Proteomic analysis of differentially expressed proteins in lymphoid organ of Fenneropenaeus chinensis response to Vibrio anguillarum stimulation

To gain an insight into the function of shrimp lymphoid organ at protein level, we analyzed the proteome of lymphoid organ in healthy Chinese shrimp Fenneropenaeus chinensis (F. chinensis) through two-dimensional gel electrophoresis (2-DE) based proteomic approach. A total of 95 spots representing 75 protein entries were identified by liquid chromatography tandem mass spectrometry (LC-MS/MS) with both online and in-house database. According to Gene Ontology (GO) annotation of biological process, the identified proteins were classified into 13 categories. Among them, approximately 36% of proteins related to cytoskeleton are noticeable. Then, a comparative proteomic approach was employed to investigate the differentially expressed proteins in lymphoid organ of Vibrio anguillarum-challenged F. chinensis. At 24 h post-injection (hpi), 17 differentially expressed protein spots were successfully identified, including 4 up-regulated protein spots (represent 4 proteins: cathepsin L protein similar to squid CG16901-PC, protein kinase C and protein similar to T-complex Chaperonin 5 CG8439-PA), and 13 down-regulated protein spots (represent 9 proteins: actin, beta-actin, cytoplasmic actin CyII, alpha tubulin, beta tubulin, protein similar to proteasome delta, vacuolar ATP synthase subunit B, elongation factor 2, carboxypeptidase B). These data may help us to understand the function of lymphoid organ and the molecular immune mechanism of shrimp responsive to pathogen infection. (C) 2010 Elsevier Ltd. All rights reserved.

Food utilization of adult flatfishes co-occurring in the Bohai Sea of China

Stomach contents were examined of 4527 adult individuals of 12 flatfish species collected during the 1982 - 1983 Bohai Sea Fisheries Resources Investigation. Their food habits, diet diversity, similarity of prey taxa, trophic niche breadth and diet overlap were systematically analysed. Ninety-seven prey species belonging to the Coelenterata, Nemertinea, Polychaeta, Mollusca, Crustacea, Echinodermata, Hemichordata and fish were found and five of them were considered to be principal prey for flatfishes: Alpheus japonicus, Oratosquilla oratoria, Alpheus distinguendus, Loligo japonicus and Crangon affinis. Among the flatfishes, Paralichthys olivaceus was piscivorous, whereas Pseodopleuronectes yokohamae and Pseudopleuronectes herzensteini both had polychaetes and molluscs as their main prey groups. Pleuronichthys cornutus was classified as a polychaete-mollusc eater, with a strong preference for crustaceans. Verasper variegatus, Cynoglossus semilaevis, Eopsetta grigorjewi and Cleisthenes herzensteini ate crustaceans. Kareius bicoloratus was classified as a mollusc-crustacean eater: Cynoglossus abbreviatus, Cynoglossus joyneri and Zebrias zebra were grouped as crustacean-fish eaters. However, Z. zebra also took polychaetes and C. abbreviatus and C. joyneri preyed on some molluscs. Trophic relationships among the flatfishes were complicated, but they occupied distinctive microhabitats in different seasons and selected their specific prey items, which was favourable to the stability of the flatfish community in the Bohai Sea.

Trophic role of small cetaceans and seals in Irish waters

Understanding the role of marine mammals in specific ecosystems and their interactions with fisheries involves, inter alia, an understanding of their diet and dietary requirements. In this thesis, the foraging ecology of seven marine mammal species that regularly occur in Irish waters was investigated by reconstructing diet using hard parts from digestive tracts and scats. Of the species examined, two (striped and Atlantic white-sided dolphin) can be considered offshore species or species inhabiting neritic waters, while five others usually inhabit more coastal areas (white-beaked dolphin, harbour porpoise, harbour seal and grey seal); the last species studied was the bottlenose dolphin whose population structure is more complex, with coastal and offshore populations. A total of 13,028 prey items from at least 81 different species (62 fish species, 14 cephalopods, four crustaceans, and a tunicate) were identified. 28% of the fish species were identified using bones other than otoliths, highlighting the importance of using all identifiable structures to reconstruct diet. Individually, each species of marine mammal presented a high diversity of prey taxa, but the locally abundant Trisopterus spp. were found to be the most important prey item for all species, indicating that Trisopterus spp. is probably a key species in understanding the role of these predators in Irish waters. In the coastal marine mammals, other Gadiformes species (haddock, pollack, saithe, whiting) also contributed substantially to the diet; in contrast, in pelagic or less coastal marine mammals, prey was largely comprised of planktivorous fish, such as Atlantic mackerel, horse mackerel, blue whiting, and mesopelagic prey. Striped dolphins and Atlantic white-sided dolphins are offshore small cetaceans foraging in neritic waters. Differences between the diet of striped dolphins collected in drift nets targeting tuna and stranded on Irish coasts showed a complex foraging behaviour; the diet information shows that although this dolphin forages mainly in oceanic waters it may occasionally forage on the continental shelf, feeding on available prey. The Atlantic white-sided dolphin diet showed that this species prefers to feed over the continental edge, where planktivorous fish are abundant. Some resource partitioning was found in bottlenose dolphins in Irish waters consistent with previous genetic and stable isotope analysis studies. Bottlenose dolphins in Irish waters appears to be generalist feeders consuming more than 30 prey species, however most of the diet comprised a few locally abundant species, especially gadoid fish including haddock/pollack/saithe group and Trisopterus spp., but the contribution of Atlantic hake, conger eels and the pelagic planktivorous horse mackerel were also important. Stomach content information suggests that three different feeding behaviours might occur in bottlenose dolphin populations in Irish waters; firstly a coastal behaviour, with animals feeding on prey that mainly inhabit areas close to the coast; secondly an offshore behaviour where dolphins feed on offshore species such as squid or mesopelagic fish; and a third more complex behaviour that involves movements over the continental shelf and close to the shelf edge. The other three coastal marine mammal species (harbour porpoise, harbour seal and grey seal) were found to be feeding on similar prey and competition for food resources among these sympatric species might occur. Both species of seals were found to have a high overlap (more than 80%) in their diet composition, but while grey seals feed on large fish (>110mm), harbour seals feed mostly on smaller fish (<110mm), suggesting some spatial segregation in foraging. Harbour porpoises and grey seals are potentially competing for the same food resource but some differences in prey species were found and some habitat partitioning might occur. Direct interaction (by catch) between dolphins and fisheries was detected in all species. Most of the prey found in the stomach contents from both stranded and by catch dolphins were smaller sizes than those targeted by commercial fisheries. In fact, the total annual food consumption of the species studied was found to be very small (225,160 tonnes) in comparison to fishery landings for the same area (~2 million tonnes). However, marine mammal species might be indirectly interacting with fisheries, removing forage fish. Incorporating the dietary information obtained from the four coastal species, an ECOPATH food web model was established for the Irish Sea, based on data from 2004. Five trophic levels were found, with bottlenose dolphins and grey and harbour seals occurring at the highest trophic level. A comparison with a previous model based on 1973 data suggests that while the overall Irish Sea ecosystem appears to be “maturing”, some indices indicate that the 2004 fishery was less efficient and was targeting fish at higher trophic levels than in 1973, which is reflected in the mean trophic level of the catch. Depletion or substantial decrease of some of the Irish Sea fish stocks has resulted in a significant decline in landings in this area. The integration of diet information in mass-balance models to construct ecosystem food-webs will help to understand the trophic role of these apex predators within the ecosystem.

Cephalopods of the South Georgia slope

During January 2003 the bathymetric distribution of the cephalopod fauna of the South Georgia and Shag Rocks slope (100-900 m) was investigated using a commercial bottom trawl. Forty-four trawl stations caught 193 cephalopod specimens including six species of octopod and seven of squid. The benthic octopods Pareledone turqueti and Adelieledone polymorpha were abundant in shallow water at South Georgia, being replaced by Thaumeledone gunteri in greater depths. However, neither A. polymorpha nor T gunteri were caught on the adjacent Shag Rocks area. Two specimens of the deep-sea genus Graneledone were caught on the South Georgia slope. The most abundant squid species caught were Moroteuthis knipovitchi, Psychroteuthis glacialis and Slosarczykovia circumantarctica, which are primarily pelagic and may have been taken when their vertical migrations impinged on the slope.

Magnetic properties of copper hexadecaphthalocyanine (F16CuPc) thin films and powders

The structural and magnetic properties of F16CuPc thin films and powder, including x-ray diffraction (XRD), superconducting quantum interference device (SQUID) magnetometry, and theoretical modelling of exchange interactions are reported. Analysis of XRD from films, with thickness ranging between 100 and 160 nm, deposited onto Kapton and a perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride (PTCDA) interlayer shows that the stacking angle (defined in the text) of the film is independent of the thickness, but that the texture is modified by both film thickness and substrate chemistry. The SQUID measurements suggest that all samples are paramagnetic, a result that is confirmed by our theoretical modelling including density functional theory calculations of one-dimensional molecular chains and Green's function perturbation theory calculations for a molecular dimer. By investigating theoretically a range of different geometries, we predict that the maximum possible exchange interaction between F16CuPc molecules is twice as large as that in unfluorinated copper-phthalocyanine (CuPc). This difference arises from the smaller intermolecular spacing in F16CuPc. Our density functional theory calculation for isolated F16CuPc molecule also shows that the energy levels of Kohn-Sham orbitals are rigidly shifted similar to 1 eV lower in F16CuPc compared to CuPc without a significant modification of the intramolecular spin physics, and that therefore the two molecules provide a suitable platform for independently varying magnetism and charge transport. 

Chemical tuning of the interlayer magnetic coupling in TlCo2Se2-xSx

The system TlCo2Se2-xSx has been thoroughly investigated by neutron powder diffraction and SQUID magnetometry. TlCo2Se2-xSx is a layered tetragonal structure containing atomic cobalt layers separated by a distance of 6.4 angstrom in the sulphide and 6.8 angstrom in the selenide. The solid solubility of isovalent selenium and sulphur atoms in the structure makes it possible to continuously vary the interlayer distance and thereby tune the magnetic coupling between the Co-layers. At low temperatures, the Co-atoms are ferromagnetically ordered within the layers and magnetic moments lie in the ab-plane. However, these Co-moments form a helical magnetic structure that prevails for 0 <= x <= 1.5 with a gradual decrease of the angle between adjacent Co-layers from 122 degrees to 39 degrees. For x >= 1.75, a collinear ferromagnetic structure is stable. The relationship between the coupling angle and the Co-interlayer separation shows an almost linear behaviour. The helical phase contains no net spontaneous magnetic moment up to TlCo2SeS, where a small net magnetic moment appears that increases until the ferromagnetic structure is found for 1.75 <= x <= 2.0. (C) 2005 Elsevier B.V. All rights reserved.

Crystal structure and magnetic properties of the new phase Mn3IrSi

A new phase in the ternary Ir-Mn-Si system has been synthesised. From powder neutron diffraction data the crystal structure was determined to be of the AlAu4 type and to be described in the cubic space group P2(1)3 with the unit cell a = 6.4973(3) Angstrom. Susceptibility measurements using a SQUID-magnetometer showed a transition typical of anti ferromagnetism, with T-N = 210 K. Low temperature antiferromagnetic order is confirmed by extra peaks in neutron diffractograms recorded at 10 and 80 K. (C) 2004 Elsevier B.V. All rights reserved.

Evaluation of La1−xSrxMnO3 (0 ≤ x < 0.4) synthesised via a modified sol–gel method as mediators for magnetic fluid hyperthermia

A range of lanthanum strontium manganates (La1−xSrxMnO3–LSMO) where 0 ≤ x < 0.4 were prepared using a modified peroxide sol–gel synthesis method. The magnetic nanoparticle (MNP) clusters obtained for each of the materials were characterised using scanning electron microscopy (SEM), X-ray powder diffraction (XRD) and infra-red (IR) spectroscopy in order to confirm the crystalline phases, crystallite size and cluster morphology. The magnetic properties of the materials were assessed using the Superconducting quantum interference device (SQUID) to evaluate the magnetic susceptibility, Curie temperature (Tc) and static hysteretic losses. Induction heating experiments also provided an insight into the magnetocaloric effect for each material. The specific absorption rate (SAR) of the materials was evaluated experimentally and via numerical simulations. The magnetic properties and heating data were linked with the crystalline structure to make predictions with respect to the best LSMO composition for mild hyperthermia (41 °C ≤ T ≤ 46 °C). La0.65Sr0.35MnO3, with crystallite diameter of 82.4 nm, (agglomerate size of ∼10 μm), Tc of 89 °C and SAR of 56 W gMn−1 at a concentration 10 mg mL−1 gave the optimal induction heating results (Tmax of 46.7 °C) and was therefore deemed as most suitable for the purposes of mild hyperthermia, vide infra.

Properties of self-assembled diluted magnetic semiconductor nanostructures

Este trabalho centra-se na investigação da possibilidade de se conseguir um semicondutor magnético diluído (SMD) baseado em ZnO. Foi levado a cabo um estudo detalhado das propriedades magnéticas e estruturais de estruturas de ZnO, nomeadamente nanofios (NFs), nanocristais (NCs) e filmes finos, dopadas com metais de transição (MTs). Foram usadas várias técnicas experimentais para caracterizar estas estruturas, designadamente difracção de raios-X, microscopia electrónica de varrimento, ressonância magnética, SQUID, e medidas de transporte. Foram incorporados substitucionalmente nos sítios do Zn iões de Mn2+ e Co2+ em ambos os NFs e NCs de ZnO. Revelou-se para ambos os iões dopantes, que a incorporação é heterogénea, uma vez que parte do sinal de ressonância paramagnética electrónica (RPE) vem de iões de MTs em ambientes distorcidos ou enriquecidos com MTs. A partir das intensidades relativas dos espectros de RPE e de modificações da superfície, demonstra-se ainda que os NCs exibem uma estrutura core-shell. Os resultados, evidenciam que, com o aumento da concentração de MTs, a dimensão dos NCs diminui e aumentam as distorções da rede. Finalmente, no caso dos NCs dopados com Mn, obteve-se o resultado singular de que a espessura da shell é da ordem de 0.3 nm e de que existe uma acumulação de Mn na mesma. Com o objectivo de esclarecer o papel dos portadores de carga na medição das interacções ferromagnéticas, foram co-dopados filmes de ZnO com Mn e Al ou com Co e Al. Os filmes dopados com Mn, revelaram-se simplesmente paramagnéticos, com os iões de Mn substitucionais nos sítios do Zn. Por outro lado, os filmes dopados com Co exibem ferromagnetismo fraco não intrínseco, provavelmente devido a decomposição spinodal. Foram ainda efectuados estudos comparativos com filmes de ligas de Zn1-xFexO. Como era de esperar, detectaram-se segundas fases de espinela e de óxido de ferro nestas ligas; todas as amostras exibiam curvas de histerese a 300 K. Estes resultados suportam a hipótese de que as segundas fases são responsáveis pelo comportamento magnético observado em muitos sistemas baseados em ZnO. Não se observou nenhuma evidência de ferromagnetismo mediado por portadores de carga. As experiências mostram que a análise de RPE permite demonstrar directamente se e onde estão incorporados os iões de MTs e evidenciam a importância dos efeitos de superfície para dimensões menores que ~15 nm, para as quais se formam estruturas core-shell. As investigações realizadas no âmbito desta tese demonstram que nenhuma das amostras de ZnO estudadas exibiram propriedades de um SMD intrínseco e que, no futuro, são necessários estudos teóricos e experimentais detalhados das interacções de troca entre os iões de MTs e os átomos do ZnO para determinar a origem das propriedades magnéticas observadas.

Study of multiferroic materials

The present PhD work aims the research and development of materials that exhibit multiferroic properties, in particular having a significant interaction between ferromagnetism and ferroelectricity; either directly within an intrinsic single phase or by combining extrinsic materials, achieving the coupling of properties through mechanic phenomena of the respective magnetostriction and piezoelectricity. These hybrid properties will allow the cross modification of magnetic and electric polarization states by the application of cross external magnetic and/or electric fields, giving way to a vast area for scientific investigation and potential technological applications in a new generation of electronic devices, such as computer memories, signal processing, transducers, sensors, etc. Initial experimental work consisted in chemical synthesis of nano powders oxides by urea pyrolysis method: A series of ceramic bulk composites with potential multiferroic properties comprised: of LuMnO3 with La0.7Sr0.3MnO3 and BaTiO3 with La0.7Ba0.3MnO3; and a series based on the intrinsic multiferroic LuMn1-zO3 phase modified with of Manganese vacancies. The acquisition of a new magnetron RF sputtering deposition system, in the Physics Department of Aveiro University, contributed to the proposal of an analogous experimental study in multiferroic thin films and multilayer samples. Besides the operational debut of this equipment several technical upgrades were completed like: the design and construction of the heater electrical contacts; specific shutters and supports for the magnetrons and for the substrate holder and; the addition of mass flow controllers, which allowed the introduction of N2 or O2 active atmosphere in the chamber; and the addition of a second RF generator, enabling co-deposition of different targets. Base study of the deposition conditions and resulting thin films characteristics in different substrates was made from an extensive list of targets. Particular attention was given to thin film deposition of magnetic phases La1-xSrxMnO3, La1-xBaxMnO3 and Ni2+x-yMn1-xGa1+y alloy, from the respective targets: La0.7Sr0.3MnO3, La0.7Ba0.3MnO3; and NiGa with NiMn. Main structural characterization of samples was performed by conventional and high resolution X-Ray Diffraction (XRD); chemical composition was determined by Electron Dispersion Spectroscopy (EDS); magnetization measurements recur to a Vibrating Sample Magnetometer (VSM) prototype; and surface probing (SPM) using Magnetic-Force (MFM) and Piezo-Response (PFM) Microscopy. Results clearly show that the composite bulk samples (LuM+LSM and BTO+LBM) feat the intended quality objectives in terms of phase composition and purity, having spurious contents below 0.5 %. SEM images confirm compact grain packaging and size distribution around the 50 nm scale. Electric conductivity, magnetization intensity and magneto impedance spreading response are coherent with the relative amount of magnetic phase in the sample. The existence of coupling between the functional phases is confirmed by the Magnetoelectric effect measurements of the sample “78%LuM+22%LSM” reaching 300% of electric response for 1 T at 100 kHz; while in the “78%BTO+22%LBM” sample the structural transitions of the magnetic phase at ~350 K result in a inversion of ME coefficient the behavior. A functional Magneto-Resistance measurement system was assembled from the concept stage until the, development and operational status; it enabled to test samples from 77 to 350 K, under an applied magnetic field up to 1 Tesla with 360º horizontal rotation; this system was also designed to measure Hall effect and has the potential to be further upgraded. Under collaboration protocols established with national and international institutions, complementary courses and sample characterization studies were performed using Magneto-Resistance (MR), Magneto-Impedance (MZ) and Magneto-Electric (ME) measurements; Raman and X-ray Photoelectron Spectroscopy (XPS); SQUID and VSM magnetization; Scanning Electron Microscopy (SEM) and Rutherford Back Scattering (RBS); Scan Probe Microscopy (SPM) with Band Excitation Probe Spectroscopy (BEPS); Neutron Powder Diffraction (NPD) and Perturbed Angular Correlations (PAC). Additional collaboration in research projects outside the scope of multiferroic materials provided further experience in sample preparation and characterization techniques, namely VSM and XPS measurements were performed in cubane molecular complex compounds and enable to identify the oxidation state of the integrating cluster of Ru ions; also, XRD and EDS/SEM analysis of the acquired targets and substrates implied the devolution of some items not in conformity with the specifications. Direct cooperation with parallel research projects regarding multiferroic materials, enable the assess to supplementary samples, namely a preliminary series of nanopowder Y1-x-yCaxØyMn1O3 and of Eu0.8Y0.2MnO3, a series of micropowder composites of LuMnO3 with La0.625Sr0.375MnO3 and of BaTiO3 with hexagonal ferrites; mono and polycrystalline samples of Pr1-xCaxMnO3, La1-xSrxMnO3 and La1-xCaxMnO3.

Population dynamics and fisheries assessment of the bigeye thresher (Alopias superciliosus) in the Atlantic: a comparison between North Atlantic and South Atlantic stocks

Tese de doutoramento, Ciências do Mar, da Terra e do Ambiente (Biologia Pesqueira), Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Fleet dynamics in multispecies trawlers: a study based on fisheries-dependent data

Tese de doutoramento, Ciências do Mar, da Terra e do Ambiente (Avaliação e Gestão de Recursos), Faculdade das Ciências do Mar e do Ambiente, Universidade do Algarve, 2013

Aspectos biológico - pesqueros de los recursos pelágicos peruanos. Crucero BIC Humboldt y BIC SNP-1 9508-09

El Crucero de Evaluación de la Biomasa Desovante de anchoveta y sardina en 1995 empleó el Método de Producción de Huevos (MPH), abarcando el área comprendida entre Tambo de Mora y Paita, entre las 0 y 60 mn y 4 perfiles hidrográficos hasta las150 mn. La información analizada proviene de las capturas y muestreos biológicos de los 89 lances de comprobación ejecutados (66 del BIC Humboldt y 23 del SNP-1). La composición por especies estuvo conformada principalmente por anchoveta (Engraulis ringens), sardina (Sardinops sagax sagax), jurel (Trachurus picturatus murphyi) y caballa (Scomber japonicus). Especies capturadas incidentalmente fueron el "bagre con faja" (Galeichthys peruvianus) y el calamar (Loligo gahi). La distribución latitudinal de la anchoveta abarcó toda el área explorada y longitudinalmente hasta las 60 mn. La sardina, el jurel y la caballa mostraron una distribución amplia y dispersa hasta las 120 millas de la costa. La estructura por tamaños de anchoveta indicó la predominancia de ejemplares adultos, siendo escasa la presencia de juveniles. La sardina fue predominantemente juvenil, observada tanto en área costera como lejos de ésta. Las capturas de jurel y caballa estuvieron constituidas por ejemplares adultos. Las especies anchoveta y sardina se encontraban en pleno desove principal de invierno.

Características biológicas de la merluza y otras especies demersales en el invierno de 1996

Describe las actividades del crucero de evaluación del stock de merluza BIC SON-1 9607-08, que tuvo como objetivo determinar la distribución, concentración y características biológicas de la merluza y su fauna acompañante en el invierno de 1996. Las especies más frecuentes en las capturas fueron merluza (Merluccius gayi peruanus); vocador (Prionotus stephanophrys); lenguado ojón (Hippoglossina macrops); bereche (Larinus pacificus) y calamar (Loligo gahi). El rango de tallas de merluza varió entre 16 y 80 cm de longitud total, con una moda en 27 cm. Se le encontró en proceso de madurez sexual, al igual que el vocador y lenguado. En las subáreas A, D y E, la merluza evidenció una tendencia creciente de la proporción de hembras conforme se incrementa la profundidad. Las tallas del vocador fluctuaron entre 13 y 28 cm con una medida de 19,25 cm. El lenguado ojón presentó rangos de tallas entre 19 y 28 cm con talla media muestral de 22,7 cm. Las longitudes del bereche variaron de 9 a 26 cm, con talla de 17,2 cm. En el calamar se observaron tallas comprendidas entre 12 y 14 cm y talla media de 13,9 cm.

Caracteristicas de distribución, concentración y biologicas de los recursos costeros

Describe el desarrollo de una prospección pesquera aplicando la metodología del área barrida y rastreo acústico para estimar la abundancia relativa de los recursos demersales – costeros, respectivamente, así como para determinar aspectos biológicos de los mismos. Las mejores concentraciones de recursos pelágico-costeros se ubicaron entre el extremo norte y Callao. Se destaca la presencia sostenida del "bagre con faja" (Galeichthys peruvianus) entre Punta Fallas y Punta Colorado; el "calamar" (Loligo gahi) y el "pejerrey", se mostraron concurrentes en gran parte del área evaluada. La lorna y el mis-mis, mostraron comportamiento demersal y pelágico en función de su estratificación latitudinal de tallas. El "camaroncito rojo" (Pleuroncodes monodon) destacó notablemente desde el Callao hasta Camaná, circunstancia favorecida por el influjo de las Aguas Templadas de la Sub-antártica, especialmente entre Pisco e Ilo.