Growth, survival, gene expression, microbiota and tryptic activity during feeding of Scophthalmus maximus first feeding larvae with beta-glucan (MacroGard)

Reflecting the natural biology of mass spawning fish aquaculture production of fish larvae is often hampered by high and unpredictable mortality rates. The present study aimed to enhance larval performance and immunity via the oral administration of an immunomodulator, beta-glucan (MacroGard®) in turbot (Scophthalmus maximus). Rotifers (Brachionus plicatilis) were incubated with or without yeast beta-1,3/1,6-glucan in form of MacroGard® at a concentration of 0.5 g/L. Rotifers were fed to first feeding turbot larvae once a day. From day 13 dph onwards all tanks were additionally fed untreated Artemia sp. nauplii (1 nauplius ml/L). Daily mortality was monitored and larvae were sampled at 11 and 24 dph for expression of 30 genes, trypsin activity and size measurements. Along with the feeding of beta-glucan daily mortality was significantly reduced by ca. 15% and an alteration of the larval microbiota was observed. At 11 dph gene expression of trypsin and chymotrypsin was elevated in the MacroGard® fed fish, which resulted in heightened tryptic enzyme activity. No effect on genes encoding antioxidative proteins was observed, whilst the immune response was clearly modulated by beta-glucan. At 11 dph complement component c3 was elevated whilst cytokines, antimicrobial peptides, toll like receptor 3 and heat shock protein 70 were not affected. At the later time point (24 dph) an anti-inflammatory effect in form of a down-regulation of hsp 70, tnf-alpha and il-1beta was observed. We conclude that the administration of beta-glucan induced an immunomodulatory response and could be used as an effective measure to increase survival in rearing of turbot.

Proteome analysis of extracellular proteins regulated by the las and rhl quorum sensing systems in Pseudomonas aeruginosa PAO1

The las and rhl quorum sensing (QS) systems regulate the expression of several genes in response to cell density changes in Pseudomonas aeruginosa. Many of these genes encode surface-associated or secreted virulence factors. Proteins from stationary phase culture supernatants were collected from wild-type and P. aeruginosa PAO1 mutants deficient in one or more of the lasRI, rhIRI and vfr genes and analysed using two-dimensional gel electrophoresis. All mutants released significantly lower amounts of protein than the wild-type. Protein spot patterns from each strain were compared using image analysis and visible spot differences were identified using mass spectrometry. Several previously unknown OS-regulated proteins were characterized, including an aminopeptidase (PA2939), an endoproteinase (PrpL) and a unique 'hypothetical' protein (PA0572), which could not be detected in the culture supernatants of Delta/as mutants, although they were unaffected in Deltarhl mutants. Chitin-binding protein (CbpD) and a hypothetical protein (PA4944) with similarity to host factor I (HF-1) could not be detected when any of the lasRI or rhIRI genes were disrupted. Fourteen proteins were present at significantly greater levels in the culture supernatants of OS mutants, suggesting that QS may also negatively control the expression of some genes. Increased levels of two-partner secretion exoproteins (PA0041 and PA4625) were observed and may be linked to increased stability of their cognate transporters in a CS-defective background. Known QS-regulated extracellular proteins, including elastase (lasB), LasA protease (lasA) and alkaline metalloproteinase (aprA) were also detected.

Response and function of cutaneous mucosal and serum antibodies in barramundi (Lates calcarifer) acclimated in seawater and freshwater

Mucosal and serum antibody responses were studied in sibling barramundi (Lates calcarifer) acclimated in either seawater or freshwater following vaccination by intraperitoneal injection or direct immersion in an inactivated Streptococcus iniae vaccine. As expected, route of vaccination had a marked effect on immune response, with direct immersion resulting in low serum antibody levels against S. iniae by ELISA detected 21 days post vaccination at 26 degrees C, whilst a significant response was detected in mucus. A strong specific antibody response was detected in both mucus and serum 21 days following intraperitoneal injection. Fish acclimated in seawater prior to vaccination showed a markedly higher specific mucosal antibody response than sibling fish acclimated in freshwater, regardless of the route of vaccination, whilst the serum antibody response was not affected by salinity. Both mucosal and serum antibodies from fish in seawater and freshwater were capable of binding antigen at salinities similar to full strength seawater in a modified ELISA assay. These results indicate that this euryhaline fish species is riot only able to mount significant specific antibody response in cutaneous mucus, but that these antibodies will function in the marine environment. (c) 2005 Elsevier Ltd. All rights reserved.

Viruses: agents of coral disease?

The potential role of viruses in coral disease has only recently begun to receive attention. Here we describe our attempts to determine whether viruses are present in thermally stressed corals Pavona danai, Acropora formosa and Stylophora pistillata and zoanthids Zoanthus sp., and their zooxanthellae. Heat-shocked P. danai, A. formosa and Zoanthus sp. all produced numerous virus-like particles (VLPs) that were evident in the animal tissue, zooxanthellae and the surrounding seawater; VLPs were also seen around heat-shocked freshly isolated zooxanthellae (FIZ) from P. danai and S. pistillata. The most commonly seen VLPs were tail-less, hexagonal and about 40 to 50 nm in diameter, though a diverse range of other VLP morphotypes (e.g. rounded, rod-shaped, droplet-shaped, filamentous) were also present around corals. When VLPs around heat-shocked FIZ from S. pistillata were added to non-stressed FIZ from this coral, they resulted in cell lysis, suggesting that an infectious agent was present; however, analysis with transmission electron microscopy provided no clear evidence of viral infection. The release of diverse VLPs was again apparent when flow cytometry was used to enumerate release by heat-stressed A. formosa nubbins. Our data support the infection of reef corals by viruses, though we cannot yet determine the precise origin (i.e. coral, zooxanthellae and/or surface microbes) of the VLPs seen. Furthermore, genome sequence data are required to establish the presence of viruses unequivocally.

Cloning, mapping and identification of the Aeromonas salmonicida fstA, fepA and irpA genes, encoding the 86, 82 and 74 kDa iron-regulated outer membrane proteins, respectively

Three iromps (iron-regulated outer membrane proteins) of Aeromonas salmonicida were identified by the use of specific antibodies together with Southern hybridization analysis and limited nucleotide sequencing of their genes. The results of these experiments together with a search of the international database for homologous sequences led to their identification as follows: -86 kDa iromp (FstA) as a Vibrio anguillarum Fat A homologue -82 kDa iromp (FepA) as an Escherichia coli FepA homologue -74 kDa iromp (IrpA) as an Escherichia coli Cir homologue.

Taxonomy and distribution of taxa in the genus Gomphonema from the Florida Everglades, U.S.A.

Located at a subtropical latitude, the expansive Florida Everglades contains a mixture of tropical and temperate diatom taxa, as well as a unique flora adapted to the calcareous, often excessively hot, seasonally flooded wetland conditions. This flora has been poorly documented taxonomically, although diatoms are recognized as important indicators of environmental change in this threatened ecosystem. Gomphonema is a dominant genus in the freshwater marsh, and is represented by highly variable species complexes, including Gomphonema gracile Ehrenberg, Gomphonema intricatum var. vibrio Ehrenberg sensu Fricke, Gomphonema vibrioides Reichardt & Lange-Bertalot and Gomphonema parvulum (Kützing) Grunow. These taxa have been shown to exhibit wide morphological variation in other regions, resulting in considerable nomenclatural confusion. We collected Gomphonema from 237 sites distributed throughout the freshwater Everglades and used qualitative and quantitative morphological data to identify 20 distinguishable populations. Taxonomie assignments were based on descriptions and/or observations of type material of relevant taxa when possible, but deviations from original morphological range descriptions were common. We then compared morphological variation in Everglades Gomphonema taxa to that reported for the same taxa in other regions and suggest revisions of taxonomie concepts when necessary.

Design and synthesis of S-ribosylhomocysteine analogues

Bacteria are known to release a large variety of small molecules known as autoinducers (AI) which effect quorum sensing (QS) initiation. The interruption of QS effects bacterial communication, growth and virulence. ^ Three novel classes of S-ribosylhomocysteine (SRH) analogues as potential inhibitors of S-ribosylhomocysteinase (LuxS enzyme) and AI-2 modulators of QS were developed. The synthesis of 2-deoxy-2-bromo-SRH analogues was attempted by coupling of the corresponding 2-bromo-2-deoxypentafuranosyl precursors with the homocysteinate anion. The displacement of the bromide from C2 rather than the expected substitution of the mesylate from C5 was observed. The synthesis of 4-C-alkyl/aryl-S-ribosylhomocysteine analogues involved the following steps: (i) conversion of the D-ribose to the ribitol-4-ulose; (ii) diastereoselective addition of various alkyl or aryl or vinyl Grignard reagents to 4-ketone intermediate; (iii) oxidation of the primary hydroxyl group at C1 followed by the intramolecular ring closure to the corresponding 4-C-alkyl/aryl-substituted ribono-1,4-lactones; (iv) displacement of the activated 5-hydroxyl group with the protected homocysteinate. Treatment of the 4-C-alkyl/aryl-substituted SRH analogues with lithium triethylborohydride effected reduction of the ribonolactone to the ribose (hemiacetal) and subsequent global deprotection with trifluoroacetic acid provided 4-C-alkyl/aryl-SRHs. ^ The 4-[thia]-SRH were prepared from the 1-deoxy-4-thioribose through the coupling of the &agr;-fluoro thioethers (thioribosyl fluorides) with homocysteinate anion. The 4-[thia]-SRH analogues showed concentration dependent effect on the growth on las (50% inhibitory effect at 200 µg/mL). The most active was 1-deoxy-4-[thia]-SRH analogue with sufur atom in the ring oxidized to sulfoxide decreasing las gene activity to approximately 35% without affecting rhl gene. Neither of the tested compounds had effect on bioluminescence nor on total growth of V. harveyi, but had however slight inhibition of the QS.^

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Avaliação da sensibilidade ao H2O2 de diferentes linhas celulares humanas: estabelecimento de modelos celulares para avaliação da capacidade antioxidante de moléculas ou extratos

Os organismos marinhos são considerados uma fonte de novos compostos bioativos com enorme potencial biotecnológico. As bactérias associadas a macroalgas têm vindo a ser estudadas devido à produção de metabolitos secundários com atividades biológicas. Neste trabalho foram isoladas e identificadas 90 bactérias associadas às macroalgas Asparagopsis armata, Bifurcaria bifurcata e Sphaerococcus coronopifolius com diferentes características fenotípicas, sendo identificadas relativamente ao seu género através da sequenciação do gene 16S RNA. A extração de compostos bioativos foi realizada com os solventes metanol e diclorometano (1:1). A capacidade antioxidante dos extratos das bactérias associadas foi avaliada através do método fluorimétrico ORAC (oxygen radical absorbent capacity), da quantificação total de polifenóis (QTP) e da capacidade de redução do radical 2,2-diphenyl-1-picrylhydrazyl (DPPH). O efeito citotóxico do H2O2 foi testado nos modelos celulares SH-SY5Y, MCF-7 e HepG-2, representativos de células humanas neuronais, epiteliais da glândula mamária e hepáticas, respetivamente. Os extratos com maior capacidade antioxidante foram testados nos modelos celulares em condições de stress oxidativo induzido pelo H2O2. Os resultados foram revelados pelo método de 3-[4,5- dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide (MTT). O género de bactérias mais representativo identificado em associação com Asparagopsis armata, Bifurcaria Bifurcata e Sphaerococcus coronopifolius foi Vibrio sp. com 40%, 48,72% e 28,57%, respetivamente. Os géneros de bactérias menos representativos identificados em associação com Asparagopsis armata foram Bacillus sp., Cobetia sp. e Erwinia sp., com uma ocorrência de 3,33%. Por sua vez, Citricoccus sp., Cellulophaga sp., Ruegeria sp. e Staphylococcus sp. foram os géneros de bactérias menos representativos associados a Bifurcaria Bifurcata (2,56%). Os géneros menos representativos identificados em associação com Sphaerococcus coronopifolius foram Bacillus sp. e Holomonas sp. com uma ocorrência de 9,52%. O extrato da bactéria associada que apresentou maior potencial antioxidante avaliado pelos métodos de ORAC (3603,66 ± 80,14 μmol eq. Trolox/g extrato), QTP (53,854 ± 3,02 mg eq. ácido gál./g extrato) e DPPH (20,21 (14,41-28,34) μg.mL-1) foi a BB16 (Shewanella sp.), associada à alga Bifurcaria bifurcata. O efeito induzido pelo H2O2 foi bastante distinto na redução da viabilidade celular, com IC50 distintos, nas células SH-SY5Y (206,0 μM (150,4 – 282,2)), MCF-7 (450,2 μM (388,0 – 522,5)) e HepG-2 (1058,0 μM (847,3 – 1321,0)).A elevada atividade antioxidante do extrato da bactéria associada à alga Bifurcaria bifurcata (0,1mg.mL-1; BB16 – Shewanella sp.) permitiu a prevenção do efeito induzido pelo H2O2 na linha celular SH-SY5Y (IC50 - 431,7 μM (360,1 – 517,6). Em conclusão, as bactérias associadas das macroalgas Asparagopsis armata, Bifurcaria bifurcata e Sphaerococcus coronopifolius podem ser uma excelente e interessante fonte de compostos marinhos naturais com um elevado potencial antioxidante.

Exploring Mechanisms of Bacterial Adaptation to Seasonal Temperature Change

This research examines three potential mechanisms by which bacteria can adapt to different temperatures: changes in strain-level population structure, gene regulation and particle colonization. For the first two mechanisms, I utilize bacterial strains from the Vibrionaceae family due to their ease of culturability, ubiquity in coastal environments and status as a model system for marine bacteria. I first examine vibrio seasonal dynamics in temperate, coastal water and compare the thermal performance of strains that occupy different thermal environments. Our results suggest that there are tradeoffs in adaptation to specific temperatures and that thermal specialization can occur at a very fine phylogenetic scale. The observed thermal specialization over relatively short evolutionary time-scales indicates that few genes or cellular processes may limit expansion to a different thermal niche. I then compare the genomic and transcriptional changes associated with thermal adaptation in closely-related vibrio strains under heat and cold stress. The two vibrio strains have very similar genomes and overall exhibit similar transcriptional profiles in response to temperature stress but their temperature preferences are determined by differential transcriptional responses in shared genes as well as temperature-dependent regulation of unique genes. Finally, I investigate the temporal dynamics of particle-attached and free-living bacterial community in coastal seawater and find that microhabitats exert a stronger forcing on microbial communities than environmental variability, suggesting that particle-attachment could buffer the impacts of environmental changes and particle-associated communities likely respond to the presence of distinct eukaryotes rather than commonly-measured environmental parameters. Integrating these results will offer new perspectives on the mechanisms by which bacteria respond to seasonal temperature changes as well as potential adaptations to climate change-driven warming of the surface oceans.

Immunostimulatory effects of different aspects of aquaculture on the host response in the edible sea urchin, paracentrotus lividus

Aquaculture is a fast-growing industry contributing to global food security and sustainable aquaculture, which may reduce pressures on capture fisheries. The overall objective of this thesis was to look at the immunostimulatory effects of different aspects of aquaculture on the host response of the edible sea urchin, Paracentrotus lividus, which are a prized delicacy (roe) in many Asian and Mediterranean countries. In Chapter 1, the importance of understanding the biology, ecology, and physiology of P. lividus, as well as the current status in the culture of this organism for mass production and introducing the thesis objectives for following chapters is discussed. As the research commenced, the difficulties of identifying individuals for repeat sampling became clear; therefore, Chapter 2 was a tagging experiment that indicated PIT tagging was a successful way of identifying individual sea urchins over time with a high tag retention rate. However, it was also found that repeat sampling via syringe to measure host response of an individual caused stress which masked results and thus animals would be sampled and sacrificed going forward. Additionally, from personal observations and discussion with peers, it was suggested to look at the effect that diet has on sea urchin immune function and the parameters I measured which led to Chapter 3. In this chapter, both Laminaria digitata and Mytilus edulis were shown to influence measured immune parameters of differential cell counts, nitric oxide production, and lysozyme activity. Therefore, trials commencing after Trial 5 in Chapter 4, were modified to include starvation in order to remove any effect of diet. Another important aspect of culturing any organism is the study of their immune function and its response to several immunostimulatory agents (Chapter 4). Zymosan A was shown to be an effective immunostimulatory agent in P. lividus. Further work on handled/stored animals (Chapter 5) showed Zymosan A reduced the measured levels of some immune parameters measured relative to the control, which may reduce the amount of stress in the animals. In Chapter 6, animals were infected with Vibrio anguillarum and, although V. anguillarum, impacted immune parameters of P. lividus, it did not cause mortality as predicted. Lastly, throughout this thesis work, it was noted that the immune parameters measured produced different values at different times of the year (Chapter 7); therefore, using collated baseline (control) data, results were compiled to observe seasonal effects. It was determined that both seasonality and sourcing sites influenced immune parameter measurements taken at different times throughout the year. In conclusion, this thesis work fits into the framework of development of aquaculture practices that affect immune function of the host and future research focusing on the edible sea urchin, P. lividus.

Microbial community composition and bacterioplankton at time series station Helgoland Roads, North Sea

A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the alphaproteobacterial Roseobacter clade. This study explores such successions during spring phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. The surface water samples were taken at Helgoland Island about 40 km offshore in the southeastern North Sea in the German Bight at the station 'Kabeltonne' (54° 11.3' N, 7° 54.0' E) between the main island and the minor island, Düne (German for 'dune') using small research vessels (http://www.awi.de/en/expedition/ships/more-ships.html). Water depths at this site fluctuate from 6 to 10 m over the tidal cycle. Samples were processed as described previously (Teeling et al., 2012; doi:10.7554/eLife.11888.001) in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Assessment of absolute cell numbers and bacterioplankton community composition was carried out as described previously (Thiele et al., 2011; doi:10.1016/B978-0-444-53199-5.00056-7). To obtain total cell numbers, DNA of formaldehyde fixed cells filtered on 0.2 mm pore sized filters was stained with 4',6-diamidino-2-phenylindole (DAPI). Fluorescently labeled cells were subsequently counted on filter sections using an epifluores-cence microscope. Likewise, bacterioplankton community composition was assessed by catalyzedreporter deposition fluorescence in situ hybridization (CARD-FISH) of formaldehyde fixed cells on 0.2 mm pore sized filters.

Rational design of a (S)-selective-Transaminase for asymmetric synthesis of (1S)-1-(1,1'-biphenyl 2-yl)ethanamine

Amine transaminases offer an environmentally sustainable synthesis route for the production ofpure chiral amines. However, their catalytic efficiency towards bulky ketone substrates isgreatly limited by steric hindrance and therefore presents a great challenge for industrialsynthetic applications. Hereby we report an example of rational transaminase enzyme design tohelp alleviate these challenges. Starting from the Vibrio fluvialis amine transaminase that has nodetectable catalytic activity towards the bulky aromatic ketone 2-acetylbiphenyl, we employed arational design strategy combining in silico and in vitro studies to engineer the transaminaseenzyme with a minimal number of mutations, achieving an high catalytic activity and highenantioselectivity. We found that by introducing two mutations W57G/R415A detectableenzyme activity was achieved. The rationally designed best variant,W57F/R88H/V153S/K163F/I259M/R415A/V422A, showed an improvement in reaction rateby > 1716-fold towards the bulky ketone under study, producing the corresponding enantiomericpure (S)-amine (ee value of > 99%). 

Caractérisation du repliement en temps réel du riborégulateur adénine

Vers la fin des années 1990 et au début des années 2000, l’idée que l’ARN puisse interagir directement avec de petits métabolites pour contrôler l’expression de certains gènes devient de plus en plus acceptée. Des recherches menées à cette époque ont permis la découverte de plusieurs structures d’ARN hautement conservées nommées riborégulateurs. La structure de ces ARN leur permet de reconnaître spécifiquement un ligand. La reconnaissance du ligand entraîne ensuite un changement de conformation dans l’ARN responsable du contrôle de l’expression génétique. Le but de cette thèse est d’étudier la structure et les changements de conformation du riborégulateur associé au gène add liant l’adénine chez Vibrio vulnificus. Ce riborégulateur étant relativement simple, les informations recueillies lors de cette étude pourront servir à comprendre le fonctionnement de riborégulateurs plus complexes. Dans l’introduction, la découverte des riborégulateurs sera décrite en plus des caractéristiques particulières et de l’importance de ces ARN. Par la suite, quelques exemples démontrant l’importance des structures d’ARN seront abordés. Ensuite, les techniques de fluorescence utilisées pour étudier les structures d’ARN au cours de cette thèse seront présentées. Enfin, les recherches effectuées sur les riborégulateurs adénine seront détaillées afin d’aider le lecteur à bien comprendre le type de riborégulateur au centre de cette thèse. Le chapitre 1 traite du repliement de l’aptamère suite à la liaison avec l’adénine. Dans ce chapitre, il est démontré que l’aptamère peut adopter trois conformations. Une modification de la séquence de l’aptamère de type sauvage a permis d’isoler ces trois conformations. Il a ensuite été possible d’identifier les caractéristiques propres à chacun des états. Le chapitre 2 s’intéresse à une région précise du riborégulateur adénine. Dans ce chapitre, la conformation du cœur de l’aptamère est étudiée plus en profondeur. Il y est possible de constater que le repliement du cœur de l’aptamère influence l’interaction boucle-boucle en présence de magnésium et de ligand. De plus, la présence de ligand, en concentration suffisante, permet le repliement du cœur et favorise le rapprochement des tiges P2 et P3 dans un aptamère muté pour empêcher la formation de l’interaction boucle-boucle. Il semble donc que le repliement du cœur de l’aptamère influence la structure globale de l’aptamère. Finalement, les travaux présentés dans les chapitres 1 et 2 seront mis en contexte avec la littérature scientifique disponible. Cette discussion tentera de réconcilier certaines observations contradictoires. Il sera ensuite question de l’impact que les travaux présentés dans cette thèse peuvent avoir dans le domaine de l’ARN. Enfin, quelques études à réaliser en continuité avec ces travaux seront proposées.