Transboundary Movement of Atlantic Istiophorid Billfishes Among International and U.S. Domestic Management Areas Inferred from Mark-Recapture Studies

Billfish movements relative to the International Commission for the Conservation of Atlantic Tunas management areas, as well as U.S. domestic data collection areas within the western North Atlantic basin, were investigated with mark-recapture data from 769 blue marlin, Makaira nigricans, 961 white marlin, Tetrapturus albidus, and 1,801 sailfish, Istiophorus platypterus. Linear displacement between release and recapture locations ranged from zero (all species) to 15,744 km (mean 575, median 119, SE 44) for blue marlin, 6,523 km (mean 719, median 216, SE 33) for white marlin, and 3,845 km (mean 294, median 98, SE 13) for sailfish. In total, 2,824 (80.0%) billfish were recaptured in the same management area of release. Days at liberty ranged from zero (all species) to 4,591 (mean 619, median 409, SE 24) for blue marlin, 5,488 (mean 692, median 448, SE 22) for white marlin, and 6,568 (mean 404, median 320, SE 11) for sailfish. The proportions (per species) of visits were highest in the Caribbean area for blue marlin and white marlin, and the Florida East Coast area for sailfish. Blue marlin and sailfish were nearly identical when comparing the percent of individuals vs. the number of areas visited. Overall, white marlin visited more areas than either blue marlin or sailfish. Seasonality was evident for all species, with overall results generally reflecting the efforts of the catch and release recreational fishing sector, particularly in the western North Atlantic. This information may be practical in reducing the uncertainties in billfish stock assessments and may offer valuable insight into management consideration of time-area closure regulations to reduce bycatch mortality of Atlantic billfishes.

Home range and seasonal movements of Black Sea Bass (Centropristis striata) during their inshore residency at a reef in the mid-Atlantic Bight

Black Sea Bass (Centropristis striata) in the mid-Atlantic Bight undertake seasonal cross-shelf movements to occupy inshore rocky reefs and hardbottom habitats between spring and fall. Shelf-wide migrations of this stock are well documented, but movements and home ranges of fish during their inshore residency period have not been described. We tagged 122 Black Sea Bass with acoustic transmitters at a mid-Atlantic reef to estimate home-range size and factors that influence movements (>400 m) at a 46.1-km2 study site between May and November 2003. Activity of Black Sea Bass was greatest and most consistent during summer but declined rapidly in September as water temperatures at the bottom of the seafloor increased on the inner shelf. Black Sea Bass maintained relatively large home ranges that were fish-size invariant but highly variable (13.7–736.4 ha), underscoring the importance of large sample sizes in examination of population-level characteristics of mobile species with complex social interactions. On the basis of observed variations in movement patterns and the size of home ranges, we postulate the existence of groups of conspecifics that exhibit similar space-use behaviors. The group of males released earlier in the tagging period used larger home ranges than the group of males released later in our study. In addition, mean activity levels and the probability of movement among acoustic stations varied among groups of fish in a complex manner that depended on sex. These differences in movement behaviors may increase the vulnerability of male fish to passive fishing gears, further exacerbating variation in exploitation rates for this species among reefs.

Biology of Balanus amphitrite communis (Darwin) in the Cochin harbour waters

Seasonal viariations in the incidence on fresh surfaces, breeding season, rate of growth and mortality of Balanus amphitrite communis was studied for a period of twelve months in the Cochin harbour waters, situated 76̊ 14'E and 90̊ 57'N, and subjected to annual seasonal changes in salinity.

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication(1,2). To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data(3). Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.

Molecular evidence for diphyly of the Asian catfish family Amblycipitidae (Teleostei: Siluriformes) and exclusion of the South American Aspredinidae from Sisoroidea

Amblycipitidae Day, 1873 is an Asian family of catfishes (Siluriformes) usually considered to contain 28 species placed in three genera: Amblyceps (14 spp.), Liobagrus (12 spp.) and Xiurenbagrus (2 spp.). Morphology-based systematics has supported the monophyly of this family, with some authors placing Amblycipitidae within a larger group including Akysidae, Sisoridae and Aspredinidae, termed the Sisoroidea. Here we investigate the phylogenetic relationships among four species of Amblyceps, six species of Liobagrus and the two species of Xiurenbagrus with respect to other sisoroid taxa as well as other catfish groups using 6100 aligned base pairs of DNA sequence data from the rag1 and rag2 genes of the nuclear genome and from three regions (cyt b, COL ND4 plus tRNA-His and tRNA-Ser) of the mitochondrial genome. Parsimony and Bayesian analyses of the data indicate strong support for a diphyletic Amblycipitidae in which the genus Amblyceps is the sister group to the Sisoridae and a clade formed by genera Liobagrus and Xiurenbagrus is the sister group to Akysidae. These taxa together form a well supported monophyletic group that assembles all Asian sisoroid taxa, but excludes the South American Aspredinidae. Results for aspredinids are consistent with previous molecular studies that indicate these catfishes are not sisoroids, but the sister group to the South American doradoid catfishes (Auchenipteridae + Doradidae). The redefined sisoroid clade plus Bagridae, Horabagridae and (Ailia + Laides) make up a larger monophyletic group informally termed "Big Asia." Likelihood-based SH tests and Bayes Factor comparisons of the rag and the mitochondrial data partitions considered separately and combined reject both the hypothesis of amblycipitid monophyly and the hypothesis of aspredinid inclusion within Sisoroidea. This result for amblycipitids conflicts with a number of well documented morphological synapomorphies that we briefly review. Possible nomenclatural changes for amblycipitid taxa are noted.

Effects of brominated flame retardants and brominated dioxins on steroidogenesis in H295R human adrenocortical carcinoma cell line

Brominated flame retardants (BFRs) and brominated dioxins are emerging persistent organic pollutants that are ubiquitous in the environment and can be accumulated by wildlife and humans. These chemicals can disturb endocrine function. Recent studies have demonstrated that one of the mechanisms of endocrine disruption by chemicals is modulation of steroidogenic gene expression or enzyme activities. In this study, an in vitro assay based on the H295R human adrenocortical carcinoma cell line, which possesses most key genes or enzymes involved in steroidogenesis, was used to examine the effects of five bromophenols, two polybrominated biphenyls (PBBs 77 and 169), 2,3,7,8-tetrabromodibenzo-p-dioxin, and 2,3,7,8-tetrabromodibenzofuran on the expression of 10 key steroidogenic genes. The H295R cells were exposed to various BFR concentrations for 48 h, and the expression of specific genescytochrome P450 (CYP11A, CYP11B2, CYP17, CYP19, and CYP21), 3 beta-hydroxysteroid dehydrogenase (3PHSD2), 17 beta-hydroxysteroid dehydrogenase (17 beta HSD1 and 17 beta HSD4), steroidogenic acute regulatory protein (StAR), and 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR)-was quantitatively measured using real-time polymerase chain reaction. Cell viability was not affected at the doses tested. Most of the genes were either up- or down-regulated, to some extent, by BFR exposure. Among the genes tested, 3PHSD2 was the most markedly up-regulated, with a range of magnitude from 1.6- to 20-fold. The results demonstrate that bromophenol, bromobiphenyls, and bromodibenzo-p-dioxin/furan are able to modulate steroidogenic gene expression, which may lead to endocrine disruption.

Linear dimensionality reduction: Survey, insights, and generalizations

© 2015 John P. Cunningham and Zoubin Ghahramani. Linear dimensionality reduction methods are a cornerstone of analyzing high dimensional data, due to their simple geometric interpretations and typically attractive computational properties. These methods capture many data features of interest, such as covariance, dynamical structure, correlation between data sets, input-output relationships, and margin between data classes. Methods have been developed with a variety of names and motivations in many fields, and perhaps as a result the connections between all these methods have not been highlighted. Here we survey methods from this disparate literature as optimization programs over matrix manifolds. We discuss principal component analysis, factor analysis, linear multidimensional scaling, Fisher's linear discriminant analysis, canonical correlations analysis, maximum autocorrelation factors, slow feature analysis, sufficient dimensionality reduction, undercomplete independent component analysis, linear regression, distance metric learning, and more. This optimization framework gives insight to some rarely discussed shortcomings of well-known methods, such as the suboptimality of certain eigenvector solutions. Modern techniques for optimization over matrix manifolds enable a generic linear dimensionality reduction solver, which accepts as input data and an objective to be optimized, and returns, as output, an optimal low-dimensional projection of the data. This simple optimization framework further allows straightforward generalizations and novel variants of classical methods, which we demonstrate here by creating an orthogonal-projection canonical correlations analysis. More broadly, this survey and generic solver suggest that linear dimensionality reduction can move toward becoming a blackbox, objective-agnostic numerical technology.

Small angle scattering characterisation of micellar systems and templated architectures

The work described in this thesis reports the structural changes induced on micelles under a variety of conditions. The micelles of a liquid crystal film and dilute solutions of micelles were subjected to high pressure CO2 and selected hydrocarbon environments. Using small angle neutron scattering (SANS) techniques the spacing between liquid crystal micelles was measured in-situ. The liquid crystals studied were templated from different surfactants with varying structural characteristics. Micelles of a dilute surfactant solution were also subjected to elevated pressures of varying gas atmospheres. Detailed modelling of the in-situ SANS experiments revealed information of the size and shape of the micelles at a number of different pressures. Also reported in this thesis is the characterisation of mesoporous materials in the confined channels of larger porous materials. Periodic mesoporous organosilicas (PMOs) were synthesised within the channels of anodic alumina membranes (AAM) under different conditions, including drying rates and precursor concentrations. In-situ small angle x-ray scattering (SAXS) and transmission electron microscopy (TEM) was used to determine the pore morphology of the PMO within the AAM channels. PMO materials were also used as templates in the deposition of gold nanoparticles and subsequently used in the synthesis of germanium nanostructures. Polymer thin films were also employed as templates for the directed deposition of gold nanoparticles which were again used as seeds for the production of germanium nanostructures. A supercritical CO2 (sc-CO2) technique was successfully used during the production of the germanium nanostructures.

Wavelength division multiplexing at 2μm

This paper shows, for the first time, the implementation of a WDM subsystem at the 2μm wavelength window with mixed formats. Three wavelength channels were directly modulated withBPSK Fast-OFDM at 5Gbit/s per channel, with a fourth channel NRZ-OOK externally modulated at8.5Gbit/s giving a total capacity in excess of 20 Gbit/s.

Exploiting the diverse microbial ecology of marine sponges

Marine sponges (phylum Porifera) are the oldest extant metazoan animals on earth and host large populations of symbiotic microbes: Bacteria, Archaea and unicellular Eukaryota. Those microbes play ecological functions which are essential to the health of the host including carbon, nitrogen and sulfur cycling as well as host defence through the production of bioactive secondary metabolites which protect against infection and predation. The diversity of sponge-associated microbes is remarkable with thousands of OTUs reported from individual sponge species. Amongst those populations are sponge-specific microbes which may be specific to sponges or specific to sponge species. While marine natural product discovery concerns many animal phyla, Porifera account for the largest proportion of novel compounds. Evidence suggests that many of these compounds are the products of symbiotic microbes. Descriptions of sponge-associated microbial community structures have been advanced by the development of next-generation sequencing technologies while the discovery and exploitation of sponge derived bioactive compounds has increased due to developments in sequence-based and function-based metagenomics. Here, we use pyrosequencing to describe the bacterial communities associated with two shallow, temperate water sponges (Raspailia ramosa and Stelligera stuposa) from Irish coastal waters and to describe the bacterial and archaeal communities of a single sponge species (Inflatella pellicula) from two different depths in deep waters in the Atlantic Ocean, including at a depth of 2900m, a depth far greater than that of any previous sequence-based sponge-microbe investigation. We identified diverse microbial communities in all sponges and the presence of sponge-specific taxa recruiting to previously described and novel spongespecific clusters. We also identified archaeal communities which dominated sponge-microbe communities. We demonstrate that sponge-associated microbial communities differ from seawater communities indicating host selection processes. We used sequence-based metagenomic techniques to identify genes of potential industrial and pharmacological interest in the metagenomes of various sponge species and functionbased metagenomic screening in an attempt to identify lipolytic and antibacterial activities from metagenomic clones from the metagenome of the marine sponge Stelletta normani. In addition we have cultured diverse bacterial species from sponge tissues, many of which display antimicrobial activities against clinically relevant bacterial and yeast test strains. Other isolates represent novel species in the genus Maribacter and require emendments to the description of that genus.

Biodiscovery of natural products from microbes associated with Irish coastal sponges

Marine sponges have been an abundant source of new metabolites in recent years. The symbiotic association between the bacteria and the sponge has enabled scientists to access the bacterial diversity present within the bacterial/sponge ecosystem. This study has focussed on accessing the bacterial diversity in two Irish coastal marine sponges, namely Amphilectus fucorum and Eurypon major. A novel species from the genus Aquimarina has been isolated from the sponge Amphilectus fucorum. The study has also resulted in the identification of an α–Proteobacteria, Pseudovibrio sp. as a potential producer of antibiotics. Thus a targeted based approach to specifically cultivate Pseudovibrio sp. may prove useful for the development of new metabolites from this particular genus. Bacterial isolates from the marine sponge Haliclona simulans were screened for anti–fungal activity and one isolate namely Streptomyces sp. SM8 displayed activity against all five fungal strains tested. The strain was also tested for anti–bacterial activity and it showed activity against both against B. subtilis and P. aeruginosa. Hence a combinatorial approach involving both biochemical and genomic approaches were employed in an attempt to identify the bioactive compounds with these activities which were being produced by this strain. Culture broths from Streptomyces sp. SM8 were extracted and purified by various techniques such as reverse–phase HPLC, MPLC and ash chromatography. Anti–bacterial activity was observed in a fraction which contained a hydroxylated saturated fatty acid and also another compound with a m/z 227 but further structural elucidation of these compounds proved unsuccessful. The anti–fungal fractions from SM8 were shown to contain antimycin–like compounds, with some of these compounds having different retention times from that of an antimycin standard. A high–throughput assay was developed to screen for novel calcineurin inhibitors using yeast as a model system and three putative bacterial extracts were found to be positive using this screen. One of these extracts from SM8 was subsequently analysed using NMR and the calcineurin inhibition activity was con rmed to belong to a butenolide type compound. A H. simulans metagenomic library was also screened using the novel calcineurin inhibitor high–throughput assay system and eight clones displaying putative calcineurin inhibitory activity were detected. The clone which displayed the best inhibitory activity was subsequently sequenced and following the use of other genetic based approaches it became clear that the inhibition was being caused by a hypothetical protein with similarity to a hypothetical Na+/Ca2+ exchanger protein. The Streptomyces sp. SM8 genome was sequenced from a fragment library using Roche 454 pyrosequencing technology to identify potential secondary metabolism clusters. The draft genome was annotated by IMG/ER using the Prodigal pipeline. The Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMPN00000000. The genome contains genes which appear to encode for several polyketide synthases (PKS), non–ribosomal peptide synthetases (NRPS), terpene and siderophore biosynthesis and ribosomal peptides. Transcriptional analyses led to the identification of three hybrid clusters of which one is predicted to be involved in the synthesis of antimycin, while the functions of the others are as yet unknown. Two NRPS clusters were also identified, of which one may be involved in gramicidin biosynthesis and the function of the other is unknown. A Streptomyces sp. SM8 NRPS antC gene knockout was constructed and extracts from the strain were shown to possess a mild anti–fungal activity when compared to the SM8 wild–type. Subsequent LCMS analysis of antC mutant extracts confirmed the absence of the antimycin in the extract proving that the observed anti–fungal activity may involve metabolite(s) other than antimycin. Anti–bacterial activity in the antC gene knockout strain against P. aeruginosa was reduced when compared to the SM8 wild–type indicating that antimycin may be contributing to the observed anti–bacterial activity in addition to the metabolite(s) already identified during the chemical analyses. This is the first report of antimycins exhibiting anti–bacterial activity against P. aeruginosa. One of the hybrid clusters potentially involved in secondary metabolism in SM8 that displayed high and consistent levels of gene–expression in RNA studies was analysed in an attempt to identify the metabolite being produced by the pathway. A number of unusual features were observed following bioinformatics analysis of the gene sequence of the cluster, including a formylation domain within the NRPS cluster which may add a formyl group to the growing chain. Another unusual feature is the lack of AT domains on two of the PKS modules. Other unusual features observed in this cluster is the lack of a KR domain in module 3 of the cluster and an aminotransferase domain in module 4 for which no clear role has been hypothesised.

Exploiting the bioactive potential of marine sponge microbiota

Endospore-forming bacteria are often isolated from different marine sponges, but their abundance varies, and they are frequently missed by culture-independent studies. Within endospore-formers, Bacillus are renowned for the production of antimicrobials and other compounds of medical and industrial importance. Although this group has been well studied in many different environments, very little is known about the actual diversity and properties of sporeformers associated with marine sponges. Identification of the endospore-forming bacteria associated with the marine sponges; Haliclona simulans, Amphilectus fucorum and Cliona celata, has uncovered an abundant and diverse microbial population composed of Bacillus, Paenibacillus, Solibacillus, Halobacillus and Viridibacillus species. This diversity appears to be overlooked by other non-targeted approaches where spore-formers are masked by more dominant species within the ecosystem. In addition to the identification of two antibiotic resistant plasmids, this bank of sporeformers produce a range of bioactive compounds. New antimicrobial compounds are urgently needed to combat the spread of multidrug resistant pathogens, as few new options are entering the drug discovery pipelines for clinical trials. Based on the results of this project, endospore-formers associated with marine sponges may hold the answer. The power of coupling functional based assays with genomic approaches has enabled us to identify a novel class 1 lantibiotic, subtilomycin, which is active against several clinically relevant pathogens. Subtilomycin is encoded in the genomes of all the marine sponge B. subtilis isolates analysed. They cluster together phylogenetically and form a distinct group from other sequenced B. subtilis strains. Regardless of its potential clinical relevance, subtilomycin may be providing these strains with a specific competitive advantage(s) within the stringent confines of the marine sponge environment. This work has outlined the industrial and biotechnological potential of marine sponge endospore-formers which appear to produce a cocktail of bioactive compounds. Genome sequencing of specific marine sponge isolates highlighted the importance of mining extreme environments and habitats for new lead compounds with potential therapeutic applications.

The effectiveness of using patient-reported outcome measures as quality improvement tools

Aim: To investigate the value of using PROMs as quality improvement tools. Methods: Two systematic reviews were undertaken. The first reviewed the quantitative literature on the impact of PROMs feedback and the second reviewed the qualitative literature on the use of PROMs in practice. These reviews informed the focus of the primary research. A cluster randomised controlled trial (PROFILE) examined the impact of providing peer benchmarked PROMs feedback to consultant orthopaedic surgeons on improving outcomes for hip replacement surgery. Qualitative interviews with surgeons in the intervention arm of the trial examined the view of and reactions to the feedback. Results: The quantitative review of 17 studies found weak evidence to suggest that providing PROMs feedback to professionals improves patient outcomes. The qualitative review of 16 studies identified the barriers and facilitators to the use of PROMs based on four themes: practical considerations, attitudes towards the data, methodological concerns and the impact of feedback on care. The PROFILE trial included 11 surgeons and 215 patients in the intervention arm, and 10 surgeons and 217 patients in the control arm. The trial found no significant difference in the Oxford Hip Score between the arms (-0.7, 95% CI -1.9-0.5, p=0.2). Interviews with surgeons revealed mixed opinions about the value of the PROMs feedback and the information did not promote explicit changes to their practice. Conclusion: It is important to use PROMs which have been validated for the specific purpose of performance measurement, consult with professionals when developing a PROMs feedback intervention, communicate with professionals about the objectives of the data collection, educate professionals on the properties and interpretation of the data, and support professionals in using the information to improve care. It is also imperative that the burden of data collection and dissemination of the information is minimised.

The controlled delivery of hydrogen sulfide for the preservation of heart tissue

Gemstone Team Organ Storage and Hibernation

Fabrication of Poly (D,L-Lactic-Co-Glycolic Acid) Microparticles for Improved Human Papillomavirus Vaccine Delivery

Human papillomavirus (HPV) is the leading cause of cervical cancer and the most prevalent sexually transmitted disease worldwide. HPV vaccines require a multi-dose regimen to provide immunity, contributing to low patient compliance. We addressed this problem by formulating biodegradable poly(D,L-lactic-co-glycolic acid) (PLGA) microparticles and assessing their viability for use in controlled-release vaccines. We hypothesized that we could alter fabrication parameters to produce 1-10 μm microparticles in order to encapsulate ovalbumin (OVA) and HPV virus-like particles (VLPs). Microparticles were fabricated using a double emulsion method and used to elicit an immune response in JAWSII cells. Our results contribute to knowledge of vaccine delivery mechanisms and controlled-release technology, and could contribute to the creation of a viable controlled-release HPV vaccine.