Enzyme Optimization for Lignocellulose Hydrolysis using Mechanistic Modeling

A novel mechanistic model for the saccharification of cellulose and hemicellulose is utilized to predict the products of hydrolysis over a range of enzyme loadings and times. The mechanistic model considers the morphology of the substrate and the kinetics of enzymes to optimize enzyme concentrations for the enzymatic hydrolysis of cellulose and hemicellulose simultaneously. Substrates are modeled based on their fraction of accessible sites, glucan content, xylan content, and degree of polymerizations. This enzyme optimization model takes into account the kinetics of six core enzymes for lignocellulose hydrolysis: endoglucanase I (EG1), cellobiohydrolase I (CBH1), cellobiohydrolase II (CBH2), and endo-xylanase (EX) from Trichoderma reesei; β-glucosidase (BG), and β-xylosidase (BX) from Aspergillus niger. The model employs the synergistic action of these enzymes to predict optimum enzyme concentrations for hydrolysis of Avicel and ammonia fiber explosion (AFEX) pretreated corn stover. Glucan, glucan + xylan, glucose and glucose + xylose conversion predictions are given over a range of mass fractions of enzymes, and a range of enzyme loadings. Simulation results are compared with optimizations using statistically designed experiments. BG and BX are modeled in solution at later time points to predict the effect on glucose conversion and xylose conversion.

Asymmetric Syntheses of Analogs of Kainic Acid

Kainic acid has been used for nearly 50 years as a tool in neuroscience due to its pronounced neuroexcitatory properties. However, the significant price increase of kainic acid resulting from the disruption in the supply from its natural source, the alga Digenea Simplex, as well as inefficient synthesis of kainic acid, call for the exploration of functional mimics of kainic acid that can be synthesized in a simpler way. Aza kainoids analog could be one of them. The unsubstituted aza analog of kainoids has demonstrates its ability as an ionotropic glutamate receptor agonist and showed affinity in the chloride dependent glutamate (GluCl) binding site. This opened a question of the importance of the presence of one nitrogen or both nitrogens in the aza kainoid analogs for binding to glutamate receptors. Therefore, two different pyrrolidine analogs of kainic acid, trans-4-(carboxymethyl)pyrrolidine-3-carboxylic acid and trans-2-carboxy-3-pyrrolidineacetic acid, were synthesized through multi-step sequences. The lack of the affinity of both pyrrolidine analogs in GluCl binding site indicated that both nitrogens in aza kainoid analogs are involved in hydrogen bonding with receptors, significantly enhancing their affinity in GluCl binding site. Another potential functional mimic of kainic acid is isoxazolidine analogs of kainoids whose skeleton can be constituted directly via a 1, 3 dipolar cycloaddition as the key step. The difficulty in synthesizing N-unsubstituted isoxazolidines when applying such common protecting groups as alkyl, phenyl and benzyl groups, and the requirement of a desired enantioselectivity due to the three chiral ceneters in kainic acid, pose great challenges. Hence, several different protected nitrones were studied to establish that diphenylmethine nitrone may be a good candidate as the dipole in that the generated isoxazolidines can be deprotected in mild conditions with high yields. Our investigations also indicated that the exo/endo selectivity of the 1, 3 dipolar cycloaddition can be controlled by Lewis acids, and that the application of a directing group in dipolarophiles can accomplish a satisfied enantioselectivity. Those results demonstrated the synthesis of isoxazoldines analogs of kainic acid is very promising.

Identification of novel molecular determinants of tissue mineralization in fish

Tese de doutoramento, Ciências Biomédicas, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 2015

Electronic structure and magnetism of Mn-doped GaSb for spintronic applications: A DFT study

We have carried out first-principles spin polarized calculations to obtain comprehensive information regarding the structural, magnetic, and electronic properties of the Mn-doped GaSb compound with dopant concentrations: x¼0.062, 0.083, 0.125, 0.25, and 0.50. The plane-wave pseudopotential method was used in order to calculate total energies and electronic structures. It was found that the MnGa substitution is the most stable configuration with a formation energy of 1.60 eV/Mn-atom. The calculated density of states shows that the half-metallic ferromagnetism is energetically stable for all dopant concentrations with a total magnetization of about 4.0 lB/Mn-atom. The results indicate that the magnetic ground state originates from the strong hybridization between Mn-d and Sb-p states, which agree with previous studies on Mn-doped wide gap semiconductors. This study gives new clues to the fabrication of diluted magnetic semiconductors

Relación entre atrofia cortical difusa y desempeño cognitivo : estudio en población mayor de 60 años en un hospital universitario en la ciudad de Bogotá

El presente trabajo tuvo como objetivo evaluar la existencia de la relación entre la atrofia cortical difusa objetivada por neuroimagenes cerebrales y desempeños cognitivos determinados mediante la aplicación de pruebas neuropsicológicas que evalúan memoria de trabajo, razonamiento simbólico verbal y memoria anterógrada declarativa. Participaron 114 sujetos reclutados en el Hospital Universitario Mayor Méderi de la ciudad de Bogotá mediante muestreo de conveniencia. Los resultados arrojaron diferencias significativas entre los dos grupos (pacientes con diagnóstico de atrofia cortical difusa y pacientes con neuroimagenes interpretadas como dentro de los límites normales) en todas las pruebas neuropsicológicas aplicadas. Respecto a las variables demográficas se pudo observar que el grado de escolaridad contribuye como factor neuroprotector de un posible deterioro cognitivo. Tales hallazgos son importantes para determinar protocoles tempranos de detección de posible instalación de enfermedades neurodegenerativas primarias.

Por baixo da pele outra pele: conjunto de obras artísticas. Corpo, ecrã e interface para uma visualidade háptica interativa

A tese teórico-prática de doutoramento apresentada contempla a investigação, a criação, a produção e a conceptualização da instalação artística interativa intitulada Por baixo da pele outra pele. A Obra é constituída por três objetos tridimensionais concebidos à escala humana. Recorre a materiais flexíveis, como têxteis, convidando o público (interator), à envolvência física, numa relação corporal sensorial e sensual com a obra. Os objetos contêm dispositivos técnicos interativos e sensores tácteis, que, ao serem utilizados, desencadeiam estímulos multissensoriais no espectador. A instalação interativa focaliza a experiência háptica e íntima do interator considerando os seus mecanismos sensoriais e cognitivos como um potencial aparato na construção de experiências fenomenológicas, singulares e individuais. A autora considera a interatividade enquanto elemento potenciador da experiência estética visual háptica. Na argumentação conceitual da obra, reflete-se sobre o tema da visualidade háptica interativa a partirdos conceitos de ecrã, corpo e interface, assim como de endossensorialidade. Instrumentam-se metodologias de investigação em ação, experimentais e observacionais. Apresentam-se os processos investigativos, criativos e técnicos necessários ao desenvolvimento e à materialização da instalação artística. A investigação revela-se de grande interesse para o avanço da pesquisa de novas linguagens experimentais apresentando estratégias de criação artística que, ao privilegiarem o corpo físico e fenomenológico do interator, transpõe a experiência háptica interativa para um grau interno de imersão motoro-sensorial; Underneath the skin another skin: art installation. Body, screen and interface towards an interactive haptic visuality. Abstract: The theoretical-practical doctorate dissertation presents the research and conceptual framework behind, and the processes leading to, the creation and production of the interactive installation art piece Underneath the skin, another skin. The piece is presented in the shape of three human-scale tridimentional objects. It is made from flexible materials, such as textiles, inviting the (interacting) audience, to physically engage in a bodily sensorial, and sensuous, relationship with the artwork. The objects enclose interactive devices and tactile sensors that, when used, trigger in the interactor multiple sensorial stimuli. The interactive installation focuses on the interactor's intimate haptic experience taking in consideration his or hers sensorial and cognitive mechanisms as a potential apparatus in the construction of unique individual phenomenological experiences. The author understands interactivity as a triggering element into an haptic visual aesthetical experience. The supporting conceptual reasoning deals with thought and criticism on interactive haptic visuality applied to the concepts of screen, body and interface, as well as with that of endo-sensoriality. The dissertation describes the use of experimental and observation research methodologies. It also elaborates on the research, creative and technical processes at play in the installation's development and realization. The research at hand has shown great potential for the further development of new experimental languages, as it presents art-creation strategies privileging the interactor's physical and phenomenological body, and thus able to take the interactive haptic experience onto an greater inner level of motor-sensorial immersion.

Changes in enzymatic activity, accumulation of proteins and softening of persimmon (Diospyros kaki Thunb.) flesh as a function of pre-cooling acclimatization.

One of the major causes of ?Fuyu? persimmon loss after cold storage (CS) is the breakdown of its flesh, which results in the production of a translucent fruit (a water-soaked fruit). It is believed that the cause of this disturbance is linked to disorganization of the cytoskelet and endomembrane system, which changes the synthesis and transport of proteins and metabolites, resulting in incomplete ripening. To test this hypothesis, ?Fuyu? persimmon was subjected to three different postharvest treatments (T): Control ? harvested and kept at 23±3 ◦C and relative humidity (RH) of 85±5% (room temperature, RT) for 12 days, T1 ? harvested and kept under cold storage (CS) (1±1 ◦C and RH of 85±5%) for 30 days followed by RT storage for 2 days, T2 ? kept under RT for 2 days (acclimatization) followed by CS for 30 days. Control and T2 resulted in fruit with decreased flesh firmness (FF), and increased soluble solids (SS) and ascorbic acid (AA) contents. In these fruit the activity of endo-1,4-ß-glucanase (endo-1,4-ß-gluc), pectin methylesterase (PME), polygalacturonase (PG) and ß-galactosidase (ß-gal) increased. T1 resulted in translucent fruit with decreased FF, without any enzymatic activity changes, probably due to the physical disruption of the cytoskeleton. Further, there was an increased content of proteins corresponding to expansins in fruit kept under Control and T2 conditions, which suggests that these conditions do contribute to the synthesis and/or transport of proteins involved in the process of solubilization of the cell wall. In these fruit, there was also a major accumulation of gene transcripts corresponding to heat shock proteins (HSPs) of organelles related to endomembrane, which suggests participation of these genes in the prevention of damage caused by cold conditions. These data proved the hypotheses that acclimatization contributes to the expression of HSPs, and synthesis and transportat of proteins involved in the solubilization of the cell wall. The expression of these genes results in the normal ripening of the persimmon, as confirmed by the evolution of ethylene production.