Evidence of hook competition in longline surveys

Catch rates from surveys are used as indices of abundance for many fish species. Relative abundance estimates from surveys with longline gear do not usually account for possible effects of gear saturation, which potentially creates competition among fish for baited hooks and misrepresentations of abundance trends. We examined correlations between catch rates of sablefish (Anoplopoma fimbria) and giant grenadier (Albatrossia pectoralis) and between sablefish and shortraker (Sebastes borealis) and rougheye rockfish (Sebastes aleutianus) from 25 years of longline surveys in Alaska waters for evidence of competition for hooks. Sablefish catch rates were negatively correlated with giant grenadier catch rates in all management areas in Alaskan waters, and sablefish and rockfish were negatively correlated in five of the six areas, indicating that there is likely competition for hooks during longline surveys. Comparative analyses were done for trawl survey catch rates, and no negative correlations were observed, indicating that the negative correlations on the longline surveys are not due to differing habitat preferences or direct competition. Available adjustments for gear saturation may be biased if the probability of capture does not decrease linearly with baited hooks. A better understanding of each fish species’ catch probabilities on longline gear are needed before adjustments for hook competition can be made.

Biodiversity as an index of regime shift in the eastern Bering Sea

Data collected from an annual groundf ish survey of the eastern Bering Sea shelf from 1975 to 2002 were used to estimate biomass and biodiversity indexes for two fish guilds: f latfish and roundfish. Biomass estimates indicated that several species of f latfish (particularly rock sole, arrowtooth flounder, and f lathead sole), several large sculpins (Myoxocephalus spp.), bigmouth (Hemitripterus bolini), and skates (Bathyraja spp.) had increased. Declining species included several f latfish species and many smaller roundfish species of sculpins, eelpouts (Lycodes spp.), and sablefish (Anoplopoma fimbria). Biodiversity indexes were calculated by using biomass estimates for both guilds from 1975 through 2002 within three physical domains on the eastern Bering Sea shelf. Biodiversity trends were found to be generally declining within the roundfish guild and generally increasing within the f latfish guild and varied between inner, middle, and outer shelf domains. The trends in biodiversity indexes from this study correlated strongly with the regime shift reported for the late 1970s and 1980s.

Effects of Gear Modifications on the Trawl Performance and Catching Efficiency of the West Coast Upper Continental Slope Groundfish Survey Trawl

Since 1984, annual bottom trawl surveys of the west coast (California–Washington) upper continental slope (WCUCS) have provided information on the abundance, distribution, and biological characteristics of groundfish resources. Slope species of the deep-water complex (DWC) are of particular importance and include Dover sole, Microstomus pacificus; sablefish, Anoplopoma fimbria; shortspine thornyhead, Sebastolobus alascanus; and longspine thornyhead, S. altivelis. In the fall of 1994, we conducted an experimental gear research cruise in lieu of our normal survey because of concerns about the performance of the survey trawl. The experiment was conducted on a soft mud bottom at depths of 460–490 m off the central Oregon coast. Treatments included different combinations of door-bridle rigging, groundgear weight, and scope length. The experimental design was a 2 ´ 2 ´ 2 factorial within a randomized complete-block. Analysis of variance was used to examine the effects of gear modifications on the engineering performance of the trawl (i.e. trawl dimensions, variation in trawl dimensions, and door attitude) and to determine if catch rates in terms of weight and number of DWC species and invertebrates were affected by the gear modifications. Trawl performance was highly variable for the historically used standard trawl configuration. Improvements were observed with the addition of either a 2-bridle door or lighter ground gear. Changes in scope length had relatively little effect on trawl performance. The interaction of door bridle and ground gear weight had the most effect on trawl performance. In spite of the standard trawl’s erratic performance, catch rates of all four DWC species and invertebrates were not significantly different than the 2-bridle/heavy combination, which did the best in terms of engineering performance. The most important factor affecting DWC catch rates was ground gear. Scope length and the type of door bridle had little effect on DWC catch rates. Subsequent revisions to survey gear and towing protocol and their impact on the continuity of the slope survey time series are discussed.

Biology and Potential Use of Pacific Grenadier, Coryphaenoides acrolepis, off California

Grenadiers (family Macrouridae) are the most abundant fish on most continental slope areas worldwide. Off California the Pacific grenadier, Coryphaenoides acrolepis, occurs in relatively large numbers and may have marketing potential. This repon provides information on the biology of the species and catch results from a number of scientific cruises. Catch data on several other species found together with Pacific grenadier, panicularly sablefish, Anoplopoma fimbria, are also given. The fish were caught with a bottom trawl (15 trawls), and with free-vehicle longline gear (117 sets). The latter was a hook and line system in which the gear was dropped to the seafloor untethered to the fishing vessel, and floated to the surface, with the catch, when detachable weights were automatically released. Sablefish dominated longline catches in depths of 200-600fm (334-1,098m), while Pacific grenadier was most abundant between 600 and 1,OOOfm (1,098-1,830m). Best trawl catches of Pacific grenadier were made at depths between 615 and 675fm (1,125 and 1,235 m) and at 760fm (1,391 m). Ripe females were absent from our samples, but spent females were found during the entire year with highest numbers in the spring and early summer. Only one larva was found despite extensive sampling with plankton nets. Pacific grenadier was found to have good edible qualities by a taste-test panel, although the protein content (15 percent) and flesh yield (24 percent) were significantly lower than those of other fishes. A second species, the giant grenadier, Albatrossia pectoralis, was found to have exceptionally poor eating qualities and even lower protein content.

Comparing autonomous underwater vehicle (AUV) and vessel-based tracking performance for locating acoustically tagged fish

Autonomous underwater vehicles (AUV’s) are increasingly used to collect physical, chemical, and biological information in the marine environment. Recent efforts include merging AUV technology with acoustic telemetry to provide information on the distribution and movements of marine fish. We compared surface vessel and AUV tracking capabilities under rigorous conditions in coastal waters near Juneau, Alaska. Tracking surveys were conducted with a REMUS 100 AUV equipped with an integrated acoustic receiver and hydrophone. The AUV was programmed to navigate along predetermined routes to detect both reference transmitters at 20–500 m depths and tagged fish and crabs in situ. Comparable boat surveys were also conducted. Transmitter depth had a major impact on tracking performance. The AUV was equally effective or better than the boat at detecting reference transmitters in shallow water, and significantly better for transmitters at deeper depths. Similar results were observed for tagged animals. Red king crab, Paralithodes camtschaticus, at moderate depths were recorded by both tracking methods, while only the AUV detected Sablefish, Anoplopoma fimbria, at depths exceeding 500 m. Strong currents and deep depths caused problems with AUV navigation, position estimation, and operational performance, but reflect problems encountered by other AUV applications that will likely diminish with future advances, enhanced methods, and increased use.

Quantitative mapping of trimethyltin injury in the rat brain using magnetic resonance histology.

The growing exposure to chemicals in our environment and the increasing concern over their impact on health have elevated the need for new methods for surveying the detrimental effects of these compounds. Today's gold standard for assessing the effects of toxicants on the brain is based on hematoxylin and eosin (H&E)-stained histology, sometimes accompanied by special stains or immunohistochemistry for neural processes and myelin. This approach is time-consuming and is usually limited to a fraction of the total brain volume. We demonstrate that magnetic resonance histology (MRH) can be used for quantitatively assessing the effects of central nervous system toxicants in rat models. We show that subtle and sparse changes to brain structure can be detected using magnetic resonance histology, and correspond to some of the locations in which lesions are found by traditional pathological examination. We report for the first time diffusion tensor image-based detection of changes in white matter regions, including fimbria and corpus callosum, in the brains of rats exposed to 8 mg/kg and 12 mg/kg trimethyltin. Besides detecting brain-wide changes, magnetic resonance histology provides a quantitative assessment of dose-dependent effects. These effects can be found in different magnetic resonance contrast mechanisms, providing multivariate biomarkers for the same spatial location. In this study, deformation-based morphometry detected areas where previous studies have detected cell loss, while voxel-wise analyses of diffusion tensor parameters revealed microstructural changes due to such things as cellular swelling, apoptosis, and inflammation. Magnetic resonance histology brings a valuable addition to pathology with the ability to generate brain-wide quantitative parametric maps for markers of toxic insults in the rodent brain.

Effects of thyroxine treatment on histology and behavior using the methimazole model of congenital hypothyroidism in the rat

The timing of thyroxine (T4) replacement treatment in congenital hypothyroidism (CH) has been suggested to be important for optimizing cognitive recovery in humans; however this has not been fully established using modern animal models of CH. Consequently, the current studies investigated the ameliorating effects of postnatal T4 treatment on neuropathology and behavior in CH rats. Rat dams were administered methimazole to produce CH offspring, then brain tissue from male CH pups was analyzed to determine the effects of postnatal (P3, P7, P14 and P21) T4 treatment on hippocampal dendritic branching and the expression of nerve growth factor (NGF). Two operant behavioral procedures were employed to confirm and extend previous findings obtained using this model, and to investigate timelines for instigating T4 treatment on improved behavioral outcomes. T4 treatment initiated at P14 was protective of a reduction in dendritic branching in the hippocampus, and initiated at P7 was protective of a reduction of NGF expression in the fimbria of the hippocampus. Induction of CH did not affect the acquisition of simple operant response rules but had a significant effect on the acquisition of complex operant rules subsequently imposed. Furthermore, T4 treatment initiated at P3 protected learning deficits seen following the imposition of complex operant response rules. These findings indicate T4 treatment initiated at P7 is sufficient for the protection of hippocampal NGF expression and dendritic branching but for the protection of complex behavioral abilities T4 treatment is necessary prior to or approximating P3.

Exploring the modulatory role of A2A receptors in oligodendrogenesis derived from neural stem/progenitor cells of the subventricular zone

Tese de mestrado, Neurociências, Faculdade de Medicina, Universidade de Lisboa, 2015

Étude fonctionnelle de l’opéron fimbriaire stg de Salmonella enterica sérovar Typhi

La bactérie Salmonella enterica sérovar Typhi (S. Typhi) provoque la fièvre typhoïde chez les humains et constitue un problème de santé publique important. La majorité de nos connaissances sur la pathogenèse de cette bactérie provient du modèle de fièvre entérique chez la souris causée par le sérovar Typhimurium. Peu d’études se sont penchées sur les facteurs de virulence uniques au sérovar Typhi, ni sur la possibilité que les pseudogènes retrouvés dans son génome puissent être fonctionnels. Le fimbria stg, unique au sérovar Typhi, renferme un codon d’arrêt TAA prématuré dans le gène stgC qui code pour le placier responsable de l’assemblage des sous-unités fimbriaires à la surface de la bactérie. Ainsi, le fimbria stg a été classifié dans la liste des pseudogènes non-fonctionnels. Les objectifs de cette étude étaient d’évaluer l’implication du fimbria stg lors de l’interaction avec les cellules humaines, puis de vérifier l’importance du pseudogène stgC lors de la biogenèse fimbriaire. Dans une première partie, la transcription de stg a été évaluée à l’aide d’une fusion lacZ. Malgré des niveaux d’expression observés généralement faibles en milieu riche, la croissance en milieu minimal a favorisé la transcription de l’opéron. La délétion complète de l’opéron fimbriaire stgABCD du génome de S. Typhi a été réalisée par échange allélique, puis a été complémentée sur un plasmide. Il a été démontré que la présence de stg chez S. Typhi, S. Typhimurium et E. coli contribue à une adhérence accrue sur les cellules épithéliales humaines. De plus, ce fimbria semble agir comme une structure anti-phagocytaire lors de l’interaction avec des macrophages humains. Ainsi, l’opéron stg semble fonctionnel, malgré son codon d’arrêt prématuré, puisque des phénotypes ont été observés. La seconde partie de cette étude consistait à vérifier le rôle joué par le pseudogène stgC dans la biogenèse du fimbria. Différentes variantes de l’opéron ont été générées, clonées dans un vecteur inductible à l’arabinose, puis transformées dans la souche afimbriaire d’E. coli ORN172. La translocation de la sous-unité fimbriaire StgD à la surface de la bactérie a été évaluée chez ces différents mutants par immunobuvardage de type Western. Cette expérience a permis de démontrer que le pseudogène stgC est essentiel pour l’exportation de la sous-unité StgD à la surface. L’ajout d’une étiquette de 6-histidines en C-terminal de StgC a permis de confirmer la traduction complète du gène, malgré le codon d’arrêt TAA prématuré. Le séquençage peptidique a révélé l’insertion d’une tyrosine à ce codon. Une fusion traductionnelle avec la protéine verte fluorescente a révélé qu’environ 0.8% de l’ARNm peut être traduit et permet la production complète du placier. Ce projet a permis la caractérisation d’un facteur de virulence unique à S. Typhi et constitue une étape de plus vers la compréhension de ses mécanismes de pathogenèse. Il s’agit de la première démonstration chez les bactéries de la fonctionnalité d’un gène interrompu prématurément par un codon d’arrêt TAA.

Caractérisation et surexpression des fimbriae de type chaperon-placier de Salmonella enterica sérovar Typhi

Salmonella enterica sérovar Typhi (S. Typhi) est l’agent responsable de la fièvre typhoïde et cause environ 200 000 morts et 27 millions de cas annuellement. C’est un pathogène entérique dont le réservoir est restreint à l’Homme. Les raisons de cette restriction d’hôte sont méconnues et pourraient dépendre de l’expression de facteurs d’adhésion à des étapes importantes au cours de la pathogenèse. L’annotation bioinformatique du génome de S. Typhi identifie 12 fimbriae de type chaperon-placier (FCP), un curli ainsi qu’un pilus de type IV. L’objectif de ce projet de recherche est d’étudier ces systèmes d’adhésion peu caractérisés. D’abord, le niveau d’expression de ces gènes a été évalué dans différentes conditions de culture in vitro en utilisant une approche de gènes rapporteurs. L’expression des 14 systèmes d’adhésion a été détectée. Nos résultats indiquent qu’une carence en fer favorise l’expression des opérons bcf et csg. Indépendamment du fer, l’expression de bcf, csg, pil, sef, sta, stc, stg et sth est influencée par la richesse nutritive du milieu. L’incubation en milieu LB liquide favorise l’expression de la plupart des systèmes d’adhésion par rapport à un milieu LB liquide sans agitation ou un milieu LB solide. En somme, l’expression des systèmes d’adhésion de S. Typhi a été observée et est influencée par des conditions environnementales. Dans un second volet, nous avons tent de surexprimer les différents systèmes d’adhésion chez une souche d’E. coli ou de S. Typhi afimbriaire. Avec cette approche, nous avons été en mesure de démontrer que l’opéron tcf encode pour un fimbria fonctionnel que l’on a pu observer en microscopie électronique. L’expression de tcf chez une souche afimbriaire d’E. coli et S. Typhi a également diminué leur capacité d’adhésion à des cellules épithéliales intestinales humaines lors d’essais in vitro. Nos observations démontrent que l’expression des systèmes d’adhésion retrouvés chez S. Typhi est influencée par les conditions enviroi9onnementales. Au moins un de ces systèmes est fonctionnel. Ceci suggère une contribution des systèmes d’adhésion retrouvés chez S. Typhi lors de l’interaction de ce pathogène avec l’humain.

SEF17 fimbriae are essential for the convoluted colonial morphology of Salmonella enteritidis

Salmonella enteritidis isolated from poultry infections generated a convoluted colonial morphology after 48 h growth on colonisation factor antigen (CFA) agar at 25 degrees C. A mutant S. enteritidis defective for the elaboration of the SEF17 fimbrial antigen, in which the agf gene cluster was inactivated by insertion of an ampicillin resistance gene cassette, and other wild-type S. enteritidis transduced to this genotype failed to produce convoluted colonies. However, growth of SEF17(-) mutans at 25 degrees C on CFA agar supplemented with 0.001% Congo red resulted in partial recovery of the phenotype. Immunoelectron microscopy demonstrated that copious amounts of the SEF17 fimbrial antigen were present in the extracellular matrix of convoluted colonies of wild-type virulent S. enteritidis isolates. Bacteria were often hyperflagellated also. Immunoelectron microscopy of SEF17(-) mutants grown on CFA agar+0.001% Congo red demonstrated the elaboration of an as yet undefined fimbrial structure. Isolates of S. enteritidis which were described previously as avirulent and sensitive to environmental stress failed to express SEF17 or produce convoluted colonies. These data indicate an essential role for SEF17, and possibly for another fimbria and flagella, in the generation of the convoluted colonial phenotype. The relationship between virulence and colonial phenotype is discussed.

Short- and long-term anxiogenic effects induced by a single injection of subconvulsant doses of pilocarpine in rats: investigation of the putative role of hippocampal pathways

Behavioral consequences of convulsive episodes are well documented, but less attention was paid to changes that occur in response to subconvulsant doses of drugs. We investigated short- and long-term effects of a single systemic injection of a subconvulsant dose of pilocarpine on the behavior of rats as evaluated in the elevated plus maze. Pilocarpine induced an anxiogenic-like profile 24 h later, and this effect persisted for up to 3 months (% of time spent on open arms at 24 h, control = 35.47 +/- 3.23; pilocarpine 150 = 8.2 +/- 2.6; 3 months, control = 31.9 +/- 5.5; pilocarpine 150 = 9.3 +/- 4.9). Temporary inactivation of fimbria-fornix with lidocaine 4% promoted an anxiolytic-like effect per se, suggesting a tonic control of this pathway on the modulation of anxiety-related behaviors. Lidocaine also reduced the anxiogenic-like profile of animals tested 1 month after pilocarpine treatment (% of time spent on open arms, saline + phosphate-buffered saline (PBS) = 31.7 + 3.7; saline + lidocaine = 54.4 + 4.7; pilocarpine + PBS = 10.3 + 4.1; pilocarpine + lidocaine = 40.1 + 9.1). To determine whether the anxiogenic-like effect was mediated by septal region or by direct hippocampal projections to the diencephalon, the neural transmission of post-commissural fornix was blocked, and a similar reduction in the anxiogenic-like effect of pilocarpine was observed. Our findings suggest that a single systemic injection of pilocarpine may induce long-lasting anxiogenic-like behavior in rats, an effect that appears to be mediated, in part, through a direct path from hippocampus to medial hypothalamic sites involved in fear responses.

Pseudomonas aeruginosa PA14 cupD transcription is activated by the RcsB response regulator, but repressed by its putative cognate sensor RcsC

The opportunistic pathogen Pseudomonas aeruginosa PA14 possesses four fimbrial cup clusters, which may confer the ability to adapt to different environments. cupD lies in the pathogenicity island PAPI-1 next to genes coding for a putative phosphorelay system composed of the hybrid histidine kinase RcsC and the response regulator RcsB. The main focus of this work was the regulation of cupD at the mRNA level. It was found that the HN-S-like protein MvaT does not exert a strong influence on cupD transcript levels, as it does for cupA. cupD transcription is higher in cultures grown at 28 degrees C, which agrees with a cupD mutant presenting attenuated virulence only in a plant model, but not in a mouse model of infection. Whereas an rcsC in-frame deletion mutant presented higher levels of cupD mRNA, rcsB deletion had the opposite effect. Accordingly, overexpression of RcsB increased the levels of cupD transcription, and promoted biofilm formation and the appearance of fimbriae. A single transcription start site was determined for cupD and transcription from this site was induced by RcsB. A motif similar to the enterobacterial RcsB/RcsA-binding site was detected adjacent to the -35 region, suggesting that this could be the RcsB-binding site. Comparison of P. aeruginosa and Escherichia coli Rcs may provide insights into how similar systems can be used by different bacteria to control gene expression and to adapt to various environmental conditions.

Whole-genome expression profiling of Xylella fastidiosa in response to growth on glucose

Xylella fastidiosa is the etiologic agent of diseases in a wide range of economically important crops including citrus variegated chlorosis, a major threat to the Brazilian citrus industry. The genomes of several strains of this phytopathogen have been completely sequenced enabling large-scale functional studies. In this work we used whole-genome DNA microarrays to investigate the transcription profile of X. fastidiosa grown in defined media with different glucose concentrations. Our analysis revealed that while transcripts related to fastidian gum production were unaffected, colicin-V-like and fimbria precursors were induced in high glucose medium. Based on these results, we suggest a model for colicin-defense mechanism in X. fastidiosa.