Determining Propeller Erosion at the Stern of a Berthing Ship

This paper presents the findings from an experimental investigation in to the nature and extent of the scouring that occurs when a ship berths in front of a perpendicular quay wall within the confines of a harbor. It examines the interaction between the relative position of the quay wall to the central axis of the ship and the influence of angle of the vessel's rudder on the magnitude of the scouring produced. The experimental programme covered a range of sediment sizes, propeller diameters and speeds of rotation and rudder angles. Also, methods for calculating the depth of expected scour are presented in terms of initial semi-empirical equations for the data range under investigation.

Parasite diversity, patterns of MHC II variation and olfactory based mate choice in diverging three-spined stickleback ecotypes

Ecological speciation has been the subject of intense research in evolutionary biology but the genetic basis of the actual mechanism driving reproductive isolation has rarely been identified. The extreme polymorphism of the major histocompatibility complex (MHC), probably maintained by parasite-mediated selection, has been proposed as a potential driver of population divergence. We performed an integrative field and experimental study using three-spined stickleback river and lake ecotypes. We characterized their parasite load and variation at MHC class II loci. Fish from lakes and rivers harbor contrasting parasite communities and populations possess different MHC allele pools that could be the result of a combined action of genetic drift and parasite-mediated selection. We show that individual MHC class II diversity varies among populations and is lower in river ecotypes. Our results suggest the action of homogenizing selection within habitat type and diverging selection between habitat types. Finally, reproductive isolation was suggested by experimental evidence: in a flow channel design females preferred assortatively the odor of their sympatric male. This demonstrates the role of olfactory cues in maintaining reproductive isolation between diverging fish ecotypes.

Molecular dissection of Meis1 reveals 2 domains required for leukemia induction and a key role for Hoxa gene activation

The Hoxa9 and Meis1 genes represent important oncogenic collaborators activated in a significant proportion of human leukemias with genetic alterations in the MLL gene. In this study, we show that the transforming property of Meis1 is modulated by 3 conserved domains, namely the Pbx interaction motif (PIM), the homeodomain, and the C-terminal region recently described to possess transactivating properties. Meis1 and Pbx1 interaction domain-swapping mutants are dysfunctional separately, but restore the full oncogenic activity of Meis1 when cotransduced in primary cells engineered to overexpress Hoxa9, thus implying a modular nature for PIM in Meis1-accelerated transformation. Moreover, we show that the transactivating domain of VP16 can restore, and even enhance, the oncogenic potential of the Meis1 mutant lacking the C-terminal 49 amino acids. In contrast to Meis1, the fusion VP16-Meis1 is spontaneously oncogenic, and all leukemias harbor genetic activation of endogenous Hoxa9 and/or Hoxa7, suggesting that Hoxa gene activation represents a key event required for the oncogenic activity of VP16-Meis1.

Molecular and clinical features of the myeloproliferative neoplasm associated with JAK2 exon 12 mutations

Although approximately 95% of patients with polycythemia vera (PV) harbor the V617F mutation in JAK2 exon 14, several mutations in exon 12 have been described in the remaining patients. We conducted a European collaborative study to define the molecular and clinical features of patients harboring these mutations. Overall, 106 PVs were recruited and 17 different mutations identified. Irrespective of the mutation, two-thirds of patients had isolated erythrocytosis, whereas the remaining subjects had erythrocytosis plus leukocytosis and/or thrombocytosis. Compared with JAK2 (V617F)-positive PV patients, those with exon 12 mutations had significantly higher hemoglobin level and lower platelet and leukocyte counts at diagnosis but similar incidences of thrombosis, myelofibrosis, leukemia, and death. In a multivariable analysis, age more than 60 years and prior thrombosis predicted thrombosis. These findings suggest that, despite the phenotypical difference, the outcome of JAK2 exon 12 mutations-positive PV is similar to that of JAK2 (V617F)positive PV. (Blood. 2011; 117(10):2813-2816)

Biomonitoring aquatic environmental quality in a marine protected area: A biomarker approach

The main aims of the present study, conducted in the framework of the MONIQUA-Egadi Scientific Project, were twofold: first, to make the first step in the development and validation of an ecotoxicological approach for the assessment of marine pollution in coastal environments on the basis of a set of biomarker responses in new sentinel species; and second, to obtain preliminary information on environmental quality in an Italian marine protected area, the Egadi Islands (Sicily). Several cytochrome P450-dependent mixed-function oxidase activities were measured in the following sentinel species: rainbow wrasse Coris julis, gastropod limpet Patella caerulea, and sea urchin Paracentrotus lividus. The results suggest that specimens from the Favignana Harbor may be exposed to P450 inducers, whereas most of the other sites seem to share similar environmental quality. The proposed approach has potential for assessment of environmental quality in marine protected areas.

Antibiotic and anti-inflammatory therapies for cystic fibrosis

Cystic fibrosis (CF) lung disease is characterized by chronic bacterial infection and an unremitting inflammatory response, which are responsible for most of CF morbidity and mortality. The median expected survival has increased from <6 mo in 1940 to >38 yr now. This dramatic improvement, although not great enough, is due to the development of therapies directed at secondary disease pathologies, especially antibiotics. The importance of developing treatments directed against the vigorous inflammatory response was realized in the 1990s. New therapies directed toward the basic defect are now visible on the horizon. However, the impact of these drugs on downstream pathological consequences is unknown. It is likely that antibiotics and anti-inflammatory drugs will remain an important part of the maintenance regimen for CF in the foreseeable future. Current and future antibiotic and anti-inflammatory therapies for CF are reviewed. © 2013 Cold Spring Harbor Laboratory Press; all rights reserved.

SN 2010ay is a Luminous and Broad-lined Type Ic Supernova within a Low-metallicity Host Galaxy

We report on our serendipitous pre-discovery detection and follow-up observations of the broad-lined Type Ic supernova (SN Ic) 2010ay at z = 0.067 imaged by the Pan-STARRS1 3π survey just ~4 days after explosion. The supernova (SN) had a peak luminosity, MR ≈ -20.2 mag, significantly more luminous than known GRB-SNe and one of the most luminous SNe Ib/c ever discovered. The absorption velocity of SN 2010ay is v Si ≈ 19 × 103 km s-1 at ~40 days after explosion, 2-5 times higher than other broad-lined SNe and similar to the GRB-SN 2010bh at comparable epochs. Moreover, the velocity declines ~2 times slower than other SNe Ic-BL and GRB-SNe. Assuming that the optical emission is powered by radioactive decay, the peak magnitude implies the synthesis of an unusually large mass of 56Ni, M Ni = 0.9 M ⊙. Applying scaling relations to the light curve, we estimate a total ejecta mass, M ej ≈ 4.7 M ⊙, and total kinetic energy, EK ≈ 11 × 1051 erg. The ratio of M Ni to M ej is ~2 times as large for SN 2010ay as typical GRB-SNe and may suggest an additional energy reservoir. The metallicity (log (O/H)PP04 + 12 = 8.19) of the explosion site within the host galaxy places SN 2010ay in the low-metallicity regime populated by GRB-SNe, and ~0.5(0.2) dex lower than that typically measured for the host environments of normal (broad-lined) SNe Ic. We constrain any gamma-ray emission with E γ ~ 1048 erg. We therefore rule out the association of a relativistic outflow like those that accompanied SN 1998bw and traditional long-duration gamma-ray bursts (GRBs), but we place less-stringent constraints on a weak afterglow like that seen from XRF 060218. If this SN did not harbor a GRB, these observations challenge the importance of progenitor metallicity for the production of relativistic ejecta and suggest that other parameters also play a key role.

Contribution to the study of the Ria de Aveiro inlet morphodynamics

Over the years it was observed at the Ria de Aveiro lagoon inlet, near the head of the north breakwater, a depth increase that might threaten the stability of this structure. A trend of accretion in the navigation channel of this lagoon is observed, endangering the navigation in this region. In order to understand the origin of these and other trends observed, the knowledge of the sediment transport in the study area is imperative. The main aim of this work is understanding the dominant physical processes in the sediment transport of sediment at the Ria de Aveiro lagoon inlet and adjacent area, improving knowledge of this region morphodynamics. The methodology followed in this study consisted in the analyzes of the topohydrographic surveys performed by the Administration of the Aveiro Harbor, and in the numerical simulations results performed with the morphodynamic modeling system MORSYS2D. The analysis of the surveys was performed by studying the temporal evolution of the bathymetry. The numerical analysis was based on the implementation of the model at the study area, sensitivity analysis of the formulations used to compute the sediment transport to the variation of input parameters (e.g. depth, sediment size, tidal currents) and analysis of the sediment uxes and bathymetric changes predicted. The simulations considered as sediment transport forcing the tidal currents only and the coupled forcing of tides and waves. Considering the wave e ect as sediment transport forcing, both monochromatic waves and a wave regime were simulated. The results revealed that the observed residual sediment transport patterns are generated due to the channel con guration. Inside the lagoon the uxes are mainly induced by the tidal currents action, restricting the action of waves to the inlet and adjacent coast. In the navigation channel the residual sediment uxes predicted are directed o - shore with values between 7 and 40 m3=day generating accretions of approximately 10 m3=day for the shallower region and 35 m3=day for the region between the tidal gauge and the tri^angulo das mar es. At the inlet, the residual uxes are approximately 30 m3=day inducing trends of erosion of approximately 20 m3=day. At the North side of the nearshore accretion is predicted, while at the South side is predicted erosion, at the rates of 250 and 1500 m3=day, respectively. It was also concluded that the waves with higher contribution to the residual sediment uxes are those with heights between 4 and 5 m. However, the storm waves with heights bigger than 5 m, despite their 10% of frequency of occurrence are responsible for 25% of the observed sediment transport.

Biodiversity and conservation of subterranean fauna of Portuguese karst

As regiões cársicas de Portugal ocupam uma parte considerável do território e albergam mais de 2000 grutas, que são habitadas por animais subterrâneos com características adaptativas únicas. Estes animais estão entre os mais raros, ameaçados e desprotegidos a nível mundial, comummente pelo simples fato de serem desconhecidos, o que associado à relativa inacessibilidade do seu habitat, constitui um desafio para o seu estudo. O presente trabalho centra-se no estudo da biodiversidade subterrânea do carso de Portugal, de forma a contribuir para a sua conservação. Os invertebrados subterrâneos têm sido ignorados no que concerne à sua proteção, sobretudo porque o conhecimento era escasso e desorganizado. Este trabalho começa por apresentar uma revisão de todas as fontes bibliográficas sobre fauna subterrânea em Portugal, incluindo um catálogo de espécies troglóbias e estigóbias, acompanhado das respetivas localizações, para congregar, pela primeira vez, o estado do conhecimento da riqueza específica, biogeografia e conservação das áreas estudadas. Para compreender os padrões de biodiversidade subterrânea, foi realizado um ano de trabalho de campo intenso e padronizado em mais de 40 cavidades de 14 unidades cársicas. Deste esforço resultou a descoberta e descrição de nove novos taxa, compreendendo três novos géneros e seis novas espécies para a ciência. Utilizando sistemas de informação geográfica foram mapeadas as distribuições das espécies subterrâneas do carso de Portugal e a sua riqueza foi comparada com a de outras áreas do mundo. Para explicar a sua riqueza específica subterrânea, foram testados vários fatores ambientais e efetuada a estimativa de espécies subterrâneas, numa escala regional. A evapotranspiração e consequentemente a produtividade primária ao nível da superfície poderão ser fatores importantes na variação da riqueza específica nas diferentes unidades cársicas, mas a profundidade e as características geológicas únicas de cada maciço parecem desempenhar um papel determinante nos padrões de biodiversidade subterrânea. Com o intuito de avaliar a sensibilidade de organismos subterrâneos à contaminação, foram testados os efeitos letais de dois tóxicos em crustáceos estigóbios com diferentes graus de troglomorfismo. Foram igualmente abordados aspectos gerais de ecotoxicologia de águas subterrâneas e perspectivas de futuro. Os principais problemas relacionados com a conservação dos habitats subterrâneos em Portugal estão associados à destruição direta do habitat e à sua contaminação. Estes carecem de proteção específica, o que implica a gestão adequada à superfície e a criação de áreas prioritárias de conservação. Integrando toda a informação gerada, o presente estudo estabelece uma hierarquização de locais prioritários para a conservação da fauna subterrânea em zonas cársicas de Portugal.

An overview of chemosynthetic symbioses in bivalves from the North Atlantic and Mediterranean Sea

Deep-sea bivalves found at hydrothermal vents, cold seeps and organic falls are sustained by chemosynthetic bacteria that ensure part or all of their carbon nutrition. These symbioses are of prime importance for the functioning of the ecosystems. Similar symbioses occur in other bivalve species living in shallow and coastal reduced habitats worldwide. In recent years, several deep-sea species have been investigated from continental margins around Europe, West Africa, eastern Americas, the Gulf of Mexico, and from hydrothermal vents on the Mid-Atlantic Ridge. In parallel, numerous, more easily accessible shallow marine species have been studied. Herein we provide a summary of the current knowledge available on chemosymbiotic bivalves in the area ranging west-to-east from the Gulf of Mexico to the Sea of Marmara, and north-to-south from the Arctic to the Gulf of Guinea. Characteristics of symbioses in 53 species from the area are summarized for each of the five bivalve families documented to harbor chemosynthetic symbionts (Mytilidae, Vesicomyidae, Solemyidae, Thyasiridae and Lucinidae). Comparisons are made between the families, with special emphasis on ecology, life cycle, and connectivity. Chemosynthetic symbioses are a major adaptation to ecosystems and habitats exposed to reducing conditions. However, relatively little is known regarding their diversity and functioning, apart from a few “model species” on which effort has focused over the last 30 yr. In the context of increasing concern about biodiversity and ecosystems, and increasing anthropogenic pressure on oceans, we advocate a better assessment of the diversity of bivalve symbioses in order to evaluate the capacities of these remarkable ecological and evolutionary units to withstand environmental change.

Ecological and biotechnological potential of sponge microbiome

Marine sponges harbor microbial communities of immense ecological and biotechnological importance. Recently, they have been focus of heightened attention due to the wide range of biologically active compounds with potential application, particularly, in chemical, cosmetic and pharmaceutical industries. However, we still lack fundamental knowledge of their microbial ecology and biotechnological potential. The development of high-throughput sequencing technologies has given rise to a new range of tools that can help us explore the biotechnological potential of sponges with incredible detail. Metagenomics, in particular, has the power to revolutionize the production of bioactive compounds produced by unculturable microorganisms. It can offer the identification of biosynthetic genes or gene clusters that can be heterologously expressed on a cultivable and suitable host. This review focus on the exploration of the biotechnological potential of sponge-associated microorganisms, and integration of molecular approaches, whose increasing efficiency can play an essential role on achieving a sustainable source of natural products.

Antimicrobial activity of essential oils against multiresistant aeromonads and enterococci

Tese de mestrado. Biologia (Microbiologia Aplicada). Universidade de Lisboa, Faculdade de Ciências, 2014

Tsunami Hazard Assessment of the Strait of Juan de Fuca

This study presents and discusses the tsunami hazard posed by an updated CSZ earthquake scenerio to the coastal communities of Port Angeles and Port Townsend, based on the results of a high resolution GeoClaw simulation with 2/3 arc second resolution (about 20.56 meters) surrounding these towns. In addition, we will also present the results of a coarse regional simulation of the Strait of Juan de Fuca. This coarse study encompasses 28 regions that span the Strait’s coast, including the communities of Anacortes, Bellingham, Friday Harbor, and Victoria, BC in addition to extended areas around Port Angeles and Port Townsend. The finest grid for these 28 regions where we collected results had 2 arc sec resolution (around 62 meters). Finally, we will discuss some inherent uncertainties in the specification of the earthquake scenario, the limitations of the GeoClaw model, and the associated uncertainites in the results.

Peroxisomal beta-oxidation--a metabolic pathway with multiple functions.

Fatty acid degradation in most organisms occurs primarily via the beta-oxidation cycle. In mammals, beta-oxidation occurs in both mitochondria and peroxisomes, whereas plants and most fungi harbor the beta-oxidation cycle only in the peroxisomes. Although several of the enzymes participating in this pathway in both organelles are similar, some distinct physiological roles have been uncovered. Recent advances in the structural elucidation of numerous mammalian and yeast enzymes involved in beta-oxidation have shed light on the basis of the substrate specificity for several of them. Of particular interest is the structural organization and function of the type 1 and 2 multifunctional enzyme (MFE-1 and MFE-2), two enzymes evolutionarily distant yet catalyzing the same overall enzymatic reactions but via opposite stereochemistry. New data on the physiological roles of the various enzymes participating in beta-oxidation have been gathered through the analysis of knockout mutants in plants, yeast and animals, as well as by the use of polyhydroxyalkanoate synthesis from beta-oxidation intermediates as a tool to study carbon flux through the pathway. In plants, both forward and reverse genetics performed on the model plant Arabidopsis thaliana have revealed novel roles for beta-oxidation in the germination process that is independent of the generation of carbohydrates for growth, as well as in embryo and flower development, and the generation of the phytohormone indole-3-acetic acid and the signal molecule jasmonic acid.

Discovery and fine mapping of serum protein loci through transethnic meta-analysis.

Many disorders are associated with altered serum protein concentrations, including malnutrition, cancer, and cardiovascular, kidney, and inflammatory diseases. Although these protein concentrations are highly heritable, relatively little is known about their underlying genetic determinants. Through transethnic meta-analysis of European-ancestry and Japanese genome-wide association studies, we identified six loci at genome-wide significance (p < 5 × 10(-8)) for serum albumin (HPN-SCN1B, GCKR-FNDC4, SERPINF2-WDR81, TNFRSF11A-ZCCHC2, FRMD5-WDR76, and RPS11-FCGRT, in up to 53,190 European-ancestry and 9,380 Japanese individuals) and three loci for total protein (TNFRS13B, 6q21.3, and ELL2, in up to 25,539 European-ancestry and 10,168 Japanese individuals). We observed little evidence of heterogeneity in allelic effects at these loci between groups of European and Japanese ancestry but obtained substantial improvements in the resolution of fine mapping of potential causal variants by leveraging transethnic differences in the distribution of linkage disequilibrium. We demonstrated a functional role for the most strongly associated serum albumin locus, HPN, for which Hpn knockout mice manifest low plasma albumin concentrations. Other loci associated with serum albumin harbor genes related to ribosome function, protein translation, and proteasomal degradation, whereas those associated with serum total protein include genes related to immune function. Our results highlight the advantages of transethnic meta-analysis for the discovery and fine mapping of complex trait loci and have provided initial insights into the underlying genetic architecture of serum protein concentrations and their association with human disease.