The ultimate goal of this project has been to develop a computational model for quantifying the interactions between of a body of fluid and a fibrous surface. To achieve this goal, one has to develop a model to create virtual structures that resemble the morphology of a fibrous surface (Objective-1) as well as a model that can simulate the flow of a fluid over these virtual surfaces (Objective-2). To achieve the first objective, we treated fibers as an array of beads interconnected through viscoelastic elements (springs and dampers). The uniqueness of our algorithm lies in its ability to simulate the curvature of the fibers in terms of their rigidity, fiber diameter, and fiber orientation. Moving on to Objective-2, we considered woven screens for their geometric periodicity, as a starting point. We studied how fiber diameter, fiber spacing, and contact angle can affect the skin-friction drag of a submerged hydrophobic woven screen, and how such surfaces resist against water intrusion under elevated hydro-static pressures (a requirement for providing drag reduction benefits). We also studied the impact of surface geometry and wetting properties on droplet mobility over these surfaces. Laboratory experiment was conducted at various stages throughout this investigation, and good agreement was observed between the experimental data and the results from our numerical simulation.

Ultra-deep RNA sequencing has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We develop MATS (Multivariate Analysis of Transcript Splicing), a Bayesian statistical framework for flexible hypothesis testing of differential alternative splicing patterns on RNA-Seq data. MATS uses a multivariate uniform prior to model the between-sample correlation in exon splicing patterns, and a Markov chain Monte Carlo (MCMC) method coupled with a simulation-based adaptive sampling procedure to calculate the P value and false discovery rate (FDR) of differential alternative splicing. Importantly, the MATS approach is applicable to almost any type of null hypotheses of interest, providing the flexibility to identify differential alternative splicing events that match a given user-defined pattern. We evaluated the performance of MATS using simulated and real RNA-Seq data sets. In the RNA-Seq analysis of alternative splicing events regulated by the epithelial-specific splicing factor ESRP1, we obtained a high RT-PCR validation rate of 86% for differential alternative splicing events with a MATS FDR of < 10%. Additionally, over the full list of RT-PCR tested exons, the MATS FDR estimates matched well with the experimental validation rate. Our results demonstrate that MATS is an effective and flexible approach for detecting differential alternative splicing from RNA-Seq data.

Bakgrund                                                                                                                                               År 2009 producerade ICA ett flertal reklamfilmer i kampanjen ”Vi kan mer” som syftade till att utmana fördomar kring personer med intellektuell funktionsnedsättning. Reklamfilmerna startade en livlig debatt på Internet och väckte både frågor kring produktionernas syfte och etik. Syfte                                                                                                                                    Studiens ambition har varit att undersöka hur bloggare och bloggkommentatorer uppfattat de tre första reklamfilmerna i kampanjen. Syftet var också att utröna huruvida filmerna har genererat några konsekvenser för bilden av personer med intellektuell funktionsnedsättning. Metod                                                                                                     Studien har till största del baserats på en kvalitativ metod, då syftet har varit att nå förståelse snarare än att försöka nå statistiskt säkerställda resultat. Kritisk diskursanalys användes för att analysera studiens material som bestod av cirka 80 blogginlägg med tillhörande kommentarer. Resultat                                                                                                                                  Studien konkluderar att reklamfilmerna har uppfattats på många olika sätt när det kommer till syfte och etik. Resultatet indikerar även att reklamfilmerna kan ses både reproducera och utmana fördomar gentemot funktionsnedsatta.Företagets initiativ har inte uppnått sitt fulla syfte, men filmerna har inneburit ett viktigt första steg mot normalisering för denna grupp i samhället. / Background                                                                                                                                     In 2009 ICA, one of Sweden’s largest food store chain, produced a series of commercials in a campaign which aimed to challenge prejudices about mental disability. The commercials started a lively online debate, and raised questions regarding both the purpose and ethics of these productions. Purpose                                                                                                                                              The ambition of this study was to examine how the people that participated in the online debate perceived ICA’s three first commercials in the campaign. The aim was also to analyze whether they have generated any consequences for the perception of mental disability. Method                                                                                                                                                   A largely qualitative approach have been used, since the aim has been to reach deeper understanding rather than statistically ensured results. Critical discourse analysis was used to analyze the study’s data which consisted of about 80 blog posts with related comments. Results                                                                                                                                                The study concludes that the commercials have been perceived in many different ways when it comes to purpose and ethics. The results also indicate that ICA’s advertisement both reproduce and challenge existing prejudices towards people with mental disabilities. The company’s initiative has not fulfilled its full purpose, but it constitutes an important first step to reach normalization for this group of society.

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Biofilms are significant contributors to primary production, nutrient cycling, bio-stabilization and the food web of wetland ecosystems. Photoautotrophic biomass (PB) and primary production (PP) were determined for biofilms exposed to various treatments and materials in wetlands near Fort McMurray. Biofilm additions and oil sands process-affected materials were expected to increase the microbial colonization rates on treated substrates and subsequently PB and PP of biofilms over time as compared to controls and unaffected materials. Biofilms survived the transfers and colonized new substrates immediately. Oil sands process affected materials were found to increase PB and PP throughout the first year. A strong decreasing trend for both PB and PP in treatment microcosms occurred in year two, eventually coalescing with control conditions at a lower equilibrium. Transferred biofilms and treatment materials, therefore, increased overall wetland productivity during the initial stages of wetland development when growing conditions are most limiting. / Land Reclamation and Remediation

Este estudo apresenta os resultados de dados coletados em testemunhos de sondagem e afloramentos na sucessão aptiana-albiana da Bacia do Araripe, NE do Brasil. Carbonatos micríticos laminados se intercalam com rochas siliciclásticas, cujo índice de alteração química (CIA) é indicativo de um clima tipicamente árido a semi-árido. O Membro Crato foi formado sob regime hidrológico altamente variável, em uma laguna salina costeira sujeita a flutuações da profundidade da lâmina d´água, salinidade e grau de oxigenação. As condições ambientais estressantes favoreceram o desenvolvimento de extensos tapetes microbiais, responsáveis pela precipitação da maior parte dos carbonatos laminados. A origem microbial dos carbonatos é atestada por uma variedade de feições de esteiras microbiais, incluindo feições relativas ao crescimento (biolaminações, bioconstruções dômicas, padrões semelhantes a Kinneyia) e feições derivadas da destruição física das esteiras (estruturas “roll-up”, fissuras lineares incompletas, e fragmentos de esteiras oriundos da dessecação dos filmes microbiais). A presença de esteiras microbiais que recobriram os fósseis com EPS foi primordial na preservação extraordinária de tecidos moles. / This study presents the results on data collected in drill cores and outcrops in the Aptian-Albian succession in the Araripe Basin, NE Brazil. Laminated, micritic carbonates are interbedded with siliciclastic rocks that yielded CIA values typical of arid to semi-arid climate. The Crato Member was formed under a highly variable hydrologic regime (with fluctuating water depth, salinity and degree of oxygenation) in a coastal, saline lagoon. The stressful environmental conditions favored the development of extensive microbial mats, responsible for the precipitation of most laminated carbonates. The microbial origin of the carbonates is attested by a variety of microbial mat features, including growth-related features (biolaminations, domal buildups, patterns resembling Kinneyia) and features derived from physical mat destruction (roll-up structures, linear, incomplete fissures, and mat chips from desiccation of microbial films). The presence of microbial mats that covered the fossils with EPS was paramount for the extraordinary preservation of soft tissues.

Este estudo apresenta os resultados de dados coletados em testemunhos de sondagem e afloramentos na sucessão aptiana-albiana da Bacia do Araripe, NE do Brasil. Carbonatos micríticos laminados se intercalam com rochas siliciclásticas, cujo índice de alteração química (CIA) é indicativo de um clima tipicamente árido a semi-árido. O Membro Crato foi formado sob regime hidrológico altamente variável, em uma laguna salina costeira sujeita a flutuações da profundidade da lâmina d´água, salinidade e grau de oxigenação. As condições ambientais estressantes favoreceram o desenvolvimento de extensos tapetes microbiais, responsáveis pela precipitação da maior parte dos carbonatos laminados. A origem microbial dos carbonatos é atestada por uma variedade de feições de esteiras microbiais, incluindo feições relativas ao crescimento (biolaminações, bioconstruções dômicas, padrões semelhantes a Kinneyia) e feições derivadas da destruição física das esteiras (estruturas “roll-up”, fissuras lineares incompletas, e fragmentos de esteiras oriundos da dessecação dos filmes microbiais). A presença de esteiras microbiais que recobriram os fósseis com EPS foi primordial na preservação extraordinária de tecidos moles. / This study presents the results on data collected in drill cores and outcrops in the Aptian-Albian succession in the Araripe Basin, NE Brazil. Laminated, micritic carbonates are interbedded with siliciclastic rocks that yielded CIA values typical of arid to semi-arid climate. The Crato Member was formed under a highly variable hydrologic regime (with fluctuating water depth, salinity and degree of oxygenation) in a coastal, saline lagoon. The stressful environmental conditions favored the development of extensive microbial mats, responsible for the precipitation of most laminated carbonates. The microbial origin of the carbonates is attested by a variety of microbial mat features, including growth-related features (biolaminations, domal buildups, patterns resembling Kinneyia) and features derived from physical mat destruction (roll-up structures, linear, incomplete fissures, and mat chips from desiccation of microbial films). The presence of microbial mats that covered the fossils with EPS was paramount for the extraordinary preservation of soft tissues.

abstract: Some cyanobacteria can generate hydrogen (H2) under certain physiological conditions and are considered potential agents for biohydrogen production. However, they also present low amounts of H2 production, a reaction reversal towards H2 consumption, and O2 sensitivity. Most attempts to improve H2 production have involved genetic or metabolic engineering approaches. I used a bio-prospecting approach instead to find novel strains that are naturally more apt for biohydrogen production. A set of 36, phylogenetically diverse strains isolated from terrestrial, freshwater and marine environments were probed for their potential to produce H2 from excess reductant. Two distinct patterns in H2 production were detected. Strains displaying Pattern 1, as previously known from Synechocystis sp. PCC 6803, produced H2 only temporarily, reverting to H2 consumption within a short time and after reaching only moderately high H2 concentrations. By contrast, Pattern 2 cyanobacteria, in the genera Lyngbya and Microcoleus, displayed high production rates, did not reverse the direction of the reaction and reached much higher steady-state H2 concentrations. L. aestuarii BL J, an isolate from marine intertidal mats, had the fastest production rates and reached the highest steady-state concentrations, 15-fold higher than that observed in Synechocystis sp. PCC 6803. Because all Pattern 2 strains originated in intertidal microbial mats that become anoxic in dark, it was hypothesized that their strong hydrogenogenic capacity may have evolved to aid in fermentation of the photosynthate. When forced to ferment, these cyanobacteria display similarly desirable characteristics of physiological H2 production. Again, L. aestuarii BL J had the fastest specific rates and attained the highest H2 concentrations during fermentation, which proceeded via a mixed-acid pathway to yield acetate, ethanol, lactate, H2, CO2 and pyruvate. The genome of L. aestuarii BL J was sequenced and bioinformatically compared to other cyanobacterial genomes to ascertain any potential genetic or structural basis for powerful H2 production. The association hcp exclusively in Pattern 2 strains suggests its possible role in increased H2 production. This study demonstrates the value of bioprospecting approaches to biotechnology, pointing to the strain L. aestuarii BL J as a source of useful genetic information or as a potential platform for biohydrogen production. / Dissertation/Thesis / Ph.D. Molecular and Cellular Biology 2013