Lagrangian evolution of DMS during the Southern Ocean gas exchange experiment: The effects of vertical mixing and biological community shift

Concentrations of dimethylsulfide (DMS) and its precursor dimethylsulfoniopropionate (DMSP) are highly variable in time and space. What is driving the variability in DMS(P), and can those variability be explained by physical processes and changes in the biological community? During the Southern Ocean Gas Exchange Experiment (SO GasEx) in the austral fall of 2008, two 3He/SF6 labeled patches were created in the surface water. SF6 and DMS were surveyed continuously in a Lagrangian framework, while direct measurements of air-sea exchange further constrained the gas budgets. Turbulent diffusivity at the base of the mixed layer was estimated from SF6 profiles and used to calculate the vertical fluxes of DMS and nutrients. Increasing mixed layer nutrient concentrations due to mixing were associated with a shift in the phytoplankton community structure, which in turned likely affected the sulfur dynamics on timescales of days. DMS concentration as well as air-sea DMS flux appeared to be decoupled from the DMSP concentration, possibly due to grazing and bacterial DMS production. Contrary to expectations, in an environment with high winds and modest productivity, physical processes (air-sea exchange, photochemistry, vertical mixing) only accounted for a small fraction of DMS loss from the surface water. Among the DMS sinks, inferred biological consumption most likely dominated during SO GasEx.

Beyond long-term averages: making biological sense of a rapidly changing world

Biological responses to climate change are typically communicated in generalized terms such as poleward and altitudinal range shifts, but adaptation efforts relevant to management decisions often require forecasts that incorporate the interaction of multiple climatic and nonclimatic stressors at far smaller spatiotemporal scales. We argue that the desire for generalizations has, ironically, contributed to the frequent conflation of weather with climate, even within the scientific community. As a result, current predictions of ecological responses to climate change, and the design of experiments to understand underlying mechanisms, are too often based on broad-scale trends and averages that at a proximate level may have very little to do with the vulnerability of organisms and ecosystems. The creation of biologically relevant metrics of environmental change that incorporate the physical mechanisms by which climate trains patterns of weather, coupled with knowledge of how organisms and ecosystems respond to these changes, can offer insight into which aspects of climate change may be most important to monitor and predict. This approach also has the potential to enhance our ability to communicate impacts of climate change to nonscientists and especially to stakeholders attempting to enact climate change adaptation policies.

iMarNet: an ocean biogeochemistry model intercomparison project within a common physical ocean modelling framework

Ocean biogeochemistry (OBGC) models span a wide variety of complexities, including highly simplified nutrient-restoring schemes, nutrient–phytoplankton–zooplankton–detritus (NPZD) models that crudely represent the marine biota, models that represent a broader trophic structure by grouping organisms as plankton functional types (PFTs) based on their biogeochemical role (dynamic green ocean models) and ecosystem models that group organisms by ecological function and trait. OBGC models are now integral components of Earth system models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here we present an intercomparison of six OBGC models that were candidates for implementation within the next UK Earth system model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the ocean general circulation model Nucleus for European Modelling of the Ocean (NEMO) and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform all other models across all metrics. Nonetheless, the simpler models are broadly closer to observations across a number of fields and thus offer a high-efficiency option for ESMs that prioritise high-resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low-resolution climate dynamics and high-complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry–climate interactions.

An introduction to biological nuclear magnetic resonance spectroscopy

ABSTRACT Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful analytical techniques available to biology. This review is an introduction to the potential of this method and is aimed at readers who have little or no experience in acquiring or analyzing NMR spectra. We focus on spectroscopic applications of the magnetic resonance effect, rather than imaging ones, and explain how various aspects of the NMR phenomenon make it a versatile tool with which to address a number of biological problems. Using detailed examples, we discuss the use of 1H NMR spectroscopy in mixture analysis and metabolomics, the use of 13C NMR spectroscopy in tracking isotopomers and determining the flux through metabolic pathways (‘fluxomics’) and the use of 31P NMR spectroscopy in monitoring ATP generation and intracellular pH homeotasis in vivo. Further examples demonstrate how NMR spectroscopy can be used to probe the physical environment of a cell by measuring diffusion and the tumbling rates of individual metabolites and how it can determine macromolecular structures by measuring the bonds and distances which separate individual atoms. We finish by outlining some of the key challenges which remain in NMR spectroscopy and we highlight how recent advances— such as increased magnet field strengths, cryogenic cooling, microprobes and hyperpolarisation—are opening new avenues for today’s biological NMR spectroscopists.

Water structure and chaotropicity: their uses, abuses and biological implications

The concept of "water structure" has been invoked to explain all manner of aqueous phenomena. Here we look at the origins of this tendency to understand solute hydration in terms of structural changes in bulk water, and consider the validity of one particular example: the classification of small solutes as chaotropic or kosmotropic, and the putative relation of this terminology to notions of structure-making and structure-breaking in the solvent. We doubt whether complex phenomena such as Hofmeister and osmolyte effects on macromolecules can be understood simply on the basis of a change in solvent structure. Rather, we argue that chaotropicity, if understood in the original sense, arises from the activities that solutes exert on macromolecular systems, as well as from deviations of solvation water from bulk-like behaviour. If applied judiciously, chaotropicity remains a potent, biologically pertinent parameter useful for classifying and understanding solution phenomena in all types of living system.

Transcending epithelial and intracellular biological barriers; a prototype DNA delivery device

Microneedle technology provides the opportunity for the delivery of DNA therapeutics by a non-invasive, patient acceptable route. To deliver DNA successfully requires consideration of both extra and intracellular biological barriers. In this study we present a novel two tier platform; i) a peptide delivery system, termed RALA, that is able to wrap the DNA into nanoparticles, protect the DNA from degradation, enter cells, disrupt endosomes and deliver the DNA to the nucleus of cells ii) a microneedle (MN) patch that will house the nanoparticles within the polymer matrix, breach the skin's stratum corneum barrier and dissolve upon contact with skin interstitial fluid thus releasing the nanoparticles into the skin. Our data demonstrates that the RALA is essential for preventing DNA degradation within the poly(vinylpyrrolidone) (PVP) polymer matrix. In fact the RALA/DNA nanoparticles (NPs) retained functionality when in the MN arrays after 28days and over a range of temperatures. Furthermore the physical strength and structure of the MNs was not compromised when loaded with the NPs. Finally we demonstrated the effectiveness of our MN-NP platform in vitro and in vivo, with systemic gene expression in highly vascularised regions. Taken together this 'smart-system' technology could be applied to a wide range of genetic therapies.

Climatic patterns and physical controls of chlorophyll-a in the Northeast Atlantic

Tese de Doutoramento, Física, 17 de Dezembro de 2013, Universidade dos Açores.

The Fast Regulation of Photosynthesis in Diatoms: an inquiry into the physiological and physical origins of non-photochemical chlorophyll fluorescence quenching.

Diatoms are renowned for their robust ability to perform NPQ (Non-Photochemical Quenching of chlorophyll fluorescence) as a dissipative response to heightened light stress on photosystem II, plausibly explaining their dominance over other algal groups in turbulent light environs. Their NPQ mechanism has been principally attributed to a xanthophyll cycle involving the lumenal pH regulated reversible de-epoxidation of diadinoxanthin. The principal goal of this dissertation is to reveal the physiological and physical origins and consequences of the NPQ response in diatoms during short-term transitions to excessive irradiation. The investigation involves diatom species from different originating light environs to highlight the diversity of diatom NPQ and to facilitate the detection of core mechanisms common among the diatoms as a group. A chiefly spectroscopic approach was used to investigate NPQ in diatom cells. Prime methodologies include: the real time monitoring of PSII excitation and de-excitation pathways via PAM fluorometry and pigment interconversion via transient absorbance measurements, the collection of cryogenic absorbance spectra to measure pigment energy levels, and the collection of cryogenic fluorescence spectra and room temperature picosecond time resolved fluorescence decay spectra to study excitation energy transfer and dissipation. Chemical inhibitors that target the trans-thylakoid pH gradient, the enzyme responsible for diadinoxanthin de-epoxidation, and photosynthetic electron flow were additionally used to experimentally manipulate the NPQ response. Multifaceted analyses of the NPQ responses from two previously un-photosynthetically characterised species, Nitzschia curvilineata and Navicula sp., were used to identify an excitation pressure relief ‘strategy’ for each species. Three key areas of NPQ were examined: (i) the NPQ activation/deactivation processes, (ii) how NPQ affects the collection, dissipation, and usage of absorbed light energy, and (iii) the interdependence of NPQ and photosynthetic electron flow. It was found that Nitzschia cells regulate excitation pressure via performing a high amplitude, reversible antenna based quenching which is dependent on the de-epoxidation of diadinoxanthin. In Navicula cells excitation pressure could be effectively regulated solely within the PSII reaction centre, whilst antenna based, diadinoxanthin de-epoxidation dependent quenching was implicated to be used as a supplemental, long-lasting source of excitation energy dissipation. These strategies for excitation balance were discussed in the context of resource partitioning under these species’ originating light climates. A more detailed investigation of the NPQ response in Nitzschia was used to develop a comprehensive model describing the mechanism for antenna centred non-photochemical quenching in this species. The experimental evidence was strongly supportive of a mechanism whereby: an acidic lumen triggers the diadinoxanthin de-epoxidation and protonation mediated aggregation of light harvesting complexes leading to the formation of quencher chlorophyll a-chlorophyll a dimers with short-lived excited states; quenching relaxes when a rise in lumen pH triggers the dispersal of light harvesting complex aggregates via deprotonation events and the input of diadinoxanthin. This model may also be applicable for describing antenna based NPQ in other diatom species.

BioJADE: A Design and Simulation Tool for Synthetic Biological Systems

The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us with the ability to build cells that are capable of a plethora of activities, from computation to synthesizing nanostructures. To develop these systems, we must have a set of tools not only for synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible design and simulation platform for synthetic biology. BioJADE is a graphical design tool built in Java, utilizing a database back end, and supports a range of simulations using an XML communication protocol. BioJADE currently supports a library of over 100 parts with which it can compile designs into actual DNA, and then generate synthesis instructions to build the physical parts. The BioJADE project contributes several tools to Synthetic Biology. BioJADE in itself is a powerful tool for synthetic biology designers. Additionally, we developed and now make use of a centralized BioBricks repository, which enables the sharing of BioBrick components between researchers, and vastly reduces the barriers to entry for aspiring Synthetic Biologists.

Calidad de vida en personas con hemofilia: una revisión de la literatura

Introducción: La hemofilia es una enfermedad poco frecuente; no obstante, los avances en los tratamientos de pacientes hemofílicos en las últimas décadas han generado cambios en su calidad de vida. Esto ha motivado el desarrollo de múltiples investigaciones al respecto. Objetivo: Revisar la literatura sobre la calidad de vida en el paciente hemofílico, producida en el periodo 2008-2012. Método: Se consultaron algunas bases de datos científicas utilizando como palabras clave “hemofilia” y “calidad de vida”. Se recopiló la información encontrada y se organizó según los objetivos propuestos en “factores negativos” y “factores protectores” de la calidad de vida a nivel fisiológico, psicosocial y cultural; “instrumentos para la evaluación de la calidad de vida” a nivel específico y general; y antecedentes empíricos de los últimos cinco años en los que se evaluara la calidad de vida o se realizara alguna intervención en la misma. Resultados: En general la información disponible sobre el comportamiento epidemiológico de la hemofilia es limitada. El interés por factores protectores y negativos es principalmente de tipo fisiológico, aunque se encontraron factores de tipo psicosocial y cultural, lo que indica la importancia de profundizar en esta temática. Existen pocos instrumentos especializados para la evaluación de la calidad de vida en hemofílicos. La evidencia empírica se centra en la evaluación. Conclusión: El estudio de la calidad de vida en pacientes hemofílicos amerita ser abordado de manera interdisciplinaria.

Reflections about physiotherapist professional performance in the field of physical activity

The physiotherapist professional activities, in the beginning were focused only in the clinical field, nowadays it has many different action fields including Physical Activity. Physical activity can be viewed from two dimensions: one biological, which is defined as any activity which requires energy expenditure involving the combined action of multiple systems; on the other side social, understood as a human activity concerning subjectivity conditions influenced by the environment where the individual and the community are developed. Given these dimensions as well as national and international benchmarks this paper’s objective is to present a series of reflections that the authors have done regarding the physiotherapist professional performance in the field of physical activity and the large possibilities derived from their practice in this field.

Studies of dynamics of physical agent ecosystems

This thesis addresses the problem of learning in physical heterogeneous multi-agent systems (MAS) and the analysis of the benefits of using heterogeneous MAS with respect to homogeneous ones. An algorithm is developed for this task; building on a previous work on stability in distributed systems by Tad Hogg and Bernardo Huberman, and combining two phenomena observed in natural systems, task partition and hierarchical dominance. This algorithm is devised for allowing agents to learn which are the best tasks to perform on the basis of each agent's skills and the contribution to the team global performance. Agents learn by interacting with the environment and other teammates, and get rewards from the result of the actions they perform. This algorithm is specially designed for problems where all robots have to co-operate and work simultaneously towards the same goal. One example of such a problem is role distribution in a team of heterogeneous robots that form a soccer team, where all members take decisions and co-operate simultaneously. Soccer offers the possibility of conducting research in MAS, where co-operation plays a very important role in a dynamical and changing environment. For these reasons and the experience of the University of Girona in this domain, soccer has been selected as the test-bed for this research. In the case of soccer, tasks are grouped by means of roles. One of the most interesting features of this algorithm is that it endows MAS with a high adaptability to changes in the environment. It allows the team to perform their tasks, while adapting to the environment. This is studied in several cases, for changes in the environment and in the robot's body. Other features are also analysed, especially a parameter that defines the fitness (biological concept) of each agent in the system, which contributes to performance and team adaptability. The algorithm is applied later to allow agents to learn in teams of homogeneous and heterogeneous robots which roles they have to select, in order to maximise team performance. The teams are compared and the performance is evaluated in the games against three hand-coded teams and against the different homogeneous and heterogeneous teams built in this thesis. This section focuses on the analysis of performance and task partition, in order to study the benefits of heterogeneity in physical MAS. In order to study heterogeneity from a rigorous point of view, a diversity measure is developed building on the hierarchic social entropy defined by Tucker Balch. This is adapted to quantify physical diversity in robot teams. This tool presents very interesting features, as it can be used in the future to design heterogeneous teams on the basis of the knowledge on other teams.

Layer-by-layer electrostatic entrapment of protein molecules on superparamagnetic nanoparticle: new strategy to enhance adsorption capacity and maintain biological activity

There is a recent interest to use inorganic-based magnetic nanoparticles as a vehicle to carry biomolecules for various biophysical applications, but direct attachment of the molecules is known to alter their conformation leading to attenuation in activity. In addition, surface immobilization has been limited to monolayer coverage. It is shown that alternate depositions of negatively charged protein molecules, typically bovine serum albumin (BSA) with a positively charged aminocarbohydrate template such as glycol chitosan (GC) on magnetic iron oxide nanoparticle surface as a colloid, are carried out under pH 7.4. Circular dichroism (CD) clearly reveals that the secondary structure of the entrapped BSA sequential depositions in this manner remains totally unaltered which is in sharp contrast to previous attempts. Probing the binding properties of the entrapped BSA using small molecules (Site I and Site II drug compounds) confirms for the first time the full retention of its biological activity as compared with native BSA, which also implies the ready accessibility of the entrapped protein molecules through the porous overlayers. This work clearly suggests a new method to immobilize and store protein molecules beyond monolayer adsorption on a magnetic nanoparticle surface without much structural alteration. This may find applications in magnetic recoverable enzymes or protein delivery.