Thesis advisor: Daniel A. Kirschner / The myelin sheath of the central nervous system contains a network of interlamellar tight junctions known as the radial component. Ablation of claudin-11, a tight junction protein, results in the absence of the radial component and compromises the passive electrical properties of the myelin sheath. Although tight junctions are known to regulate paracellular diffusion, this barrier function has not been directly demonstrated for the radial component, and some evidence suggests that the radial component may also, or instead, mediate adhesion between myelin membranes. To investigate the physical properties of claudin-11 tight junctions, we first compared fresh, unfixed Claudin 11-null and control nerves using X-ray diffraction. In Claudin 11-null tissue, we detected no changes in myelin structure, stability, or membrane interactions, which argues against the notion that myelin tight junctions exhibit significant adhesive properties. To examine myelin permeability in the absence of the radial component, we measured the kinetics of osmotic compaction and recovery in knockout and control myelin. We found that myelin lacking claudin-11 responded more rapidly to osmotic stress, indicating an increase in permeability to water and small osmolytes. To further test this hypothesis, we explored the possibility of measuring the diffusion of water through myelin using neutron diffraction, a technique that had been pioneered in myelin decades ago but was largely unused because of previous limitations in neutron technology. After establishing that present-day neutron instruments were capable of measuring diffusion in myelin, we applied this technique to samples from mice lacking claudin-11. Consistent with our X-ray diffraction studies, we found that H2O-D2O exchange was more rapid in Claudin 11-null mice compared to controls. Thus, our data indicate that the radial component serves primarily as a diffusion barrier and elucidate the mechanism by which tight junctions govern myelin function. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Introdução: o estresse psicológico aumenta a permeabilidade intestinal em roedores e humanos, potencialmente levando a inflamação de baixo grau e aos sintomas em distúrbios gastrintestinais funcionais. No entanto, o efeito do estresse agudo combinado ao estresse da vida crônica, que mimetiza potencialmente melhor a situação humana, é desconhecido. Além disso, há poucos dados disponíveis sobre os efeitos do estresse em intestino delgado versus cólon. Métodos: ratos Wistar foram alocados em quatro protocolos de estresse: 1/ controles; 2/ estresse agudo (isolamento e movimentos limitados); 3/ Crowding stress:crônico e 4/ estresse agudo + estresse crônico. Amostras de jejuno e cólon foram colhidas para estudar a permeabilidade em câmaras deUssing, a expressão gênica de moléculas de junção firmes e a densidade de mastócitos. Níveis de corticosterona no plasma foram medidos. Principais resultados:corticosterona plasmática foi avaliada nas três condições de estresse, teve níveis mais altos na condição de estresse combinado. Permeabilidade do jejuno foi aumentada em todas as condições de estresse e correlacionada com os níveis de corticosterona. O aumento da expressão das claudinas 1, 5 e 8, daocludina e da ZO-1 foi detectado no estado de estresse agudo no jejuno. Em contraste, a permeabilidade do cólon foi aumentada no protocolo de estresse combinado, e a expressão de moléculas das junção firmes permaneceu inalterada. O aumento da densidade de mastócitos foi observado no cólon nos ratos submetidos aos estresses crônico e combinado. Conclusão e inferências:os estresses agudo, crônico e combinado influenciam diferentemente a permeabilidade intestinal, a expressão de moléculas de junção firmes e a atividade dos mastócitos, no jejuno e no cólon. Estes resultados fornecem uma visão mais aprofundada dos mecanismos de hiperpermeabilidade intestinal relacionadas ao estresse. / Background: Psychological stress increases intestinal permeability in rodents and humans, potentially leading to low-grade inflammation and symptoms in functional gastrointestinal disorders through disturbances in brain-gut axis. However, the effect of acute stress on the background of Crhonic life stress, potentially better approaching the human situation, is unknown. Moreover, only limited information is available on the effects in small intestine versus colon in animal model. Methods: Wistar rats were allocated to 4 stress protocols: 1/ sham; 2/ acute stress (isolation and limited movement); 3/ Crhonic crowding stress and 4/ acute + Crhonic stress (n = 8 per group). Jejunum and colon were harvested to study permeability in Ussing chambers, gene expression of tight junction molecules and mast cell density. Plasma corticosterone levels were measured. Key Results: Plasma corticosterone was elevated in all three stress conditions, with the highest levels in the combined stress condition. Permeability of the jejunum was increased in all stress conditions and correlated with corticosterone levels. Increased expression of claudin 1, 5 and 8, occludin and ZO-1 was detected in the acute stress condition in the jejunum. In contrast, colonic permeability was increased in the acute on Crhonic stress protocol only and the expression of tight junction molecules was unaltered. Increased mast cell density was observed in the Crhonic and acute on Crhonic stress condition in the colon only. Conclusion and Inferences: Acute, Crhonic and combined stress differentially affect intestinal permeability, expression of tight junction molecules and mast cells in the jejunum and the colon. These findings provide further insight in the mechanisms of stress-related intestinal hyperpermeability and barrier.

Orientador: Alexys Bruno Alfonso / Banca: Andrea Brito Latge / Banca: Jeverson Teodoro Arantes Junior / O Programa de Pós-Graduação em Ciência e Tecnologia de Materiais, PosMat, tem caráter institucional e integra as atividades de pesquisa em materiais de diversos campi da Unesp / Resumo: São calculadas as estruturas eletrônicas de arranjos atômicos periódicos unidimensionais, bidimensionais e tridimensionais, através do método de combinação linear de orbitais atômicos (método tight binding). Esses orbitais correspondem aos átomos isolados das espécies químicas que compõem o arranjo atômico sob investigação. Combinações lineares deles, com coeficientes apropriados, aproximam a forma das funções de onda eletrônicas do arranjo atômico. Nos casos em que a sobreposição dos orbitais é desprezada, a contribuição de cada orbital atômico para função de Bloch é mostrada nas representações gráficas das estruturas de bandas calculadas. Após uma brve apresentação do método tight binding, são calculadas as estruturas de bandas de cadeias lineares de átomos de Carbono que têm um ou dois átomos por célula unitária. Essas cadeias são chamadas de cumuleno e poliino, respectivamente. Dentre os arranjos atômicos bidimensionais de interesse, é calculada a estrutura de bandas do grafeno. Essas energias são comparadas com resultados disponíveis na literatura. Para este material é realizada uma breve discussão sobre as bandas 'pi' provenientes de orbitais 'p IND. z' e sobre como a sobreposição dos orbitais atômicos afeta a forma das bandas. O método também é aplicado na modelagem de cristais tridimensionais. São calculadas as estruturas de bandas doo diamante, Germânio (com estrutura de diamente), Arseneto de Gálio (com estrutura zincblend) e Nitreto de Gálio (com estrutura de wurtzita). Os resultados obtidos são comparados com aqueles reportados por outros autores que usaram métodos ab initio / Abstract: The eletronic structures of periodic arrangements of atoms in one, two and three dimensions are calculated by a linear combinations of atomic orbitals (tight binding method). Those orbitals correspond to the isolated atoms of the chemical species composing the atomic arrangement under investigation. Suitable linear combinations of such states approximate the shape of the eletronic wave functions of the atomic arrangement. When the overlapping of the atomic orbitals is disregarded, the contribution of each orbital to the Bloch state is displayed in the graphs of the band structures. After a brief description of the tight binding method, the band structures of linear chains of Carbon atoms are calculated. The cases of one and two atoms per unit cell are considered. They correspond to cumulene and polyyne, respectively. Among the two-dimensional atomic arrangements of interest, we focus the calculation of the band structure of graphene. The calculated bands are compared with available results. Some attention is devoted to the 'pi' bands associated to the 'p IND. z' orbitals is presented. The effects of the overlapping of the atomic orbitals are discussed. The method is also applied to model three-dimensional crystels. The band structures of diamong, germanium (with diamond structure), Gallium Arsenide (with zincblende structure) and Gallium Nitride (with wurtzite structure) are obtained. The results are compared with those reported by other authors who applied ab initio methods / Mestre

Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / O câncer colorretal (CCR) é o terceiro tipo de câncer mais incidente no mundo para o sexo masculino, o segundo para o sexo feminino e a radioterapia é um dos tratamentos de primeira linha no combate a este tipo de câncer. Durante a progressão do CCR as células sofrem alterações morfogenéticas, sendo a desorganização do complexo juncional apical (CJA) um dos eventos iniciais desse processo. As junções oclusivas (JTs) são um dos principais componentes da CJA e desempenham papel importante no controle do fluxo paracelular, na determinação da polaridade celular e na transdução de sinais relacionados com a progressão tumoral. As claudinas são proteínas transmembrana, constituintes das JTs e cumprem um importante papel no controle desses eventos. Alterações na expressão das claudinas são observadas em tumores de diferentes órgãos e têm sido relacionadas com a progressão tumoral. No entanto os mecanismos que regulam essas alterações e sua consequência na progressão do CCR são poucos conhecidos. Desta forma, o presente estudo teve como objetivo avaliar a influência da superexpressão da claudina-3 na radiorresposta de células CCR. Nossos resultados mostraram que a superexpressão de claudina-3 minimiza alterações morfológicas causadas pela radiação, causa diminuição da resistência elétrica transepitelial e não tem efeito na permeabilidade a macromoléculas após a irradiação. Além disso, observamos que a superexpressão de claudina-3 aumenta o potencial proliferativo das células e que esta característica torna as células mais sensíveis a radiação. Porém quando avaliamos eventos celulares relacionados a progressão tumoral observamos que apesar da radiação diminuir a capacidade migratória das progênies, as células que superexpressam claudina-3 apresentam migração mais elevada. Além disso, verificamos que a superexpressão de claudina-3 diminui a invasão e a capacidade de formação de colônias frente ao tratamento com a radiação. Em seguida fomos avaliar o efeito da inibição das vias de proliferação (MEK/ERK) e sobrevivência (PI3K-Akt) na resposta das células que superexpressam claudina-3 frente a radiação. Observamos que a inibição de MEK é capaz de sensibilizar as células que superexpressam claudina-3 à radiação no ensaio de proliferação celular, no entanto a inibição de MEK e PI3K antes da exposição à radiação é capaz aumentar a migração e a capacidade de formação de colônias de células que superexpressam claudina-3 contribuindo para o aumento do potencial maligno. Em conjunto nossos resultados mostram que a superexpressão de claudina-3 contribui para um fenótipo mais maligno, no entanto frente ao tratamento com a radiação é capaz de sensibilizar as células. / Colorectal cancer (CRC) is the third more incident cancer for males, the second for females worldwide and radiotherapy is one of the first-line treatments to fighting this type of cancer. During the progression of CRC cells undergo morphogenetic alterations and the apical junctional complex disorganization (AJC) is one of the initial events of this process. The tight junctions (TJs) is a major component of AJC and play an important role in paracellular flux control, determination of cell polarity and in signal transduction related to tumor progression. Claudins are transmembrane proteins, members of TJs and play an important role on these events. Changes on claudins expression are found in tumors of different organs and have been associated with tumor progression. However the mechanisms that regulate these changes and their consequences in the CRC progression are not completely understood. Thus, this study aimed to evaluate the influence of claudin-3 overexpression on cellular response after radiation treatment of CRC cells. Our results show that claudin-3 overexpression minimizes morphological changes caused by the radiation, decrease transepithelial electrical resistance, and has no effect on macromolecules permeability after irradiation. Moreover, we observed that claudin-3 overexpression increases the proliferation rate of cells and that this feature makes the cells more sensitive to radiation. However, when evaluating the cellular events associated tumor progression we observed that despite decrease on migratory capacity caused by radiation, cells that overexpress claudin-3 have higher migration. In addition, we found that claudin-3 overexpression decreases the invasion and the capacity to form colonies after treatment with radiation. Then we evaluate the effect of inhibition of proliferation (MEK / ERK) and survival (PI3K-Akt) pathways in cells that overexpress claudin-3 in the response to radiation. We observed that inhibition of MEK could sensitize cells overexpressing claudin-3 radiation on cell proliferation assay, but the inhibition of MEK and PI3K before radiation exposure can increase the migration and colony forming ability cells overexpressing claudin-3 contributes to the increase of malignant potential. Altogether, our results show that claudin-3 overexpression contributes to a more malignant phenotype, however, claudin-3 overexpression is able to sensitize the cells to radiation.

Introdução: A doença hepática alcóolica (DHA) e a doença hepática gordurosa não alcóolica (DHGNA) estão entre as principais causas de morte por doenças hepáticas no mundo. Apesar das etiologias distintas, sendo a DHA causada pelo consumo excessivo de álcool e a DHGNA por dieta inadequada e sedentarismo, apresentam curso de doença semelhante, que pode evoluir de esteatose, para esteato-hepatite, fibrose, cirrose e carcinoma hepatocelular. Tanto a DHA quanto a DHGNA estão relacionadas à disbiose, aumento de permeabilidade intestinal, inflamação e dano hepático. Entretanto, ainda não está claro se a doença hepática precede as alterações no epitélio intestinal ou se é o aumento da permeabilidade que promove o dano hepático. Objetivo: Avaliar a expressão gênica de Tight Junctions em modelo de DHA e DHGNA em zebrafish (Danio rerio). Métodos: No modelo de DHA, os peixes foram divididos em dois grupos: Etanol (n=30), expostos a 0,5% de etanol por 28 dias e controle (n=30). No modelo de DHGNA, os peixes foram divididos também em dois grupos: Frutose (n=24), expostos à frutose 6% durante 2 horas por 14 dias e controle (n=24). Ao término dos experimentos os animais foram eutanasiados e coletados fígados, para avaliação histológica por coloração hematoxilina-eosina (HE) e de esteatose por Oil Red, e intestinos para avaliação da expressão gênica dos marcadores de permeabilidade intestinal cldnC, cldn15a, cldn15b e f11r por Real Time qPcr. Resultados: Tanto os animais expostos ao álcool quanto à frutose apresentaram esteatose hepática por coloração HE e Oil Red quando comparados aos seus respectivos controles, sem sinais de infiltrados inflamatórios e de fibrose hepática à microscopia óptica. Não houve diferença significativa na expressão gênica das tight junctions intestinais, tanto para a DHA quanto DHGNA (p  0,05). Conclusão: Os resultados sugerem que em estágios iniciais de DHA e DHGNA não ocorre alteração da permeabilidade intestinal, e que possivelmente o dano hepático precede o dano intestinal. / Introduction: Alcoholic liver disease (ALD) and non-alcoholic fatty liver disease (NAFLD) are among the leading causes of death from liver disease worldwide. Despite the different etiologies, ALD is caused by excessive alcohol consumption and NAFLD is due to inadequate diet and sedentary lifestyle, they have a similar disease course, which can progress from steatosis to steatohepatitis, fibrosis, cirrhosis and hepatocellular carcinoma. Both ALD and NAFLD are related to dysbiosis, increased gut permeability, inflammation, and liver damage. However, it is not yet clear whether liver disease precedes changes in the intestinal epithelium or whether it is the increased permeability that promotes liver damage. Objective: To evaluate the gene expression of tight junctions in ALD and NAFLD models in zebrafish (Danio rerio). Methods: In the ALD model, fish were divided into two groups: Ethanol (n=30), exposed to 0.5% ethanol for 28 days and control (n=30). In the NAFLD model, fish were also divided into two groups: Fructose (n=24), exposed to 6% fructose for 2 hours for 14 days and control (n=24). At the end of the experiments the animals were euthanized and livers were collected for histological evaluation by hematoxylin-eosin (HE) staining and steatosis by oil red staining and intestines for evaluation of the gene expression of gut permeability markers cldnC, cldn15a, cldn15b and f11r by Real Time qPcr. Results: Both animals exposed to alcohol and fructose presented hepatic steatosis by HE and Oil Red staining when compared to their respective controls, without signs of inflammatory infiltrates under optical microscopy. There was no significant difference in the gene expression of the tight junctions for both ALD and NAFLD (p0.05) Conclusion: The results suggest that in the early stages of ALD and NAFLD there are no changes in intestinal tight junctions, and that possibly liver damage precedes intestinal damage.

<p>The existence of immune self-tolerance allows the immune system to mount responses against infectious agents, but not against self-molecular constitutes. Although self-tolerance is a robust phenomenon, in some individuals as well as in experimental models, the self-tolerance breaks down and as a result, a self-destructive autoimmune disease emerges. The underlying mechanisms for the development of autoimmune diseases are not known, but genetic, environmental and immunological factors are suggested to be involved. In this thesis, we used murine mercury-induced autoimmunity to test this suggestion.</p><p>In susceptible mice mercuric chloride induces a systemic autoimmune disease characterized by increased serum levels of IgG1 and IgE, production of anti-nucleolar autoantibodies (ANolA) and formation of renal IgG deposits. In contrast, in resistant DBA/2 (H-2^d) mice, none of these characteristics develop after exposure to mercury. By crossing and backcrossing mercury-resistant DBA/2 mice to mercury susceptible strains, we found that the resistance was inherited as a dominant trait in F1 hybrids and that one gene or a cluster of genes located in the H-2 loci determined the resistance to ANolA production, whereas resistance to the other characteristics was found to be controlled by two or three non-H-2 genes.</p><p>We further put forward the “cryptic peptide hypothesis” to investigate whether mercury and another xenobiotic metal use similar pathway(s) to induce the H-2 linked production of ANolA. We found that while mercury stimulated ANolA synthesis in all H-2 susceptible (H-2^s, H-2^q and H-2^f) mouse strains, silver induced only ANolA responses in H-2^s and H-2^q mice, but not in H-2^fmice. Further studies showed that the resistance to silver-induced ANolA production in H-2^fmice was inherited as a dominant trait.</p><p>We next tested the proposition that mercury induces more adverse immunological effects in mouse strains, which are genetically prone to develop autoimmune diseases, using tight-skin 1 mice, an animal model for human Scleroderma. It was found that in this strain, mercury induced a strong immune activation with autoimmune characteristics, but did not accelerate the development of dermal fibrosis, a characteristic in Tsk/1 mice.</p><p>Finally we addressed the Th1/Th2 cross-regulation paradigm by examining if a Th1-type of response could interact with a Th2-type of response if simultaneous induced in susceptible mice. Our findings demonstrated that mercury-induced autoimmunity (Th2-type) and collagen-induced arthritis (CIA) (Th1-type) can interact in a synergistic, antagonistic or additive fashion, depending on at which stage of CIA mercury is administered.</p>

<p>The airway epithelium plays a crucial role in protecting the underlying connective tissue (CT) from noxious agents. Damage and shedding of the epithelium are observed in the airways of asthma, cystic fibrosis and rhinitis patients. The aim of this study was to investigate the mechanisms by which epithelial damage occurs, and the consequences of such damage for the inflammatory process in the airways. In this study, cultured normal human bronchial epithelial cells, excised rat tracheae, and cultured murine mast cells were used as model systems. Metabolic alterations, morphological changes and cell-cell contact stabilities were investigated.</p><p>The T-helper (Th)-1 cytokines, tumor necrosis factor-alpha (TNF-α), interferon-gamma (IFN-γ), and interleukin (IL)-1β were found to be pro-inflammatory, leading to major morphological changes, inhibitions in desmosome formation, and accelerated cell death. The Th2 cytokines, IL-4, IL-5, and IL-13 were found to cause no changes in cell death, nitric oxide levels and desmosome formation but instead an increase in proliferation, therefore were anti-inflammatory in this respect.</p><p>Increasing the osmolarity of the airway surface liquid (ASL) altered the integrity of the tight junction (TJ) and allowed a 4-kDa compound to penetrate the epithelial layer and access the CT. This effect was reversible if the ASL was returned to 295 mOsm. Intentionally breaking the TJ with EGTA and subsequent osmolar changes in ASL demonstrated the importance of TJ and the fragility of the CT under hyperosmolar stress, leading to a disrupted CT with larger capillaries and altered elemental ion content and epithelial denudation. </p><p>Hydrocortisone was shown to downregulate IL-4-induced IL-6 upregulation in murine mast cells. Furthermore, incubating mast cells with hydrocortisone lead to a new subpopulation that was morphologically unique, that displayed new cell surface markers (CD44 and CD61) and that lacked CD54. These changes modify the interactions of mast cells with surrounding cells in the CT and epithelium.</p><p>In conclusion, the balance between pro- and anti-inflammatory cytokines and ASL osmolarity may influence the role of the airway epithelium as a barrier. The pharmacological use of hyperosmolarity to disrupt TJ reversibly may help facilitate the delivery of drugs through the airway epithelium.</p>

<p>Studies of intestinal drug permeability have traditionally been performed in the colon-derived Caco-2 cell model. However, the permeability of these cell monolayers resembles that of the colon rather than that of the small intestine, which is the major site of drug absorption following oral administration. One aim of this thesis was therefore to develop a new cell culture model that mimics the permeability of the small intestine. 2/4/A1 cells are conditionally immortalized with a temperature sensitive mutant of SV40T. These cells proliferate and form multilayers at 33°C. At cultivation temperatures of 37 – 39°C, they stop proliferating and form monolayers. 2/4/A1 cells cultivated on permeable supports expressed functional tight junctions. The barrier properties of the tight junctions such as transepithelial electrical resistance and permeability to hydrophilic markers resembled those of the human small intestine <i>in vivo</i>. These cells lacked functional expression of drug transport proteins and can therefore be used as a model to study passive drug permeability unbiased by active transport. The permeability to diverse sets of drugs in 2/4/A1 was comparable to that of the human <i>jejunum</i> for both incompletely and completely absorbed drugs, and the prediction of human intestinal permeability was better in 2/4/A1 than in Caco-2 for incompletely absorbed drugs. The small intestinal-like paracellular permeability of 2/4/A1 thus enables better predictions of drug permeability in the small intestine than does Caco-2. </p><p>The studies of the paracellular route and its importance for intestinal drug permeability was also in focus in the second part of this thesis, in which a new principle for tight junction modulation was developed, based on the primary structure of the extracellular tight junction protein occludin. Peptides corresponding to the N-terminus of the first extracellular loop increased the permeability of the tight junctions, but lacked apical effect. This problem was solved by conjugation of one peptide to a lipoamino acid, resulting in two diastereomers with different effects. The L-isomer had a sustained apical effect, while that of the D-isomer was transient. In conclusion, conjugated occludin peptides constitute a new class of tight junction modulators that can enhance the tight junction permeability.</p>

Nanoporous carbons are among the widely studied and promising materials on hydrogen storage for on-board vehicles. However, the nature of nanoporous carbon structures, as well as the relationship between local structure and hydrogen adsorption are still unclear, and hinder the design of carbon materials for optimum hydrogen storage. This dissertation presents a systematic modeling effort of hydrogen storage in nanoporous carbon materials. Tight binding molecular dynamics simulations are utilized to simulate the amorphous carbons over a wide range of density. The resulting structures are in good agreement with experimental data of ultra-microporous carbon (UMC), a wood-based activated carbon, as indicated by a comparison of the microstructure at atomic level, pair distribution function, and pore size distribution. To estimate gas adsorption in complex geometries, an efficient numerical algorithm (based on a continuum gas adsorption model) is developed for calculating the gas uptake at room temperature and moderate pressures. This algorithm is a classical approximation of the quantum mechanical model by Patchkovskii et al.1 and proven to be much faster than other commonly used methods. The gas adsorption calculations in carbon structures from tight-binding simulations demonstrate both a promising hydrogen storage capacity (1.33 wt% at 298K and 5 MPa) and a reasonable heat of adsorption (12-21 kJ/mol). To our knowledge, this is the first work to directly calculate hydrogen adsorption capacity in amorphous carbon. This work demonstrates that increasing the heat of adsorption does not necessarily increase the hydrogen uptake. In fact, the available adsorption volume is as important as the isosteric heat of adsorption for hydrogen storage in nanoporous carbons.

Various analytical, semi-analytical, and empirical models have been proposed to characterize rate and pressure behavior as a function of time in tight/shale gas systems featuring a horizontal well with multiple hydraulic fractures. Despite a small number of analytical models and published numerical studies there is currently little consensus regarding the large-scale flow behavior over time in such systems. The purpose of this work is to construct a fit-for-purpose numerical simulator which will account for a variety of production features pertinent to these systems, and to use this model to study the effects of various parameters on flow behavior. Specific features examined in this work include hydraulically fractured horizontal wells, multiple porosity and permeability fields, desorption, and micro-scale flow effects. The theoretical basis of the model is described in Chapter I, along with a validation of the model. We employ the numerical simulator to examine various tight gas and shale gas systems and to illustrate and define the various flow regimes which progressively occur over time. We visualize the flow regimes using both specialized plots of rate and pressure functions, as well as high-resolution maps of pressure distributions. The results of this study are described in Chapter II. We use pressure maps to illustrate the initial linear flow into the hydraulic fractures in a tight gas system, transitioning to compound formation linear flow, and then into elliptical flow. We show that flow behavior is dominated by the fracture configuration due to the extremely low permeability of shale. We also explore the possible effect of microscale flow effects on gas effective permeability and subsequent gas species fractionation. We examine the interaction of sorptive diffusion and Knudsen diffusion. We show that microscale porous media can result in a compositional shift in produced gas concentration without the presence of adsorbed gas. The development and implementation of the micro-flow model is documented in Chapter III. This work expands our understanding of flow behavior in tight gas and shale gas systems, where such an understanding may ultimately be used to estimate reservoir properties and reserves in these types of reservoirs.