The Ocean Colour Climate Change Initiative: III. A round-robin comparison on in-water bio-optical algorithms

Satellite-derived remote-sensing reflectance (Rrs) can be used for mapping biogeochemically relevant variables, such as the chlorophyll concentration and the Inherent Optical Properties (IOPs) of the water, at global scale for use in climate-change studies. Prior to generating such products, suitable algorithms have to be selected that are appropriate for the purpose. Algorithm selection needs to account for both qualitative and quantitative requirements. In this paper we develop an objective methodology designed to rank the quantitative performance of a suite of bio-optical models. The objective classification is applied using the NASA bio-Optical Marine Algorithm Dataset (NOMAD). Using in situRrs as input to the models, the performance of eleven semi-analytical models, as well as five empirical chlorophyll algorithms and an empirical diffuse attenuation coefficient algorithm, is ranked for spectrally-resolved IOPs, chlorophyll concentration and the diffuse attenuation coefficient at 489 nm. The sensitivity of the objective classification and the uncertainty in the ranking are tested using a Monte-Carlo approach (bootstrapping). Results indicate that the performance of the semi-analytical models varies depending on the product and wavelength of interest. For chlorophyll retrieval, empirical algorithms perform better than semi-analytical models, in general. The performance of these empirical models reflects either their immunity to scale errors or instrument noise in Rrs data, or simply that the data used for model parameterisation were not independent of NOMAD. Nonetheless, uncertainty in the classification suggests that the performance of some semi-analytical algorithms at retrieving chlorophyll is comparable with the empirical algorithms. For phytoplankton absorption at 443 nm, some semi-analytical models also perform with similar accuracy to an empirical model. We discuss the potential biases, limitations and uncertainty in the approach, as well as additional qualitative considerations for algorithm selection for climate-change studies. Our classification has the potential to be routinely implemented, such that the performance of emerging algorithms can be compared with existing algorithms as they become available. In the long-term, such an approach will further aid algorithm development for ocean-colour studies.

Effect of phytoplankton size classes on bio-optical properties of phytoplankton in the Western Iberian coast: Application of models

Chlorophyll-a satellite products are routinely used in oceanography, providing a synoptic and global view of phytoplankton abundance. However, these products lack information on the community structure of the phytoplankton, which is crucial for ecological modelling and ecosystem studies. To assess the usefulness of existing methods to differentiate phytoplankton functional types (PFT) or phytoplankton size classes from satellite data, in-situ phytoplankton samples collected in the Western Iberian coast, on the North-East Atlantic, were analysed for pigments and absorption spectra. Water samples were collected in five different locations, four of which were located near the shore and another in an open-ocean, seamount region. Three different modelling approaches for deriving phytoplankton size classes were applied to the in situ data. Approaches tested provide phytoplankton size class information based on the input of pigments data (Brewin et al., 2010), absorption spectra data (Ciotti et al., 2002) or both (Uitz et al., 2008). Following Uitz et al. (2008), results revealed high variability in microphytoplankton chlorophyll-specific absorption coefficients, ranging from 0.01 to 0.09 m2 (mg chl)− 1 between 400 and 500 nm. This spectral analysis suggested, in one of the regions, the existence of small cells (< 20 μm) in the fraction of phytoplankton presumed to be microphytoplankton (based on diagnostic pigments). Ciotti et al. (2002) approach yielded the highest differences between modelled and measured absorption spectra for the locations where samples had high variability in community structure and cell size. The Brewin et al. (2010) pigment-based model was adjusted and a set of model coefficients are presented and recommended for future studies in offshore water of the Western Iberian coast.

Dilute acid hydrolysis of cellulose and cellulosic bio-waste using a microwave reactor system

The dilute acid hydrolysis of grass and cellulose with phosphoric acid was undertaken in a microwave reactor system. The experimental data and reaction kinetic analysis indicate that this is a potential process for cellulose and hemi-cellulose hydrolysis, due to a rapid hydrolysis reaction at moderate temperatures. The optimum conditions for grass hydrolysis were found to be 2.5% phosphoric acid at a temperature of 175 degrees C. It was found that sugar degradation occurred at acid concentrations greater than 2.5% (v/v) and temperatures greater than 175 degrees C. In a further series of experiments, the kinetics of dilute acid hydrolysis of cellulose was investigated varying phosphoric acid concentration and reaction temperatures. The experimental data indicate that the use of microwave technology can successfully facilitate dilute acid hydrolysis of cellulose allowing high yields of glucose in short reaction times. The optimum conditions gave a yield of 90% glucose. A pseudo-homogeneous consecutive first order reaction was assumed and the reaction rate constants were calculated as: k(1) = 0.0813 s(-1); k(2) = 0.0075 s(-1), which compare favourably with reaction rate constants found in conventional non-microwave reaction systems. The kinetic analysis would indicate that the primary advantages of employing microwave heating were to: achieve a high rate constant at moderate temperatures: and to prevent 'hot spot' formation within the reactor, which would have cause localised degradation of glucose.

Development and characterization of self-assembling nanoparticles using a bio-inspired amphipathic peptide for gene delivery

The design of a non-viral gene delivery vehicle capable of delivering and releasing a functional nucleic acid cargo intracellularly remains a formidable challenge. For systemic gene therapy to be successful a delivery vehicle is required that protects the nucleic acid cargo from enzymatic degradation, extravasates from the vasculature, traverses the cell membrane, disrupts the endosomal vesicles and unloads the cargo at its destination site, namely the nucleus for the purposes of gene delivery. This manuscript reports the extensive investigation of a novel amphipathic peptide composed of repeating RALA units capable of overcoming the biological barriers to gene delivery both in vitro and in vivo. Our data demonstrates the spontaneous self-assembly of cationic DNA-loaded nanoparticles when the peptide is complexed with pDNA. Nanoparticles were < 100 nm, were stable in the presence of serum and were fusogenic in nature, with increased peptide α-helicity at a lower pH. Nanoparticles proved to be non-cytotoxic, readily traversed the plasma membrane of both cancer and fibroblast cell lines and elicited reporter-gene expression following intravenous delivery in vivo. The results of this study indicate that RALA presents an exciting delivery platform for the systemic delivery of nucleic acid therapeutics.

Combining Bio- and Chemo-Catalysis for the Conversion of Bio-Renewable Alcohols: Homogeneous Iridium Catalysed Hydrogen Transfer Initiated Dehydration of 1,3-Propanediol to Aldehydes

Combining whole cell biocatalysis and chemocatalysis in a single reaction sequence avoids unnecessary separations, and the associated waste and energy consumption. Bacterial fermentation has been employed to convert waste glycerol from biodiesel production into 1,3-propanediol. This 1,3-propanediol can be extracted selectively from the aqueous fermentation broth using ionic liquids. 1,3-propanediol in ionic liquid solution was converted to propanal by hydrogen transfer initiated dehydration (HTID) catalysed by a Cp*IrCl2(NHC) (Cp* = pentamethylcyclopentadienyl; NHC = carbene ligand) complex. The use of an ionic liquid solvent enabled the reaction to be performed under reduced pressure, facilitating the isolation of the product, and improving the reaction selectivity. The Ir(III) catalyst in ionic liquid was found to be highly recyclable.

Inexact-aware architecture design for ultra-low power bio-signal analysis

This study introduces an inexact, but ultra-low power, computing architecture devoted to the embedded analysis of bio-signals. The platform operates at extremely low voltage supply levels to minimise energy consumption. In this scenario, the reliability of static RAM (SRAM) memories cannot be guaranteed when using conventional 6-transistor implementations. While error correction codes and dedicated SRAM implementations can ensure correct operations in this near-threshold regime, they incur in significant area and energy overheads, and should therefore be employed judiciously. Herein, the authors propose a novel scheme to design inexact computing architectures that selectively protects memory regions based on their significance, i.e. their impact on the end-to-end quality of service, as dictated by the bio-signal application characteristics. The authors illustrate their scheme on an industrial benchmark application performing the power spectrum analysis of electrocardiograms. Experimental evidence showcases that a significance-based memory protection approach leads to a small degradation in the output quality with respect to an exact implementation, while resulting in substantial energy gains, both in the memory and the processing subsystem.

Compact simulated countercurrent chromatography for downstream processing of (bio)pharmaceuticals

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Design of bio-inspired ionic liquids for protein stabilisation

Ionic Liquids (ILs) consist in organic salts that are liquid at/or near room temperature. Since ILs are entirely composed of ions, the formation of ion pairs is expected to be one essential feature for describing solvation in ILs. In recent years, protein - ionic liquid (P-IL) interactions have been the subject of intensive studies mainly because of their capability to promote folding/unfolding of proteins. However, the ion pairs and their lifetimes in ILs in P-IL thematic is dismissed, since the action of ILs is therefore the result of a subtle equilibrium between anion-cation interaction, ion-solvent and ion-protein interaction. The work developed in this thesis innovates in this thematic, once the design of ILs for protein stabilisation was bio-inspired in the high concentration of organic charged metabolites found in cell milieu. Although this perception is overlooked, those combined concentrations have been estimated to be ~300 mM among the macromolecules at concentrations exceeding 300 g/L (macromolecular crowding) and transient ion-pair can naturally occur with a potential specific biological role. Hence the main objective of this work is to develop new bio-ILs with a detectable ion-pair and understand its effects on protein structure and stability, under crowding environment, using advanced NMR techniques and calorimetric techniques. The choline-glutamate ([Ch][Glu]) IL was synthesized and characterized. The ion-pair was detected in water solutions using mainly the selective NOE NMR technique. Through the same technique, it was possible to detect a similar ion-pair promotion under synthetic and natural crowding environments. Using NMR spectroscopy (protein diffusion, HSQC experiments, and hydrogen-deuterium exchange) and differential scanning calorimetry (DSC), the model protein GB1 (production and purification in isotopic enrichment media) it was studied in the presence of [Ch][Glu] under macromolecular crowding conditions (PEG, BSA, lysozyme). Under dilute condition, it is possible to assert that the [Ch][Glu] induces a preferential hydration by weak and non-specific interactions, which leads to a significant stabilisation. On the other hand, under crowding environment, the [Ch][Glu] ion pair is promoted, destabilising the protein by favourable weak hydrophobic interactions , which disrupt the hydration layer of the protein. However, this capability can mitigates the effect of protein crowders. Overall, this work explored the ion-pair existence and its consequences on proteins in conditions similar to cell milieu. In this way, the charged metabolites found in cell can be understood as key for protein stabilisation.

Sels d’imidazolium avec des anions catalytiques : vers le développement de nouveaux catalyseurs bio-hybrides actifs en milieu liquide ionique

Les liquides ioniques connaissent depuis quelques décennies un essor particulier en raison de leurs nombreuses propriétés physico-chimiques intéressantes, telles qu’une faible pression de vapeur saturante, une viscosité limitée, une faible miscibilité avec la plupart des solvants communs, ou encore des propriétés d’agencement supramoléculaire, qui en font des outils puissants dans de nombreux domaines de la chimie. Les sels d’imidazolium représentent la plus grande famille de liquides ioniques à ce jour. Leur modulabilité leur permet d’être dérivés pour de nombreuses applications spécifiques, notamment en synthèse organique, où ils sont utilisés majoritairement comme solvants, et plus récemment comme catalyseurs. Les travaux présentés dans cette thèse se concentrent sur leur utilisation en synthèse organique, à la fois comme solvants et principalement comme catalyseurs chiraux, catalyseurs pour lesquels l’anion du sel est l’espèce catalytique, permettant d’ajouter de la flexibilité et de la mobilité au système. En tirant parti de la tolérance des liquides ioniques envers la majorité des macromolécules naturelles, l’objectif principal des travaux présentés dans cette thèse est le développement d’un nouveau type de catalyseur bio-hybride reposant sur l’encapsulation d’un sel d’imidazolium dans une protéine. Par le biais de la technologie biotine-avidine, l’inclusion supramoléculaire de sels d’imidazolium biotinylés portant des contre-anions catalytiques dans l’avidine a été réalisée et exploitée en catalyse. Dans un premier temps, le développement et l’étude de deux sels de 1-butyl-3-méthylimidazolium possédant des anions chiraux dérivés de la trans-4-hydroxy-L-proline sont rapportés, ainsi que leur comportement dans des réactions énantiosélectives d’aldol et d’addition de Michael. Ces types de composés se sont révélés actifs et performants en milieu liquide ionique. Dans un second temps, la préparation de sels d’imidazolium dont le cation est biotinylé et portant un contre-anion achiral, a été réalisée. Le comportement de l’avidine en milieu liquide ionique et son apport en termes de chiralité sur le système bio-hybride ont été étudiés. Les résultats montrent le rôle crucial des liquides ioniques sur la conformation de la protéine et l’efficacité du catalyseur pour des réactions d’aldol. Dans un dernier temps, l’influence de la structure du cation et de l’anion sur le système a été étudiée. Différents espaceurs ont été introduits successivement dans les squelettes cationiques et anioniques des sels d’imidazolium biotinylés. Dans le cas du cation, les résultats ne révèlent aucune influence majeure sur l’efficacité du catalyseur. La structure de l’anion se montre cependant beaucoup plus importante : la préparation de différents catalyseurs bio-hybrides possédant des anions aux propriétés physico-chimiques différentes a permis d’obtenir de plus amples informations sur le mode de fonctionnement du système bio-hybride et de la coopérativité entre l’avidine et l’anion du sel d’imidazolium.La nature ionique de la liaison cation-anion offrant une liberté de mouvement accrue à l’anion dans la protéine, la tolérance à différents substrats a également été abordée après optimisation du système.

Des bio-objets pour la bioéthique. Compte rendu de Bio-Objects: Life in the 21st Century

Compte-rendu / Review

Sistemas bio-inspirados: Un marco teórico para la ingeniería de sistemas complejos

En este texto buscamos sentar las bases para el marco teórico de la ingeniería de sistemas complejos. Hasta la fecha, un marco semejante ha sido apenas enunciado, y en términos bastante generales (Wolfram, 1986). Sin embargo, hasta ahora no se ha logrado formular un marco semejante que sirva a los ingenieros, a los científicos y a los filósofos para afirmar con seguridad que se tiene ya un marco teórico para la ingeniería de sistemas complejos. Al sentar el siguiente marco trazamos claramente los límites que separan a la ingeniería clásica −incluida la ingeniería de procesos inversos− de la ingeniería de sistemas complejos. Nos encontramos en el centro de una revolución científica y teórica, en términos de T. Kuhn. Luego de separar, de manera rápida, la ingeniería clásica de la ingeniería de sistemas complejos, obtenemos una visión más clara acerca de la ingeniería bio-inspirada. A fin de plantear de manera radical un (nuevo) marco teórico para la ingeniería de sistemas complejos (ISC), procedemos en zigzag así: de un lado, sobre una base al mismo tiempo científica e ingenieril, sugerimos un perímetro orgánico para la ISC; de otra parte, sobre la base de la filosofía y las lógicas no-clásicas, alcanzamos nuevas herramientas conceptuales que profundizan las bases científicas e ingenieriles. Al final se hace claro el horizonte amplio y la visión acerca del marco de la ingeniería de sistemas complejos, a saber: se trata, ulteriormente, de una teoría general de los sistemas complejos. Así, la ISC forma parte de las ciencias de la complejidad.