Diseño e implementación de un módulo de crecimiento bacteriano dependiente de nutrientes en el simulador GRO

Hace no más de una década que empezó a escucharse el término biología sintética. Este área de estudio emergente consiste en la ingeniería y programación de sistemas biológicos, tratando la biología como una tecnología programable a la que aplican los principios y metodologías de la ingeniería, con el fin de crear nuevas funcionalidades genéticas desde cero, procurando asÍ algún beneficio como por ejemplo, programar células bacterianas para producir biocombustibles. Sin embargo, para la creación de dichas funcionalidades es necesario conocer bien al organismo sobre el que se van a implantar. Por este motivo, los biólogos sintéticos emplean bacterias en sus estudios, ya que es la forma de vida más simple, está presente en prácticamente todos los nichos ecológicos, desempeña algunas de las funcionalidades vitales para los humanos y lo mas importante, se conoce prácticamente todo su material genético. Los experimentos son costosos en tiempo y dinero, siendo necesaria la ayuda de herramientas que faciliten esta labor, los simuladores. En PLASWIRES, proyecto europeo de biología sintética en el que se engloba este este trabajo, el simulador empleado es GRO. Sin embargo, en GRO el crecimiento de las bacterias ocurre de forma exponencial y sin restricciones, generando comportamientos poco realistas. Por ello, se ha considerado relevante en biología sintética, y en el simulador GRO en particular, disponer de un modelo de crecimiento bacteriano dependiente de los nutrientes. El desarrollo de este trabajo se centra en la implementación de un módulo de consumo de nutrientes en colonias de bacterias simuladas con GRO, introduciendo así la limitación de nutrientes y evitanto que las bacterias crezcan exponencialmente. Se han introducido nutrientes en el medio y la capacidad de consumirlos, con el objetivo de obtener un crecimiento ajustado al que ocurre en la naturaleza. Además, se ha desarrollado en GRO una nueva función de adquisición de volumen, que condiciona el volumen adquirido por cada bacteria en función de los nutrientes. La implentación de las dos aportaciones presentadas ha supuesto la adición de funcionalidad extra a GRO, convirtiéndolo en el único simulador de bacterias que tiene en cuenta el crecimiento bacteriano dependiente de nutrientes.---ABSTRACT---It has been in this last decade that the synthetic biology term began to be heard. This emergent area of study consists in the engineering and programming of biological systems, dealing with biology as a programable technology in which the engineering principles and methodologies are applied in order to create novel genetic functinalities from scratch, obtaining some advatages such as programmed bacteria in order to produce biofuels. However, to create this functionalities, it is necessary to know well the organisms in which they are going to be implemented. For this reason, synthetic biology researchers use bacteria, because it is the simplest life form, it can be found in almost all the ecological niche, it does some vital function to humans and, most important, almost all of its genetic information is known. Experiments are expensive in time and money, making it necessary to use tools to ease this task: the simulators. In PLASWIRES, the european synthetic biology project in which this work is included, the simulator used is GRO. However, the bacterial growth in GRO is exponential and it does not have restrictions, generating unrealistic behaviours. Therefore, it has been considered relevant in synthetic biology, and in a particular way in GRO, to provide a bacterial growth model dependent on nutrient. This work focuses on the implementation of a nutrient consumption module in bacteria colonies simulated with GRO, introducing a nuntrient limitation and avoiding the bacteria exponential growth. The module introduces nutrients and the capacity for bacteria to consume them, aiming to obtain realistic growth simulations that fit the observations made in nature. Moreover, an adquisition volumen function has been developed in GRO, determining the volumen depending on nutrients. This two contributions make GRO the only bacteria simulator that computes growth depending on nutrients

Hybridizing concentrated solar power (CSP) with biogas and biomethane as an alternative to natural gas: Analysis of environmental performance using LCA

Concentrating Solar Power (CSP) plants typically incorporate one or various auxiliary boilers operating in parallel to the solar field to facilitate start up operations, provide system stability, avoid freezing of heat transfer fluid (HTF) and increase generation capacity. The environmental performance of these plants is highly influenced by the energy input and the type of auxiliary fuel, which in most cases is natural gas (NG). Replacing the NG with biogas or biomethane (BM) in commercial CSP installations is being considered as a means to produce electricity that is fully renewable and free from fossil inputs. Despite their renewable nature, the use of these biofuels also generates environmental impacts that need to be adequately identified and quantified. This paper investigates the environmental performance of a commercial wet-cooled parabolic trough 50 MWe CSP plant in Spain operating according to two strategies: solar-only, with minimum technically viable energy non-solar contribution; and hybrid operation, where 12 % of the electricity derives from auxiliary fuels (as permitted by Spanish legislation). The analysis was based on standard Life Cycle Assessment (LCA) methodology (ISO 14040-14040). The technical viability and the environmental profile of operating the CSP plant with different auxiliary fuels was evaluated, including: NG; biogas from an adjacent plant; and BM withdrawn from the gas network. The effect of using different substrates (biowaste, sewage sludge, grass and a mix of biowaste with animal manure) for the production of the biofuels was also investigated. The results showed that NG is responsible for most of the environmental damage associated with the operation of the plant in hybrid mode. Replacing NG with biogas resulted in a significant improvement of the environmental performance of the installation, primarily due to reduced impact in the following categories: natural land transformation, depletion of fossil resources, and climate change. However, despite the renewable nature of the biofuels, other environmental categories like human toxicity, eutrophication, acidification and marine ecotoxicity scored higher when using biogas and BM.

Irrigation efficiency and water-policy implications for river-basin resilience

Rising demand for food, fiber, and biofuels drives expanding irrigation withdrawals from surface water and groundwater. Irrigation efficiency and water savings have become watchwords in response to climate-induced hydrological variability, increasing freshwater demand for other uses including ecosystem water needs, and low economic productivity of irrigation compared to most other uses. We identify three classes of unintended consequences, presented here as paradoxes. Ever-tighter cycling of water has been shown to increase resource use, an example of the efficiency paradox. In the absence of effective policy to constrain irrigated-area expansion using "saved water", efficiency can aggravate scarcity, deteriorate resource quality, and impair river basin resilience through loss of flexibility and redundancy. Water scarcity and salinity effects in the lower reaches of basins (symptomatic of the scale paradox) may partly be offset over the short-term through groundwater pumping or increasing surface water storage capacity. However, declining ecological flows and increasing salinity have important implications for riparian and estuarine ecosystems and for non-irrigation human uses of water including urban supply and energy generation, examples of the sectoral paradox. This paper briefly considers three regional contexts with broadly similar climatic and water-resource conditions – central Chile, southwestern US, and south-central Spain – where irrigation efficiency directly influences basin resilience. The comparison leads to more generic insights on water policy in relation to irrigation efficiency and emerging or overdue needs for environmental protection.

The decomposition of peroxynitrite does not yield nitroxyl anion and singlet oxygen

In a recent article [Khan, A. U., Kovacic, D., Kolbanovsky, A., Desai, M., Frenkel, K. & Geacintov, N. E. (2000) Proc. Natl. Acad. Sci. USA 97, 2984–2989], the authors claimed that ONOO−, after protonation to ONOOH, decomposes into 1HNO and 1O2 according to a spin-conserved unimolecular mechanism. This claim was based partially on their observation that nitrosylhemoglobin is formed via the reaction of peroxynitrite with methemoglobin at neutral pH. However, thermochemical considerations show that the yields of 1O2 and 1HNO are about 23 orders of magnitude lower than those of ⋅NO2 and ⋅OH, which are formed via the homolysis of ONOOH. We also show that methemoglobin does not form with peroxynitrite any spectrally detectable product, but with contaminations of nitrite and H2O2 present in the peroxynitrite sample. Thus, there is no need to modify the present view of the mechanism of ONOOH decomposition, according to which initial homolysis into a radical pair, [ONO⋅ ⋅OH]cage, is followed by the diffusion of about 30% of the radicals out of the cage, while the rest recombines to nitric acid in the solvent cage.

Nitrogen management and the future of food: Lessons from the management of energy and carbon

The food system dominates anthropogenic disruption of the nitrogen cycle by generating excess fixed nitrogen. Excess fixed nitrogen, in various guises, augments the greenhouse effect, diminishes stratospheric ozone, promotes smog, contaminates drinking water, acidifies rain, eutrophies bays and estuaries, and stresses ecosystems. Yet, to date, regulatory efforts to limit these disruptions largely ignore the food system. There are many parallels between food and energy. Food is to nitrogen as energy is to carbon. Nitrogen fertilizer is analogous to fossil fuel. Organic agriculture and agricultural biotechnology play roles analogous to renewable energy and nuclear power in political discourse. Nutrition research resembles energy end-use analysis. Meat is the electricity of food. As the agriculture and food system evolves to contain its impacts on the nitrogen cycle, several lessons can be extracted from energy and carbon: (i) set the goal of ecosystem stabilization; (ii) search the entire production and consumption system (grain, livestock, food distribution, and diet) for opportunities to improve efficiency; (iii) implement cap-and-trade systems for fixed nitrogen; (iv) expand research at the intersection of agriculture and ecology, and (v) focus on the food choices of the prosperous. There are important nitrogen-carbon links. The global increase in fixed nitrogen may be fertilizing the Earth, transferring significant amounts of carbon from the atmosphere to the biosphere, and mitigating global warming. A modern biofuels industry someday may produce biofuels from crop residues or dedicated energy crops, reducing the rate of fossil fuel use, while losses of nitrogen and other nutrients are minimized.

Dinâmica do microbioma ruminal de ovinos (Ovis aries) e sua relação com a degradação de biomassa

Considerando a dieta como um fator modulador do microbioma ruminal, neste trabalho objetivou-se investigar o impacto do bagaço da cana-de-açúcar sobre a composição e funcionalidade das espécies microbianas residentes no rúmen de carneiros (Ovis aries). Foram utilizados seis animais machos fistulados de O. aries, dos quais três foram alimentados com uma dieta composta por 70% de volumoso e 30% de concentrado (tratamento controle) e outros três animais alimentados com uma dieta similar a anterior, mas com 14% do volumoso substituído por bagaço de cana-de-açúcar (tratamento bagaço). O conteúdo ruminal (líquido e fibra) foram amostrados quinzenalmente durante 60 dias. A partir dessas amostras foram acessadas a estrutura e a composição da comunidade microbiana pela extração de DNA total e amplificação das regiões V3 e V6-V7 do gene 16S rRNA bacteriano e a região intergênica fúngica (ITS2). Além disso, foram feitas análises metagenômicas e metatranscriptômicas de comunidade microbianas enriquecidas em fibra ruminal para identificar enzimas lignocelulolíticas expressas. As frações líquida e fibrosa do conteúdo ruminal de O. aries revelaram uma comunidade bacteriana dominada principalmente por Bacteroidetes e Firmicutes ao longo de todo período experimental. Dois gêneros, Prevotella e Ruminococcus representaram 20% e 4% da comunidade bacteriana ruminal, respectivamente. Para a comunidade fúngica o filo Neocallimastigomycota representou 91% das sequências e os principais gêneros deste filo foram Piromyces, Neocallimastix, Orpinomyces, Anaeromyces, Caecomyces e Cyllamyces aderidos a fibra ruminal. O gênero Caecomyces, foi significativamente mais abundante na fibra ruminal de animais que se alimentaram de bagaço de cana-de açúcar. Além disso, foi observado um aumento significativo na frequência de enzimas como, por exemplo, 1,4-α-glucano, α-galactosidase, endo 1,4-β-xilanase, β- xilosidase, xilose isomerase, celobiose fosforilase e α-N-arabinofuranosidase no tratamento com bagaço de cana-de-açúcar. Considerando que a recuperação de enzimas a partir de comunidades microbianas naturalmente selecionadas para a degradação de biomassa é uma estratégia promissora para superar a atual ineficiência da ação enzimática na produção industrial de biocombustíveis, os resultados deste trabalho representam a possibilidade de aumentar a capacidade de recuperação ou descoberta de enzimas a partir de ruminantes, ou ainda, a possibilidade de manipular a estrutura do microbioma do rúmen para usá-lo como fonte de inóculo enriquecido em processos industriais de degradação de biomassa.

Gaseificação de microalgas: estudo termogravimétrico e modelagem matemática do processo em reator solar.

Devido ao esgotamento de recursos não renováveis e o aumento das preocupações sobre as alterações climáticas, a produção de combustível renovável a partir de microalgas continua a atrair muita a atenção devido ao seu potencial para taxas rápidas de crescimento, alto teor de óleo, capacidade de crescer em cenários não convencionais e a neutralidade de carbono, além de eliminar a preocupação da disputa com as culturas alimentares. Em virtude disso, torna-se importante o desenvolvimento de um processo de conversão das microalgas em gás combustível, em destaque o gás de síntese. Visando essa importância, estudou-se a reação de gaseificação da microalga Chlorella vulgaris através de experimentos de análise termogravimétrica para estimar os parâmetros cinéticos das reações e através da simulação de um modelo matemático dinâmico termoquímico do processo usando equações de conservação de massa e energia acoplados a cinética de reação. Análises termogravimétricas isotérmicas e dinâmicas foram realizadas usando dois diferentes tipos de modelos cinéticos: isoconversionais e reações paralelas independentes (RPI). Em ambos os modelos, os valores dos parâmetros cinéticos estimados apresentaram bons ajustes e permaneceram dentro daqueles encontrados na literatura. Também foram analisados os efeitos dos parâmetros cinéticos do modelo RPI sobre a conversão da microalga no intuito de observar quais mais se pronunciavam diante a variação de valores. Na etapa de simulação do sistema controlado pelo reator solar, o modelo matemático desenvolvido foi validado por meio da comparação dos valores de temperatura e concentrações de produtos obtidos medidos experimentalmente pela literatura, apresentando boa aproximação nos valores e viabilizando, juntamente com a etapa experimental de termogravimetria, a produção de gás de síntese através da gaseificação da microalga Chlorella vulgaris.

Soil quality response to land-use change for sugarcane expansion in Brazil

Globally, increasing demands for biofuels have intensified the rate of land-use change (LUC) for expansion of bioenergy crops. In Brazil, the world\'s largest sugarcane-ethanol producer, sugarcane area has expanded by 35% (3.2 Mha) in the last decade. Sugarcane expansion has resulted in extensive pastures being subjected to intensive mechanization and large inputs of agrochemicals, which have direct implications on soil quality (SQ). We hypothesized that LUC to support sugarcane expansion leads to overall SQ degradation. To test this hypothesis we conducted a field-study at three sites in the central-southern region, to assess the SQ response to the primary LUC sequence (i.e., native vegetation to pasture to sugarcane) associated to sugarcane expansion in Brazil. At each land use site undisturbed and disturbed soil samples were collected from the 0-10, 10-20 and 20-30 cm depths. Soil chemical and physical attributes were measured through on-farm and laboratory analyses. A dataset of soil biological attributes was also included in this study. Initially, the LUC effects on each individual soil indicator were quantified. Afterward, the LUC effects on overall SQ were assessed using the Soil Management Assessment Framework (SMAF). Furthermore, six SQ indexes (SQI) were developed using approaches with increasing complexity. Our results showed that long-term conversion from native vegetation to extensive pasture led to soil acidification, significant depletion of soil organic carbon (SOC) and macronutrients [especially phosphorus (P)] and severe soil compaction, which creates an unbalanced ratio between water- and air-filled pore space within the soil and increases mechanical resistance to root growth. Conversion from pasture to sugarcane improved soil chemical quality by correcting for acidity and increasing macronutrient levels. Despite those improvements, most of the P added by fertilizer accumulated in less plant-available P forms, confirming the key role of organic P has in providing available P to plants in Brazilian soils. Long-term sugarcane production subsequently led to further SOC depletions. Sugarcane production had slight negative impacts on soil physical attributes compared to pasture land. Although tillage performed for sugarcane planting and replanting alleviates soil compaction, our data suggested that the effects are short-term with persistent, reoccurring soil consolidation that increases erosion risk over time. These soil physical changes, induced by LUC, were detected by quantitative soil physical properties as well as by visual evaluation of soil structure (VESS), an on-farm and user-friendly method for evaluating SQ. The SMAF efficiently detected overall SQ response to LUC and it could be reliably used under Brazilian soil conditions. Furthermore, since all of the SQI values developed in this study were able to rank SQ among land uses. We recommend that simpler and more cost-effective SQI strategies using a small number of carefully chosen soil indicators, such as: pH, P, K, VESS and SOC, and proportional weighting within of each soil sectors (chemical, physical and biological) be used as a protocol for SQ assessments in Brazilian sugarcane areas. The SMAF and SQI scores suggested that long-term conversion from native vegetation to extensive pasture depleted overall SQ, driven by decreases in chemical, physical and biological indicators. In contrast, conversion from pasture to sugarcane had no negative impacts on overall SQ, mainly because chemical improvements offset negative impacts on biological and physical indicators. Therefore, our findings can be used as scientific base by farmers, extension agents and public policy makers to adopt and develop management strategies that sustain and/or improving SQ and the sustainability of sugarcane production in Brazil.

Concepção de um receptor de cavidade para concentração de energia solar para aplicação em reatores químicos.

Este trabalho dimensionou um receptor de cavidade para uso como reator químico de um ciclo de conversão de energia solar para energia química. O vetor energético proposto é o hidrogênio. Isso implica que a energia solar é concentrada em um dispositivo que absorve a radiação térmica e a transforma em energia térmica para ativar uma reação química endotérmica. Essa reação transforma o calor útil em gás hidrogênio, que por sua vez pode ser utilizado posteriormente para geração de outras formas de energia. O primeiro passo foi levantar os pares metal/óxido estudados na literatura, cuja finalidade é ativar um ciclo termoquímico que possibilite produção de hidrogênio. Esses pares foram comparados com base em quatro parâmetros, cuja importância determina o dimensionamento de um receptor de cavidade. São eles: temperatura da reação; estado físico de reagentes e produtos; desgaste do material em ciclos; taxa de reação de hidrólise e outros aspectos. O par escolhido com a melhor avaliação no conjunto dos parâmetros foi o tungstênio e o trióxido de tungstênio (W/WO3). Com base na literatura, foi determinado um reator padrão, cujas características foram analisadas e suas consequências no funcionamento do receptor de cavidade. Com essa análise, determinaram-se os principais parâmetros de projeto, ou seja, a abertura da cavidade, a transmissividade da janela, e as dimensões da cavidade. Com base nos resultados anteriores, estabeleceu-se um modelo de dimensionamento do sistema de conversão de energia solar em energia útil para um processo químico. Ao se analisar um perfil de concentração de energia solar, calculou-se as eficiências de absorção e de perdas do receptor, em função da área de abertura de um campo de coleta de energia solar e da radiação solar disponível. Esse método pode ser empregado em conjunto com metodologias consagradas e dados de previsão de disponibilidade solar para estudos de concentradores de sistemas de produção de hidrogênio a partir de ciclos termoquímicos.

Steam reforming of ethanol over bimetallic RhPt/La2O3: Long-term stability under favorable reaction conditions

Recently, the steam reforming of biofuels has been presented as a potential hydrogen source for fuel cells. Because this scenario represents an interesting opportunity for Colombia (South America), which produces large amounts of bioethanol, the steam reforming of ethanol was studied over a bimetallic RhPt/La2O3 catalyst under bulk mass transfer conditions. The effect of temperature and the initial concentrations of ethanol and water were evaluated at space velocities above 55,000 h−1 to determine the conditions that maximize the H2/CO ratio and reduce CH4 production while maintaining 100% conversion of ethanol. These requirements were accomplished when 21 mol% H2O and 3 mol% C2H5OH (steam/ethanol molar ratio = 7) were reacted at 600 °C. The catalyst stability was assessed under these reaction conditions during 120 h on stream, obtaining ethanol conversions above 99% during the entire test. The effect of both H2 and air flows as catalyst regeneration treatments were evaluated after 44 and 67 h on stream, respectively. The results showed that H2 treatment accelerated catalyst deactivation, and air regeneration increased both the catalyst stability and the H2 selectivity while decreasing CH4 generation. Fresh and spent catalyst samples were characterized by TEM/EDX, XPS, TPR, and TGA. Although the Rh and Pt in the fresh catalyst were completely reduced, the spent samples showed a partial oxidation of Rh and small amounts of carbonaceous residue. A possible Rh–Pt–Rh2O3 structure was proposed as the active site on the catalyst, which was regenerated by air treatment.

Las transformaciones del territorio derivadas de la producción de cultivos para biocombustibles

El aumento de la plantación de diversos cultivos destinados a la producción de biocombustibles representa en muchos territorios, principalmente en aquellos destinados a la agricultura y a la ganadería, un conflicto socioeconómico de excepcional relevancia, lo cual conlleva cambios profundos tanto en la evolución del paisaje como en la articulación del territorio. Con ello se pretende contribuir al debate sobre las repercusiones territoriales de los biocombustibles en el medio rural y en sus consecuencias socioeconómicas a diversas escalas.

The combined effect of plastics and food waste accelerates the thermal decomposition of refuse-derived fuels and fuel blends

Mechanical treatments such as shredding or extrusion are applied to municipal solid wastes (MSW) to produce refuse-derived fuels (RDF). In this way, a waste fraction (mainly composed by food waste) is removed and the quality of the fuel is improved. In this research, simultaneous thermal analysis (STA) was used to investigate how different mechanical treatments applied to MSW influence the composition and combustion behaviour of fuel blends produced by combining MSW or RDF with wood in different ratios. Shredding and screening resulted in a more efficient mechanical treatment than extrusion to reduce the chlorine content in a fuel, which would improve its quality. This study revealed that when plastics and food waste are combined in the fuel matrix, the thermal decomposition of the fuels are accelerated. The combination of MSW or RDF and woody materials in a fuel blend has a positive impact on its decomposition.

Characterization and Degradation of Fatty Acid Methyl Esters and Biodiesel in Artificial Seawater Under UV Exposure Using Raman Spectroscopy

Thesis (Master's)--University of Washington, 2016-06

A methodology for the generation and evaluation of biorefinery process chains, in order to identify the most promising biorefineries for the EU

The topic of bioenergy, biofuels and bioproducts remains at the top of the current political and research agenda. Identification of the optimum processing routes for biomass, in terms of efficiency, cost, environment and socio-economics is vital as concern grows over the remaining fossil fuel resources, climate change and energy security. It is known that the only renewable way of producing conventional hydrocarbon fuels and organic chemicals is from biomass, but the problem remains of identifying the best product mix and the most efficient way of processing biomass to products. The aim is to move Europe towards a biobased economy and it is widely accepted that biorefineries are key to this development. A methodology was required for the generation and evaluation of biorefinery process chains for converting biomass into one or more valuable products that properly considers performance, cost, environment, socio-economics and other factors that influence the commercial viability of a process. In this thesis a methodology to achieve this objective is described. The completed methodology includes process chain generation, process modelling and subsequent analysis and comparison of results in order to evaluate alternative process routes. A modular structure was chosen to allow greater flexibility and allowing the user to generate a large number of different biorefinery configurations The significance of the approach is that the methodology is defined and is thus rigorous and consistent and may be readily re-examined if circumstances change. There was the requirement for consistency in structure and use, particularly for multiple analyses. It was important that analyses could be quickly and easily carried out to consider, for example, different scales, configurations and product portfolios and so that previous outcomes could be readily reconsidered. The result of the completed methodology is the identification of the most promising biorefinery chains from those considered as part of the European Biosynergy Project.

Biomass fuelled combined heat and power:situation in the UK and the Netherlands

Combined Heat and Power (CHP) is the simultaneous generation of usable heat and power in a single process. Despite its obvious advantages in terms of increased efficiency when compared to a single heat or power generation unit, there are a number of technical and economic reasons that have limited their selection. Biomass resources can be, and actually are used as fuel in CHP installations; however several hurdles have to be sorted beforehand, among the most important is the fact that biomass energy sources are not as energy intense as conventional CHP fuels. The ultimate outcome is a limited number of CHP units making use of biomass as fuel. Even fewer CHP units use bioliquids (e.g.: fast pyrolysis biomass liquids, biodiesel and vegetable oil). The Bioliquid-CHP project is carried out by a consortium of seven European and Russian complementary partners, funded by the EU and by the Federal Agency for Science and Innovation of the Russian Federation. The project aim is to develop microturbine and internal combustion engine adaptations in order to adjust these prime movers to bioliquids for CHP applications. This paper will show a summary of the current biomass CHP installations in the UK and the Netherlands, making reference to number of units, capacity, fuel used, the conversion technology involved and the preferred prime movers. The information will give an insight of the current market, with probable future trends and areas where growth could be expected. A similar paper describing the biomass CHP situation in Italy and Russia will be prepared in the near future.