Satellite remote sensing reveals a positive impact of living oyster reefs on microalgal biofilm development

Satellite remote sensing (RS) is routinely used for the large-scale monitoring of microphytobenthos (MPB) biomass in intertidal mudflats and has greatly improved our knowledge of MPB spatio-temporal variability and its potential drivers. Processes operating on smaller scales however, such as the impact of benthic macrofauna on MPB development, to date remain underinvestigated. In this study, we analysed the influence of wild Crassostrea gigas oyster reefs on MPB biofilm development using multispectral RS. A 30-year time series (1985-2015) combining high-resolution (30 m) Landsat and SPOT data was built in order to explore the relationship between C. gigas reefs and MPB spatial distribution and seasonal dynamics, using the normalized difference vegetation index (NDVI). Emphasis was placed on the analysis of a before-after control-impact (BACI) experiment designed to assess the effect of oyster killing on the surrounding MPB biofilms. Our RS data reveal that the presence of oyster reefs positively affects MPB biofilm development. Analysis of the historical time series first showed the presence of persistent, highly concentrated MPB patches around oyster reefs. This observation was supported by the BACI experiment which showed that killing the oysters (while leaving the physical reef structure, i.e. oyster shells, intact) negatively affected both MPB biofilm biomass and spatial stability around the reef. As such, our results are consistent with the hypothesis of nutrient input as an explanation for the MPB growth-promoting effect of oysters, whereby organic and inorganic matter released through oyster excretion and biodeposition stimulates MPB biomass accumulation. MPB also showed marked seasonal variations in biomass and patch shape, size and degree of aggregation around the oyster reefs. Seasonal variations in biomass, with higher NDVI during spring and autumn, were consistent with those observed on broader scales in other European mudflats. Our study provides the first multi-sensor RS satellite evidence of the promoting and structuring effect of oyster reefs on MPB biofilms

Formal security analysis of registration protocols for interactive systems: a methodology and a case of study

In this work we present and formally analyze CHAT-SRP (CHAos based Tickets-Secure Registration Protocol), a protocol to provide interactive and collaborative platforms with a cryptographically robust solution to classical security issues. Namely, we focus on the secrecy and authenticity properties while keeping a high usability. In this sense, users are forced to blindly trust the system administrators and developers. Moreover, as far as we know, the use of formal methodologies for the verification of security properties of communication protocols isn't yet a common practice. We propose here a methodology to fill this gap, i.e., to analyse both the security of the proposed protocol and the pertinence of the underlying premises. In this concern, we propose the definition and formal evaluation of a protocol for the distribution of digital identities. Once distributed, these identities can be used to verify integrity and source of information. We base our security analysis on tools for automatic verification of security protocols widely accepted by the scientific community, and on the principles they are based upon. In addition, it is assumed perfect cryptographic primitives in order to focus the analysis on the exchange of protocol messages. The main property of our protocol is the incorporation of tickets, created using digests of chaos based nonces (numbers used only once) and users' personal data. Combined with a multichannel authentication scheme with some previous knowledge, these tickets provide security during the whole protocol by univocally linking each registering user with a single request. [..]Comment: 32 pages, 7 figures, 8 listings, 1 tabl

Electroweak Tests at Beta-beams

We explore the possibility of measuring the Weinberg angle from (anti)neutrino-electron scattering using low energy beta beams, a method that produces single flavour neutrino beams from the beta-decay of boosted radioactive ions. We study how the sensitivity of a possible measurement depends on the intensity of the ion beam and on a combination of different Lorentz boosts of the ions.Comment: 10 pages, 6 figure

Breathers in inhomogeneous nonlinear lattices: an analysis via centre manifold reduction

We consider an infinite chain of particles linearly coupled to their nearest neighbours and subject to an anharmonic local potential. The chain is assumed weakly inhomogeneous. We look for small amplitude discrete breathers. The problem is reformulated as a nonautonomous recurrence in a space of time-periodic functions, where the dynamics is considered along the discrete spatial coordinate. We show that small amplitude oscillations are determined by finite-dimensional nonautonomous mappings, whose dimension depends on the solutions frequency. We consider the case of two-dimensional reduced mappings, which occurs for frequencies close to the edges of the phonon band. For an homogeneous chain, the reduced map is autonomous and reversible, and bifurcations of reversible homoclinics or heteroclinic solutions are found for appropriate parameter values. These orbits correspond respectively to discrete breathers, or dark breathers superposed on a spatially extended standing wave. Breather existence is shown in some cases for any value of the coupling constant, which generalizes an existence result obtained by MacKay and Aubry at small coupling. For an inhomogeneous chain the study of the nonautonomous reduced map is in general far more involved. For the principal part of the reduced recurrence, using the assumption of weak inhomogeneity, we show that homoclinics to 0 exist when the image of the unstable manifold under a linear transformation intersects the stable manifold. This provides a geometrical understanding of tangent bifurcations of discrete breathers. The case of a mass impurity is studied in detail, and our geometrical analysis is successfully compared with direct numerical simulations

Contexts for questioning: Two zones of teaching and learning in undergraduate science

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ Springer Science+Business Media B.V. 2012.Higher education institutions are currently undertaking a challenging process in moving from teacher-orientated to student-focused approaches. Students’ ability to asking questions is fundamental to developing critical reasoning, and to the process of scientific enquiry itself. Our premise is that questioning competences should become a central focus of current reforms in higher education. This study, part of a broader naturalistic research project, aims at developing a theoretical framework for conceptualizing different contexts for questioning, illustrating the application of the proposed framework (contextual questioning zones) and reflecting about some of the dimensions of teaching and learning, for overcoming some of the challenges that higher education institutions are facing presently. The discussion of two ‘opposite’ contexts of enquiry is based on qualitative data, gathered through close collaboration with four teachers of undergraduate biology at a Portuguese university. These teachers were observed during their ‘daily activity’ during an academic year. Data was also gathered by interviewing these teachers and 8 selected students, at the end of the year, and used to sustain the argumentation. The paper concludes with some reflections and suggestions to promote authentic enquiry-based learning experiences.Portuguese Fundação para a Ciência e a Tecnologi

Development of mass spectrometry techniques for analysis of biomedical systems

2020 Spring.Includes bibliographical references.The advances of modern mass spectrometry (MS) have allowed MS to become one of the essential analytical tools for biological and biomedical research. Mass spectrometry's ability to provide rapid and sensitive analysis of many types of analytes made it an excellent candidate to study the polysaccharide dextran, biodegradable poly(organophosphazene) and polyester derived polymers, as well as interfering species in commonly used cell viability studies. Electrospray ionization time-of-flight mass spectrometry (ESI-TOF MS) was used to analyze the polysaccharide dextran. Polysaccharides, including dextran, are difficult to ionize due to their inherent neutrality. Ionization efficiency is poor in negative polarity ESI because they lack acidic groups typically needed for proton abstraction, and ionization efficiency in positive polarity ESI is poor because polysaccharides have low proton affinity. In efforts to circumvent the issue of low ionization efficiency, dextran was derivatized to try mimicking protein-like ionization. Dextran was derivatized using a one-pot derivatization procedure with ethylenediamine, thus, giving dextran free terminal amine groups. The derivatization procedure attached up to four ethylenediamine groups and allowed dextran to have up to four protonations (or positive charges). The ability to carry up to four charges shifted the molecular weight of dextran to a lower m/z, similar to protein supercharging ionization. Mass spectrometric analysis was successfully applied to identify potential degradation products during the catalytic release of nitric oxide (NO) from S-nitrosoglutathione (GSNO) when it was exposed to metal-organic frameworks (MOFs) embedded onto chitosan polymer support systems. Oxidized glutathione (GSSG) was confirmed to be the reaction byproduct of the release of NO from GSNO, and glucosamine and N-acetylglucosamine were identified as the degradation products from the chitosan polymer support system. In a similar use of MS, potential interferences in the commonly used CellTiter Blue and MTT cell viability assays were studied. When the UV-vis spectroscopic assays suggested interferences or produced inconclusive results, mass spectrometric analyses accurately determined whether selected small molecules were responsible for conversion of resazurin to resorufin, MTT to formazan, or if they were responsible for severe signal suppression on the UV-vis spectroscopic assays. MS was also successfully used to study the biodegradable poly(phosphazene), polyester polymers and their nitrosated analogues. The purpose of the studies was to investigate the potential degradation products from the degradation of these polymers. In-depth understanding of the degradation products from these polymers may aid in determining potential unwanted side effects that may render the polymeric devices unusable. A combination of direct flow injection MS, liquid chromatography mass spectrometry (LC-MS), and tandem mass spectrometry (LC-MS/MS) were successfully applied to identify the degradation products from each polymer system investigated. Identification of each degradation product from these polymers strongly suggests the implementation of LC-MS/MS when biodegradable polymers are developed for biomedical applications. Particularly because these methods can be used when a device intended for medical use undergoes the ISO 10993 series Biological Evaluation of Medical Devices. Additionally, in a highly collaborative effort, a chiral metal-organic framework (MOF) was used as a chiral stationary phase (CSP) for chiral resolution. The chiral-MOF (TAMOF-1) was packed in-house into an empty HPLC column and successfully used to resolve chiral compounds efficiently using normal and reversed phase solvent systems, highlighting the versatility of the chiral-MOF

Chromatographic analysis of fatty acids using 9-chloromethyl-anthracene and 2-bromomethyl-anthraquinone

Fatty acids are carboxylic acids with long alkane or alkene chains and are important components of living organisms. The presence of the carboxylic acid is analytically very important since it allows for derivatization with fluorescence reagents such as 9-chloromethyl-anthracene (9-CMA) for HPLC analysis. A method for the analysis of fatty acids using 9-CMA and 2-bromomethyl-anthraquinone (MAQ-Br) was developed. The method utilizes a modified protocol previously used for the analysis of short-chain carboxylic acids with 9-CMA. The modified protocol was applied to medium- and long-chain fatty acids for analysis by HPLC with UV-visible and fluorescence detection. After successful derivatization and analysis using 9-CMA, MAQ-Br was used for derivatization with successful results. Six fatty acid standards were derivatized with 9-CMA and utilized to develop a separation method and quantification. With the use of a Zorbax Rx C8 column, good separation was achieved and calibration curves ranging from 1 to 100 pmol with good linearity and R2 values. The limit of detection was approximately 50 fmol and the maximum limit of quantitation was approximately 100 pmol for the 9-CMA derivatives. After successful separation and quantitation, analyses of fat-free cooking spray and cloprostenol, a prostaglandin, were performed