Design, synthesis, and characterization of a photoactivatable flavocytochrome molecular maquette

We report the construction of a synthetic flavo-heme protein that incorporates two major physiological activities of flavoproteins: light activation of flavin analogous to DNA photolyase and rapid intramolecular electron transfer between the flavin and heme cofactors as in several oxidoreductases. The functional tetra-α-helix protein comprises two 62-aa helix-loop-helix subunits. Each subunit contains a single cysteine to which flavin (7-acetyl-10-methylisoalloxazine) is covalently attached and two histidines appropriately positioned for bis-his coordination of heme cofactors. Both flavins and hemes are situated within the hydrophobic core of the protein. Intramolecular electron transfer from flavosemiquinone generated by photoreduction from a sacrificial electron donor in solution was examined between protoporphyrin IX and 1-methyl-2-oxomesoheme XIII. Laser pulse-activated electron transfer from flavin to meso heme occurs on a 100-ns time scale, with a favorable free energy of approximately −100 meV. Electron transfer from flavin to the lower potential protoporphyrin IX, with an unfavorable free energy, can be induced after a lag phase under continuous light illumination. Thus, the supporting peptide matrix provides an excellent framework for the positioning of closely juxtaposed redox groups capable of facilitating intramolecular electron transfer and begins to clarify in a simplified and malleable system the natural engineering of flavoproteins.

Signals and signs in the nervous system: The dynamic anatomy of electrical activity is probably information-rich

The dichotomy between two groups of workers on neuroelectrical activity is retarding progress. To study the interrelations between neuronal unit spike activity and compound field potentials of cell populations is both unfashionable and technically challenging. Neither of the mutual disparagements is justified: that spikes are to higher functions as the alphabet is to Shakespeare and that slow field potentials are irrelevant epiphenomena. Spikes are not the basis of the neural code but of multiple codes that coexist with nonspike codes. Field potentials are mainly information-rich signs of underlying processes, but sometimes they are also signals for neighboring cells, that is, they exert influence. This paper concerns opportunities for new research with many channels of wide-band (spike and slow wave) recording. A wealth of structure in time and three-dimensional space is different at each scale—micro-, meso-, and macroactivity. The depth of our ignorance is emphasized to underline the opportunities for uncovering new principles. We cannot currently estimate the relative importance of spikes and synaptic communication vs. extrasynaptic graded signals. In spite of a preponderance of literature on the former, we must consider the latter as probably important. We are in a primitive stage of looking at the time series of wide-band voltages in the compound, local field, potentials and of choosing descriptors that discriminate appropriately among brain loci, states (functions), stages (ontogeny, senescence), and taxa (evolution). This is not surprising, since the brains in higher species are surely the most complex systems known. They must be the greatest reservoir of new discoveries in nature. The complexity should not deter us, but a dose of humility can stimulate the flow of imaginative juices.

Limnologia, balneabilidade e impactos ambientais: uma análise temporal e espacial na represa do Lobo (Broa), Itirapina/Brotas - SP

Considerando a importância da represa do Lobo, os indícios de eutrofização encontrados na área e tendo a recreação como seu principal uso, buscou-se, neste trabalho, avaliar a qualidade da água nos rios tributários e na represa, e sua adequação a balneabilidade. Para os afluentes do sistema, estimando-se, ainda, a contribuição dos mesmos ao aporte de materiais à represa, foram amostrados o córrego do Geraldo, a confluência dos córregos Água Branca e Limoeiro, o rio Itaqueri (antes da mineradora), o ribeirão do Lobo, o córrego das Perdizes, avaliando-se parâmetros físicos, químicos e biológicos da água e a vazão dos rios, em dois períodos (agosto/setembro e dezembro) de 2002. Os resultados, com base no índice de estado trófico, indicam que a maioria dos tributários, com exceção do córrego Água Branca (eutrófico), é oligotrófico. Na represa o estudo teve avaliações mensais para alguns parâmetros (nutrientes totais e dissolvidos, clorofila total e material em suspensão) e semanais para outros (pH, condutividade elétrica, temperatura da água, oxigênio dissolvido e coliformes fecais) ao longo de um ano (dezembro de 2001 a dezembro de 2002), em nove pontos, abrangendo a região de foz do rio Itaqueri, córrego do Geraldo e ribeirão do Lobo, quatro pontos distribuídos na praia do balneário Santo Antônio e um ponto a jusante da represa. A foz do rio Itaqueri apresentou-se meso-eutrófica no período, enquanto os outros pontos avaliados, oligotróficos. Apesar da condição favorável apresentada, a análise temporal dos dados (com estudos realizados nos últimos 30 anos), mostra uma evidente e preocupante alteração nas condições originárias desse sistema, indicando um evidente processo de eutrofização do reservatório, associado aos usos e ocupação da bacia hidrográfica (resíduos domiciliares, turismo, agricultura e pecuária). Em relação a balneabilidade os principais pontos de contaminação fecal na represa são as entradas dos tributários, enquanto o corpo da represa foi considerado excelente em todo o período amostrado. O córrego Água Branca, como corpo receptor do esgoto de Itirapina, é o mais comprometido dos corpos de água avaliados, além de ser o principal contribuinte de nutrientes e coliformes fecais para a represa do Lobo, através do rio Itaqueri.

Evidence of different thermoregulatory mechanisms between two sympatric Scarabaeus species using infrared thermography and micro-computer tomography

In endotherms insects, the thermoregulatory mechanisms modulate heat transfer from the thorax to the abdomen to avoid overheating or cooling in order to obtain a prolonged flight performance. Scarabaeus sacer and S. cicatricosus, two sympatric species with the same habitat and food preferences, showed daily temporal segregation with S. cicatricosus being more active during warmer hours of the day in opposition to S. sacer who avoid it. In the case of S. sacer, their endothermy pattern suggested an adaptive capacity for thorax heat retention. In S. cicatricosus, an active ‘heat exchanger’ mechanism was suggested. However, no empirical evidence had been documented until now. Thermographic sequences recorded during flight performance showed evidence of the existence of both thermoregulatory mechanisms. In S. sacer, infrared sequences showed a possible heat insulator (passive thermal window), which prevents heat transfer from meso- and metathorax to the abdomen during flight. In S. cicatricosus, infrared sequences revealed clear and effective heat flow between the thorax and abdomen (abdominal heat transfer) that should be considered the main mechanism of thermoregulation. This was related to a subsequent increase in abdominal pumping (as a cooling mechanism) during flight. Computer microtomography scanning, anatomical dissections and internal air volume measurements showed two possible heat retention mechanisms for S. sacer; the abdominal air sacs and the development of the internal abdominal sternites that could explain the thermoregulation between thorax and abdomen. Our results suggest that interspecific interactions between sympatric species are regulated by very different mechanisms. These mechanisms create unique thermal niches for the different species, thereby preventing competition and modulating spatio-temporal distribution and the composition of dung beetle assemblages.

Ciberperiodismo: definiciones, desarrollo y tipología

La aparición de Internet ha cambiado los medios de comunicación. En un primer momento, el desconocimiento de las posibilidades que ofrecía marcaron el paso del mundo analógico al mundo digital, pero después los diarios, las radios y las televisiones se han introducido masivamente en la Red y también han aparecido nuevos medios creados específicamente para Internet. Estos cambios han sido objeto de estudio de los investigadores y se ha hecho necesaria la consolidación de una nueva terminología. Se explican en este trabajo las cuestiones terminológicas que afectan el ciberperiodismo, se define el concepto de estudio, para hacer después un breve recorrido por la historia de la ciberprensa y las diferentes etapas y tipologías de cibermedios que han establecido los investigadores.

Spatial Distribution of Marine Epibenthic Communities in the Hola Trough (Vesterålen, Northern Norway)

The Lofoten-Vesterålen marine shelf is one of the most geologically diverse coast and offshore margin areas in Norway. This leads to huge heterogeneity in marine environments, and often high biodiversity. However, little is known yet about the benthic communities in this region. Within the ARCTOS LoVe MarineEco project the epibenthic communities of the Hola trough (Vesterålen) are analysed to give a first description of their spatial distribution. In this trough both a complex hydrodynamic system and varied topographic submarine elements occur. Trawling samples were collected for two different approaches: one in a meso-scale and another in a small-scale. For the broad scale a transect consisting in three stations was developed, while for the fine scale a small area on a sand wave field, consisting in five stations called HolaBox, was sampled. All organisms were intended to be identified to species level and colonial fauna was discarded for the analysis. Different diversity indexes were assessed (Shannon index (H’) and Pielou’s eveness (J’)). Clustering and nMDS analyses identified four statistically significant groups in terms of abundance (ind./100m2). A total amount of 211 different taxa were found within all stations. The more outer part of the transect (close to the shelf edge) presented a huge abundance of organisms and was dominated by the hemi sessile tube-builder polychaetes Nothria conchylega and Eunice dubitata and the sea urchin Gacilechinus acutus, while the more inner parts presented less abundance of individuals. Probably some upwelling produced by the Norwegian Atlantic Current (NWAC) is influencing the shelf edge increasing the primary production and, therefore, enriching the seafloor in this region. The sand wave field presented two different groups with few amount of individuals. Small-scale variability could be produced by the high heterogeneity within the different types of sand waves, while the scarce abundance of animals can be produced by the permanent changing environment that movable sand waves produce. Here more active and mobile fauna was found such as brittle stars and hermit crabs (among others). Finally, a fourth group was found in the most inner station of the transect, laying on a ridge in the central part of the trough. This station, with coarse substrate, was mainly dominated again by brittle stars and sea urchins. We can conclude that this is a really heterogeneous trough in environments and therefore in communities (even in a local scale). More detailed studies that focus in the local environmental drivers have to be carried out to get an integrated understanding of the structure of benthic communities in this system.

Análisis computacional del comportamiento termo-mecánico de materiales con aplicación a la industria automotriz

Para la supervivencia de cualquier industria en un mercado cada vez más competitivo resulta esencial mejorar la calidad del producto y reducir costos. Como parte de esa tendencia, el proceso de diseño, tanto de bienes como de procesos de manufactura, debe ser confiable e insumir el menor tiempo posible para permitir agilidad y eficacia en los cambios y las innovaciones que requiere el mercado. Es necesario abandonar los procesos de desarrollo basados en largas y costosas secuencias de prueba y error y reemplazarlos por procedimientos más cortos y eficientes. Las herramientas informáticas y los modelos computacionales han contribuido en gran medida a lograr dicho objetivo. Estos métodos son cada vez más utilizados en industrias tan importantes como la automotriz o la de maquinaria y equipamiento agrícola, ambas de relevante importancia en la actividad económica de nuestra provincia. En las mencionadas industrias, con la intención de mejorar las prestaciones del producto, de reducir costos de mantenimiento para igual prestación y, sobre todo, con el objetivo de disminuir el peso total del vehículo, factor importante en relación con el ahorro de combustible, es habitual la sustitución de algunos materiales tradicionalmente utilizados por otros con mejor relación prestación/costo y prestación/peso. Dentro de este grupo de nuevos materiales que se emplean en la industria automotriz se encuentran los compuestos, las aleaciones ligeras y la fundición dúctil, los cuales han estado substituyendo al acero o a la fundición gris en algunas piezas. La meta de esta investigación es generar modelos computacionales multiescala de: a) el proceso de tratamiento térmico de austemperizado de la fundición dúctil, b) el comportamiento mecánico de elementos de fundición dúctil y c) el comportamiento mecánico de material compuesto de matriz epoxi y fibra de vidrio con daño higrotérmico. Se usarán simulaciones acopladas de meso y macromecánica. El principal postulado es que la representación de la mesomecánica del material acoplada a la macromecánica conduce a resultados que mejoran las predicciones con respecto a modelos planteados sólo a nivel macroscópico. El dominio macroscópico se representará con elementos finitos y en ese nivel se resolverán problemas térmicos y mecánicos. En la mesoescala se emplearán leyes fenomenológicas para el aspecto metalúrgico del austemperizado y elementos finitos para el análisis del comportamiento micromecánico de la fundición dúctil y del material compuesto. Los productos resultantes de la investigación serán software y metodologías que puedan ser utilizadas en la mejora del diseño de piezas de fundición dúctil y de materiales compuestos y en el ajuste del tratamiento de austemperizado de la fundición dúctil que permita obtener la microestructura requerida. Desde un punto de vista académico y en relación con la temática planteada en el proyecto, tres integrantes llevarán a cabo sus estudios doctorales y se publicarán resultados en revistas internacionales

U, FE, AND LI ISOTOPE RATIOS IN THE MINERALIZED AND BARREN AREAS OF THE KOMBOLGIE BASIN

The Paleo- to Meso-Proterozoic Jabiluka unconformity related uranium mine is located within the Alligator River Uranium Field, found in the Northern Territories, Australia. The uranium ore is hosted in the late middle Paleoproterozoic Cahill Formation, which is unconformably overlain by a group of unmetamorphosed conglomerates known as the Kombolgie subgroup. The Kombolgie subgroup provided the source for oxidized basinal brines, carrying U as the mobile form U(VI), which interacted with reducing lithologies in the Cahill formation, thus reducing U(VI) to the solid U(IV), and leading to the precipitation of uraninite (UO2). In order to characterize fluid interaction with the ore body and compare that to areas without mineralization, several isotopic tracers were studied on a series of clay samples from drill core at Jabiluka as well as in barren areas throughout the ARUF. Among the potential tracers, three were selected: U (redox sensitive and recent fluid mobilization), Fe (redox sensitive), and Li (fractionated by hydrothermal fluids and adsorption reactions). δ238U values were found to be closely linked to the mineralogy, with samples with higher K/Al ratios (indicating high illite and low chlorite concentrations) having higher δ238U values. This demonstrates that 235U preferentially absorbs onto the surface of chlorite during hydrothermal circulation. In addition, δ234U values lie far from secular equilibrium (δ234U of 30‰), indicating there was addition or removal of 234U from the surface of the samples from recent (<2.5Ma) interactions of mobile fluids. δ57Fe values were found to be related to lithology and spatially to known uranium deposits. Decreasing δ57Fe values were found with increasing depth to the unconformity in a drill hole directly above the ore zone, but not in drill holes in the barren area. Similarly to δ238U, δ7Li is found to correlate with mineralogy, with higher δ7Li values associated with samples with more chlorite. In addition, higher δ7Li values are found at greater depth throughout the basin, indicating that the direction of the mineralizing fluid circulation was upwards from the Cahill formation to the Kombolgie subgroup.

Between violent and non-violent action strategies: a study on extreme-right organizations in Italy and Spain. IHS Political Science Series No. 130, July 2012

This paper focuses on the different forms of action adopted by extreme right organizations (both political parties and non-party groups) in Italy and Spain during their recent mobilization and links them to the environmental conditions and internal organizational factors which might affect them. With particular attention paid to the actors’ perceptions of reality, the macro-level factors (such as the favourable or unfavourable political opportunities of the context, the availability of allies in power, the degree of repression by authorities, etc.) as well as the meso-level factors (such as the internal characteristics of extreme right groups and their dynamics) will be explored in order to understand the action strategies of extreme right organizations and their recourse to violence. This paper, drawing on a combination of qualitative and quantitative research techniques, will be based on 20 semi-structured interviews with extreme right representatives of the main right wing organizations in Italy and Spain as well as a protest event analysis of newspapers dating from 2005 to 2009.

Palaeoenvironmental and palaeoceanographic changes during the lower to middle Jurassic (Toarcian-Aalenian, ~183-171 Ma). : new evidences from calcareous nannofossils of the Lusitanian Basin

Tese de doutoramento (co-tutela), Geologia (Paleontologia e Estratigrafia), Faculdade de Ciências da Universidade de Lisboa, Université Claude Bernard Lyon 1, 2016

Émergence et développement de l’oncologie au Québec : collaboration, compétition et défis organisationnels, 1900-2005

Objectifs : le principal objectif de notre projet doctoral consiste à mettre en relief les transformations qui ont marqué le développement de l’oncologie et de la lutte contre le cancer au Québec au 20e siècle. Pour ce faire, nous nous sommes penchées sur trois niveaux d’analyse : 1) le niveau micro aborde l’organisation des services médicaux au sein d’une organisation hospitalière, soit l’Hôtel-Dieu de Québec. 2) Le niveau méso analyse une lutte professionnelle, soit la lutte entre les hématologues et les oncologues médicaux pour la reconnaissance de l’oncologie médicale. 3) Le niveau macro s’intéresse à l’organisation de la lutte contre le cancer à travers la province de Québec et aux différents modèles organisationnels créés. Principale hypothèse : l’émergence et la transformation de l’oncologie et de la lutte contre le cancer ont été influencées des rapports de collaboration et de compétition entre les acteurs impliqués en oncologie. En effet, il apparaît que ce champ se trouve en tension entre l’obligation de collaborer pour offrir des services de qualité aux patients et les dynamiques professionnelles et/ou organisationnelles. Cadre théorique : un cadre théorique a été développé pour chacun des niveaux d’analyse. Le niveau micro s’inspire des travaux de Frickel, Abbott et Strauss et s’intéresse plus particulièrement aux négociations entourant l’ordre social au sein d’un hôpital universitaire; le niveau méso emploie les travaux de Bourdieu et Abbott pour analyser la lutte entre deux spécialités médicales pour le contrôle des agents de chimiothérapie; et le niveau macro, de la sociologie des organisations et de la théorie néo-institutionnaliste pour mettre en relief l’émergence et la transformation de la lutte contre le cancer au Québec au 20e siècle. Méthodologie : l’approche de l’étude de cas a été adoptée et chaque niveau d’analyse constitue une étude de cas à part entière. Le corpus de données se compose de données archivistiques recueillies dans 10 centres d’archives canadiens, et de données d’entrevues. Une soixantaine d’entrevues avec des oncologues, des professionnels de la santé, des gestionnaires, des chercheurs et des fonctionnaires ont été réalisées. Conclusion : les différents niveaux d’analyse offrent différentes contributions qui leurs sont propres, mais l’ensemble de la thèse tend à mettre en relief la complexité du changement organisationnel à travers un perpétuel processus de définition et de redéfinition des frontières professionnelles et des organisations en raison du développement des connaissances scientifiques, des technologies, des expertises professionnelles et de l’environnement social, politique et économique.

List of size fractionated eukaryotic plankton community samples and associated metadata (Database W1)

The present data set provides an Excel file in a zip archive. The file lists 334 samples of size fractionated eukaryotic plankton community with a suite of associated metadata (Database W1). Note that if most samples represented the piconano- (0.8-5 µm, 73 samples), nano- (5-20 µm, 74 samples), micro- (20-180 µm, 70 samples), and meso- (180-2000 µm, 76 samples) planktonic size fractions, some represented different organismal size-fractions: 0.2-3 µm (1 sample), 0.8-20 µm (6 samples), 0.8 µm - infinity (33 samples), and 3-20 µm (1 sample). The table contains the following fields: a unique sample sequence identifier; the sampling station identifier; the Tara Oceans sample identifier (TARA_xxxxxxxxxx); an INDSC accession number allowing to retrieve raw sequence data for the major nucleotide databases (short read archives at EBI, NCBI or DDBJ); the depth of sampling (Subsurface - SUR or Deep Chlorophyll Maximum - DCM); the targeted size range; the sequences template (either DNA or WGA/DNA if DNA extracted from the filters was Whole Genome Amplified); the latitude of the sampling event (decimal degrees); the longitude of the sampling event (decimal degrees); the time and date of the sampling event; the device used to collect the sample; the logsheet event corresponding to the sampling event ; the volume of water sampled (liters). Then follows information on the cleaning bioinformatics pipeline shown on Figure W2 of the supplementary litterature publication: the number of merged pairs present in the raw sequence file; the number of those sequences matching both primers; the number of sequences after quality-check filtering; the number of sequences after chimera removal; and finally the number of sequences after selecting only barcodes present in at least three copies in total and in at least two samples. Finally, are given for each sequence sample: the number of distinct sequences (metabarcodes); the number of OTUs; the average number of barcode per OTU; the Shannon diversity index based on barcodes for each sample (URL of W4 dataset in PANGAEA); and the Shannon diversity index based on each OTU (URL of W5 dataset in PANGAEA).

Chlorophyll-a concentrations in phytoplankton fractions in waters of the Black Sea

Comparison of daily and diel variability of chlorophyll-a concentration at three long-term stations in meso- and eutrophic regions indicates that their values are similar. Daily patterns of deviation in chlorophyll concentration in small and large phytoplankton fraction from average daily values are presented. In conformity with a hypothesis of daily removal rhythms correlated with changes in diel light-dark periods, it was concluded that the mesotrophic region during the dark period is characterized by predominance of grazing on large phytoplankton in the upper layers and accumulation of detritus from cell fragments in the lower layer, while during the light period smaller phytoplankton predominantly grazed. The eutrophic region is characterized by predominance of grazing on small phytoplankton fraction in the upper layers during the dark period and settling out of fecal pellets containing chlorophyll into deeper depths; but during the light period, large phytoplankton predominantly grazed throughout the whole water layer.

Thyroid hormones and halogenated organic compounds in black-legged kittiwake (Rissa tridactyla) and northern fulmar (Fulmarus glacialis)

Thyroid hormones are essential for normal growth and development and disruption of thyroid homeostasis can be critical to young developing individuals. The aim of the present study was to assess plasma concentrations of halogenated organic contaminants (HOCs) in chicks of two seabird species and to investigate possible correlations of HOCs with circulating thyroid hormone (TH) concentrations. Plasma from black-legged kittiwake (Rissa tridactyla) and northern fulmar (Fulmarus glacialis) chicks were sampled in Kongsfjorden, Svalbard in 2006. The samples were analyzed for thyroid hormones and a wide range of HOCs (polychlorinated biphenyls (PCBs), hydroxylated (OH-) and methylsulphoned (MeSO-) PCB metabolites, organochlorine pesticides (OCPs), brominated flame retardants (BFRs), and perfluorinated compounds (PFCs)). Concentrations of HOCs were generally low in kittiwake and fulmar chicks compared to previous reports. HOC concentrations were five times higher in fulmar chicks compared to in kittiwake chicks. PFCs dominated the summed HOCs concentrations in both species (77% in kittiwakes and 69% in fulmars). Positive associations between total thyroxin (TT4) and PFCs (PFHpS, PFOS, PFNA) were found in both species. Although correlations do not implicate causal relationships per se, the correlations are of concern as disruption of TH homeostasis may cause developmental effects in young birds.

Sedimentology and paleontology on core Lz1104 from Lake Hjort, Greenland

Two sediment cores of 70 and 252 cm length were recovered from Hjort Sø, a small lake on Store Koldewey, Northeast Greenland, and studied with a multidisciplinary approach in order to reconstruct the local environmental history and to test the relevance of proxies for paleoenvironmental information. The basal sediments from the longer core are dominated by clastic matter, which was likely deposited during deglaciation of the lake basin. These clastic sediments are overlain by gyttja, which is also present throughout the shorter core. AMS radiocarbon dating was conducted on plant macrofossils of 11 samples from the gyttja in both cores. A reliable chronology was established for both cores, which dated the onset of organic accumulation at 9,500 cal. year BP. The Holocene temperature development, with an early to mid Holocene thermal maximum, is best reflected in the grain-size composition. Nutrient availability was apparently low during the early Holocene and led to low productivity in the lake and its vicinity. From ca. 7,000 cal. year BP, productivity in the lake increased significantly, probably induced by external nutrient input from goose excrements. From this time, micro- and macrofossil remains reflect relatively well the climate history of East Greenland, with a cooling during the middle Holocene, the medieval warming, and the Little Ice Age. The amount of organic matter in the sequence seems to be more affected by lake ice cover or by nutrient supply from the catchment than by temperature changes. The record from Hjort Sø thus reveals the difficulties in interpreting sedimentary records from high arctic regions.