Monitoring and conservation of the largest loggerhead turtle (Caretta caretta) nesting population in Africa: successes and challenges.

[EN] The Republic of Cape Verde is situated about 500 km off the coast of Senegal, West Africa. The islands of Sal, Boa Vista and Maio constitute the Eastern group and harbour the most important nesting beaches for loggerhead turtles in the Archipelago. During 1998-2004 nesting seasons, fieldwork has been focused on the eastern beaches of Boa Vista and, occasionally, in other beaches of Boa Vista and in the islands of Maio, Sal and Santa Luzia. The main study area includes a total extension of 3.1 km of suitable nesting beaches. All through these years, a tagging program has been carried out, alongside recording of biological data and monitoring of nests.

Population structure and conservation implications for the loggerhead sea turtle of the Cape Verde Islands

[EN] The Cape Verde Islands harbour the second largest nesting aggregation of the globally endangered loggerhead sea turtle in the Atlantic. To characterize the unknown genetic structure, connectivity, and demographic history of this population, we sequenced a segment of the mitochondrial (mt) DNA control region (380 bp, n = 186) and genotyped 12 microsatellite loci (n = 128) in females nesting at three islands of Cape Verde. No genetic differentiation in either haplotype or allele frequencies was found among the islands (mtDNA FST = 0. 001, P > 0. 02; nDNA FST = 0. 001, P > 0. 126). However, population pairwise comparisons of the mtDNA data revealed significant differences between Cape Verde and all previously sequenced Atlantic and Mediterranean rookeries (FST = 0. 745; P < 0. 000).

Phocid seal leptin: tertiary structure and hydrophobic receptor binding site preservation during distinct leptin gene evolution

The cytokine hormone leptin is a key signalling molecule in many pathways that control physiological functions. Although leptin demonstrates structural conservation in mammals, there is evidence of positive selection in primates, lagomorphs and chiropterans. We previously reported that the leptin genes of the grey and harbour seals (phocids) have significantly diverged from other mammals. Therefore we further investigated the diversification of leptin in phocids, other marine mammals and terrestrial taxa by sequencing the leptin genes of representative species. Phylogenetic reconstruction revealed that leptin diversification was pronounced within the phocid seals with a high dN/dS ratio of 2.8, indicating positive selection. We found significant evidence of positive selection along the branch leading to the phocids, within the phocid clade, but not over the dataset as a whole. Structural predictions indicate that the individual residues under selection are away from the leptin receptor (LEPR) binding site. Predictions of the surface electrostatic potential indicate that phocid seal leptin is notably different to other mammalian leptins, including the otariids. Cloning the grey seal leptin binding domain of LEPR confirmed that this was structurally conserved. These data, viewed in toto, support a hypothesis that phocid leptin divergence is unlikely to have arisen by random mutation. Based upon these phylogenetic and structural assessments, and considering the comparative physiology and varying life histories among species, we postulate that the unique phocid diving behaviour has produced this selection pressure. The Phocidae includes some of the deepest diving species, yet have the least modified lung structure to cope with pressure and volume changes experienced at depth. Therefore, greater surfactant production is required to facilitate rapid lung re-inflation upon surfacing, while maintaining patent airways. We suggest that this additional surfactant requirement is met by the leptin pulmonary surfactant production pathway which normally appears only to function in the mammalian foetus.

Using passive acoustics and shore based surveys to investigate the use of Lundy Island’s near shore water by small odontocetes

The use of waters around Lundy by dolphins and porpoises was measured using summer shore-based watches and passive acoustic surveillance between July 2011 and July 2012. Common dolphins (Delphinus delphis) were the only cetacean species observed during shore-based surveys. C-PODs moored on the Ethel and MV Robert wrecks close to the Lundy coast showed a peak in delphinid vocal activity during August 2011. Passive acoustic detections of harbour porpoises (Phocoena phocoena) were highest during ebb tidal phases and most often associated with the tidal rip at the south of the island. These findings show tidal and monthly influences on odontocete behaviour and highlight the value of continuous, passive acoustic monitoring for these highly mobile marine predators around Lundy.

O microbioma humano

O organismo humano encontra-se colonizado por uma complexa diversidade de microrganismos. O conjunto destes microrganismos, que incluem as bactérias, fungos, vírus e protozoários, no homem denomina- se microbioma humano. Estima-se que entre a superfície interna e externa, o microbioma humano seja composto por 100 triliões de microrganismos. O microbioma humano varia muito nas mais diversas regiões do nosso corpo, dependendo de condições ambientais. Sabe-se, por exemplo, que nas regiões mais húmidas e quentes encontram-se uma maior concentração de microrganismos, enquanto que nas regiões menos húmidas, existe uma quantidade menor de microrganismos. O microbioma é de vital importância para a saúde humana, e o seu estudo conduz a um melhor conhecimento da sua complexa dinâmica, podendo conduzir ao desenvolvimento de novas formas de diagnóstico e até mesmo de tratamento de certas patologias. Assim sendo, a compreensão da diversidade fisiológica humana, bem como a de outros animais, passa pelo conhecimento da distribuição destes microrganismos nos diferentes órgãos e seu papel biológico. O desenvolvimento de técnicas de genética permitiram o estudo metagenómico importante para descrever a diversidade do microbioma humano, que não seria possível através da cultura das espécies pois um grande número destas não é cultivável. Esta dissertação tem como principal objetivo descrever o microbioma humano e de que forma esta influência o sistema imunitário. E numa segunda parte dar uma visão sobre a importância da análise metagenómica na identificação e caraterização do microbioma Humano.

Study of feeding competition between invasion ctenophore (M. leidyi) and anchovy (C. engrauliformis) in the Southern Caspian Sea (Mazandran Coast)

Mnemiopsis leidyi one species of phylum Ctenophora, is a native species in America. It has most likely moved across the Atlantic in the ballast water of cargo ships to the Black sea in 1982, and then to the Caspian Sea thought the Volga-Don Channel, in Nov 1999. The population of M. leidyi rows rapidly and by end of 2000, the entire sea was teeming with them. This survey was arranged In order to study the relationship between the invasion of M. leidyi and sharp decline in main stocks pelagic fish such as Kilka. Dietary analysis was conducted on Anchovy Killka (Clupeonella engrauliformis) and M. leidyi from August 2001 to October 2002 in two stations, located at the costal water near Babolsar (52.38° E ,36.42° N ) and Noshahar (51.33° E,36.39° N) in the Caspian Sea province of Mazandaran, Iran. M. leidyi was caught by plankton net, at three vertical strata of both station at surface 5 in, 10m, and 15 m the Kilka was caught by fisheries boat at Babolasar fishery harbour. Samples of M. leidyi were not fixed in its common fixative, we used 96% Ethanol In order to study of M. leidyi digestion system some alive samples, directly, were studied by the fluorescence microscope which was connected to a computer prepared specially for this process. In many cases, the light was directly reflected on the sample and microscopic image was prepared in dark background. We found that there were some common organisms in diet of both species. The Schoener index analysis reflected these similarities, as values more than critical level of overlap (>89 in Babolsar samples and >84 in Noshahar samples) were found. Results from this study suggests that M. leidyi and Anchovy have a similar feeding niche and computation between them is one of the reasons to decline in anchovy stocks. Economical effects of M. leidyi s invasion in research area were studied by data on kilka caught before and after introducing M. leidyi.

New morpho-bathymetric and tectono-stratigraphic data on Naples and Salerno gulfs (southern tyrrhenian sea, Italy) derived from bathymetric and seismic data analysis and integrated geological interpretation

New morpho-bathymetric and tectono-stratigraphic data on Naples and Salerno Gulfs, derived from bathymetric and seismic data analysis and integrated geologic interpretation are here presented. The CUBE(Combined Uncertainty Bathymetric Estimator) method has been applied to complex morphologies, such as the Capri continental slope and the related geological structures occurring in the Salerno Gulf.The bathymetric data analysis has been carried out for marine geological maps of the whole Campania continental margin at scales ranging from 1:25.000 to 1:10.000, including focused examples in Naples and Salerno Gulfs, Naples harbour, Capri and Ischia Islands and Salerno Valley. Seismic data analysis has allowed for the correlation of main morpho-structural lineaments recognized at a regional scale through multichannel profiles with morphological features cropping out at the sea bottom, evident from bathymetry.Main fault systems in the area have been represented on a tectonic sketch map, including the master fault located northwards to the Salerno Valley half graben. Some normal faults parallel to the master fault have been interpreted from the slope map derived from bathymetric data. A complex system of antithetic faults bound two morpho-structural highs located 20km to the south of the Capri Island. Some hints of compressional reactivation of normal faults in an extensional setting involving the whole Campania continental margin have been shown from seismic interpretation.

Typologie de la flottille chalutière du port de Sète par une méthode de segmentation

This work aims to define a typology of trawler f1eet in Sète, the main fishing harbour along the French Mediterranean coast, using several multivariate analysis methods. The fishing ships taken to account are represented by annual profiles of landing specific compositions. Five fishing strategies have been identified. A segmentation method using symbolic objects allows a formaI characterisation of the different strategies. These strategies are studied according to several general characteristics usually used for management rules elaboration (power, length, ship age). The typological analysis allows to characterise two main exploitation ways, one directed to the catch of a few species (Engraulis encrasicolus, Sardina pilchardus), the other characterised by the exploitation of a great diversity of species. By this way, it is possible to estimate how the catch of low represented species can significantly contribute to the exploitation of a resource.

The RGBarrier assay: the parallel study of gene regulatory element performance at defined chromosomal locations

Vertebrate genomes are organised into a variety of nuclear environments and chromatin states that have profound effects on the regulation of gene transcription. This variation presents a major challenge to the expression of transgenes for experimental research, genetic therapies and the production of biopharmaceuticals. The majority of transgenes succumb to transcriptional silencing by their chromosomal environment when they are randomly integrated into the genome, a phenomenon known as chromosomal position effect (CPE). It is not always feasible to target transgene integration to transcriptionally permissive “safe harbour” loci that favour transgene expression, so there remains an unmet need to identify gene regulatory elements that can be added to transgenes which protect them against CPE. Dominant regulatory elements (DREs) with chromatin barrier (or boundary) activity have been shown to protect transgenes from CPE. The HS4 element from the chicken beta-globin locus and the A2UCOE element from a human housekeeping gene locus have been shown to function as DRE barriers in a wide variety of cell types and species. Despite rapid advances in the profiling of transcription factor binding, chromatin states and chromosomal looping interactions, progress towards functionally validating the many candidate barrier elements in vertebrates has been very slow. This is largely due to the lack of a tractable and efficient assay for chromatin barrier activity. In this study, I have developed the RGBarrier assay system to test the chromatin barrier activity of candidate DREs at pre-defined isogenic loci in human cells. The RGBarrier assay consists in a Flp-based RMCE reaction for the integration of an expression construct, carrying candidate DREs, in a pre-characterised chromosomal location. The RGBarrier system involves the tracking of red, green and blue fluorescent proteins by flow cytometry to monitor on-target versus off-target integration and transgene expression. The analysis of the reporter (GFP) expression for several weeks gives a measure of the protective ability of each candidate elements from chromosomal silencing. This assay can be scaled up to test tens of new putative barrier elements in the same chromosomal context in parallel. The defined chromosomal contexts of the RGBarrier assays will allow for detailed mechanistic studies of chromosomal silencing and DRE barrier element action. Understanding these mechanisms will be of paramount importance for the design of specific solutions for overcoming chromosomal silencing in specific transgenic applications.

Explaining dinophysis cf. acuminata abundance in Antifer (Normandy, France) using dynamic linear regression

Classical regression analysis can be used to model time series. However, the assumption that model parameters are constant over time is not necessarily adapted to the data. In phytoplankton ecology, the relevance of time-varying parameter values has been shown using a dynamic linear regression model (DLRM). DLRMs, belonging to the class of Bayesian dynamic models, assume the existence of a non-observable time series of model parameters, which are estimated on-line, i.e. after each observation. The aim of this paper was to show how DLRM results could be used to explain variation of a time series of phytoplankton abundance. We applied DLRM to daily concentrations of Dinophysis cf. acuminata, determined in Antifer harbour (French coast of the English Channel), along with physical and chemical covariates (e.g. wind velocity, nutrient concentrations). A single model was built using 1989 and 1990 data, and then applied separately to each year. Equivalent static regression models were investigated for the purpose of comparison. Results showed that most of the Dinophysis cf. acuminata concentration variability was explained by the configuration of the sampling site, the wind regime and tide residual flow. Moreover, the relationships of these factors with the concentration of the microalga varied with time, a fact that could not be detected with static regression. Application of dynamic models to phytoplankton time series, especially in a monitoring context, is discussed.

Impact of Hypoxia on the Community Structure of Benthic Macroinvertebrates of Lagos Lagoon, Nigeria

Study of the Lagos lagoon was conducted for two years to investigate the impact of hypoxia on the benthic macroinvertebrates. Water and benthic samples were collected monthly along the study stretch and analysed in a standard laboratory. Temporal variation in water physico-chemistry was largely controlled by rainfall pattern while the spatial variation was influenced by proximity to the Harbour as well as the pollution sources and types. A total of 3,159 individuals comprising three phyla, five classes, nineteen families and twenty three species were recorded. Iddo I, Iddo II, Ogudu and Agboyi study stations recorded very low individuals, but relatively high number of polychaetes. Benthic macro- invertebrate community was dominated by the molluscs. Margalef’s index of species richness ranged from 0.79 to 2.57 while Shannon-Wiener index ranged from 0.40 to 2.19. Species evenness index ranged from 0.29 to 0.80. There was generally low biodiversity indicating the stressed nature of the study area.

A cidade e o rio: origem e evolução da frente ribeirinha de Lisboa

Em Lisboa, ao longo dos séculos, o homem foi conquistando as águas do Tejo. Hoje, após os diversos aterros, a frente ribeirinha da cidade é uma consolidada faixa de terreno, rematada por muros que, contra a «ondulação» do Tejo, definem uma expandida área que acolhe uma intensa actividade portuária. Foi nesta faixa junto do rio que se desenrolou parte importante da história de Lisboa, desde as ocupações romana e muçulmana, e também muito particularmente aquando do período dos Descobrimentos, da reconstrução pombalina pós-terramoto e do surto industrial do século XIX. Alguns destes momentos históricos encontram-se reflectidos nas inúmeras plantas, cartas e mapas disponíveis neste estudo, desde a Planta da Cidade de Lisboa : 1650, de João Nunes Tinoco, até ao Plano de Melhoramentos do Porto de Lisboa, de 1946. É com base nessas plantas, mas também em cartas manuscritas, relatos de época, gravuras e fotografias antigas – documentos em grande parte inéditos –, que este trabalho de investigação propõe cartografar este território, realizando desenhos originais que possibilitam um novo olhar sobre o seu processo de crescimento e consolidação. Assim, este estudo concilia todos estes elementos, constituindo uma análise completa que se debruça sobre a evolução da frente ribeirinha de Lisboa e que permite descobrir inúmeros aspectos até aqui desconhecidos, ajudando a responder à pergunta que hoje se coloca: perante o cenário que o porto actual atravessa, como melhor poderá Lisboa recuperar a relação com o rio?; THE CITY AND THE RIVER: ORIGIN AND EVOLUTION OF LISBON'S RIVERFRONT ABSTRACT: In Lisbon, over the centuries, man was conquering the waters of the Tagus. Today, after the various landfills, the city's riverfront is a consolidated strip of land, finished by walls that, against the "ripple" of the Tagus, define an expanded area that hosts an intense port activity. It was in this band along the river that unfolded important part of the history of Lisbon, from the Roman and Muslim occupations, and also very particularly during the period of the Discoveries, the post-earthquake reconstruction, and the industrial boom of the nineteenth century. Some of these historical moments are reflected in many plans, charts and maps available in this study, since the plan designated Planta da Cidade de Lisboa : 1650, made by João Nunes Tinoco, to the plan called Plano de Melhoramentos do Porto de Lisboa, drawn in the year of 1946. Based on these plans, but also in handwritten letters, time reports, antique prints and photographs – documents that are mostly unpublished – this research work proposes map this territory, performing original drawings that provide a new look at their growth process and consolidation. Thereby, this study combines all these elements, providing a complete analysis which focuses on the evolution of the Lisbon riverfront and that allows you to discover many aspects unknown until now, helping to answer the question that now arises: according to the present scenario that the harbour is going through, how can Lisbon recover the relationship with the river?

A sketch of the operations before Charlestown, the capital of South Carolina.

Scale ca. 1:11,800.

Ecotoxicological assessment of sediments from the Santos and São Vicente estuarine system- Brazil

O sedimento representa um importante depósito de contaminantes e uma fonte de contaminação para a cadeia alimentar aquática. Testes de toxicidade usando anfípodos como organismos-teste são empregados para avaliar sedimentos marinhos e estuarinos, juntamente com análises químicas. O presente trabalho tem como objetivo avaliar a qualidade de sedimentos de seis estações situadas no Sistema Estuarino e Portuário de Santos e São Vicente (São Paulo-Brasil), usando testes de toxicidade aguda com sedimento com anfípodos (Tiburonella viscana) e análises químicas de metais, PCB, e PAH. Outros parâmetros do sedimento foram analisados, como carbono orgânico e granulometria. Foram observados níveis de contaminação mais altos na porção interna do estuário onde se localiza o Porto de Santos e a zona industrial. Os testes de toxicidade mostraram resultados adversos significantes para a maioria das amostras testadas, e os sedimentos da porção interna do estuário apresentaram toxicidade mais alta. As análises de componentes principais indicaram uma relação forte entre contaminação do sedimento e toxicidade. As correlações positivas destes fatores nas amostras estudadas foram usadas para estabelecer os pesos das concentrações químicas que estão associadas com os efeitos adversos. Tais análises permitiram estimar valores limiares de efeito para a contaminação de sedimento através de análises multivariadas, identificando os contaminantes associados com o efeito biológico. Estes valores sugeridos são: Cu, 69.0; Pb, 17.4; Zn, 73.3(mg.kg-1); PAHs, 0.5 (mg.kg-1) e PCBs, 0.1 (µg.kg-1).

Whole genome sequence of Klebsiella pneumoniae U25, a hypermucoviscous, multidrug resistant, biofilm producing isolate from India

Klebsiella pneumoniae U25 is a multidrug resistant strain isolated from a tertiary care hospital in Chennai, India. Here, we report the complete annotated genome sequence of strain U25 obtained using PacBio RSII. This is the first report of the whole genome of K. pneumoniae species from Chennai. It consists of a single circular chromosome of size 5,491,870-bp and two plasmids of size 211,813 and 172,619-bp. The genes associated with multidrug resistance were identified. The chromosome of U25 was found to have eight antibiotic resistant genes [blaOXA-1, blaSHV-28, aac(6’)1b-cr, catB3, oqxAB, dfrA1]. The plasmid pMGRU25-001 was found to have only one resistant gene (catA1) while plasmid pMGRU25-002 had 20 resistant genes [strAB, aadA1, aac(6’)-Ib, aac(3)-IId, sul1,2, blaTEM-1A,1B, blaOXA-9, blaCTX-M-15, blaSHV-11, cmlA1, erm(B), mph(A)]. A mutation in the porin OmpK36 was identified which is likely to be associated with the intermediate resistance to carbapenems in the absence of carbapenemase genes. U25 is one of the few K. pneumoniae strains to harbour clustered regularly interspaced short palindromic repeats (CRISPR) systems. Two CRISPR arrays corresponding to Cas3 family helicase were identified in the genome. When compared to K. pneumoniae NTUHK2044, a transposase gene InsH of IS5-13 was found inserted.