East of the barrier; or, Sidelights on the Manchuria mission, by the Rev. J. Miller Graham.

http://www.archive.org/details/eastofthebarrier00grahuoft

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.

P-glycoprotein inhibition as a strategy to increase drug delivery across the blood-brain barrier: focus on antidepressants

Depression is among the leading causes of disability worldwide. Currently available antidepressant drugs have unsatisfactory efficacy, with up to 60% of depressed patients failing to respond adequately to treatment. Emerging evidence has highlighted a potential role for the efflux transporter P-glycoprotein (P-gp), expressed at the blood-brain barrier (BBB), in the aetiology of treatment-resistant depression. In this thesis, the potential of P-gp inhibition as a strategy to enhance the brain distribution and pharmacodynamic effects of antidepressant drugs was investigated. Pharmacokinetic studies demonstrated that administration of the P-gp inhibitors verapamil or cyclosporin A (CsA) enhanced the BBB transport of the antidepressants imipramine and escitalopram in vivo. Furthermore, both imipramine and escitalopram were identified as transported substrates of human P-gp in vitro. Contrastingly, human P-gp exerted no effect on the transport of four other antidepressants (amitriptyline, duloxetine, fluoxetine and mirtazapine) in vitro. Pharmacodynamic studies revealed that pre-treatment with verapamil augmented the behavioural effects of escitalopram in the tail suspension test (TST) of antidepressant-like activity in mice. Moreover, pre-treatment with CsA exacerbated the behavioural manifestation of an escitalopram-induced mouse model of serotonin syndrome, a serious adverse reaction associated with serotonergic drugs. This finding highlights the potential for unwanted side-effects which may occur due to increasing brain levels of antidepressants by P-gp inhibition, although further studies are needed to fully elucidate the mechanism(s) at play. Taken together, the research outlined in this thesis indicates that P-gp may restrict brain concentrations of escitalopram and imipramine in patients. Moreover, we show that increasing the brain distribution of an antidepressant by P-gp inhibition can result in an augmentation of antidepressant-like activity in vivo. These findings raise the possibility that P-gp inhibition may represent a potentially beneficial strategy to augment antidepressant treatment in clinical practice. Further studies are now warranted to evaluate the safety and efficacy of this approach.

Usability-enhanced coordination design of geovisualisations to communicate coastal flood risk information

For at least two millennia and probably much longer, the traditional vehicle for communicating geographical information to end-users has been the map. With the advent of computers, the means of both producing and consuming maps have radically been transformed, while the inherent nature of the information product has also expanded and diversified rapidly. This has given rise in recent years to the new concept of geovisualisation (GVIS), which draws on the skills of the traditional cartographer, but extends them into three spatial dimensions and may also add temporality, photorealistic representations and/or interactivity. Demand for GVIS technologies and their applications has increased significantly in recent years, driven by the need to study complex geographical events and in particular their associated consequences and to communicate the results of these studies to a diversity of audiences and stakeholder groups. GVIS has data integration, multi-dimensional spatial display advanced modelling techniques, dynamic design and development environments and field-specific application needs. To meet with these needs, GVIS tools should be both powerful and inherently usable, in order to facilitate their role in helping interpret and communicate geographic problems. However no framework currently exists for ensuring this usability. The research presented here seeks to fill this gap, by addressing the challenges of incorporating user requirements in GVIS tool design. It starts from the premise that usability in GVIS should be incorporated and implemented throughout the whole design and development process. To facilitate this, Subject Technology Matching (STM) is proposed as a new approach to assessing and interpreting user requirements. Based on STM, a new design framework called Usability Enhanced Coordination Design (UECD) is ten presented with the purpose of leveraging overall usability of the design outputs. UECD places GVIS experts in a new key role in the design process, to form a more coordinated and integrated workflow and a more focused and interactive usability testing. To prove the concept, these theoretical elements of the framework have been implemented in two test projects: one is the creation of a coastal inundation simulation for Whitegate, Cork, Ireland; the other is a flooding mapping tool for Zhushan Town, Jiangsu, China. The two case studies successfully demonstrated the potential merits of the UECD approach when GVIS techniques are applied to geographic problem solving and decision making. The thesis delivers a comprehensive understanding of the development and challenges of GVIS technology, its usability concerns, usability and associated UCD; it explores the possibility of putting UCD framework in GVIS design; it constructs a new theoretical design framework called UECD which aims to make the whole design process usability driven; it develops the key concept of STM into a template set to improve the performance of a GVIS design. These key conceptual and procedural foundations can be built on future research, aimed at further refining and developing UECD as a useful design methodology for GVIS scholars and practitioners.

Environmental and biological characteristics of lagoons on the southwest coast of Ireland

Coastal lagoons are defined as shallow coastal water bodies partially separated from the adjacent sea by a restrictive barrier. Coastal lagoons are protected under Annex I of the European Habitats Directive (92/43/EEC). Lagoons are also considered to be “transitional water bodies” and are therefore included in the “register of protected areas” under the Water Framework Directive (2000/60/EC). Consequently, EU member states are required to establish monitoring plans and to regularly report on lagoon condition and conservation status. Irish lagoons are considered relatively rare and unusual because of their North Atlantic, macrotidal location on high energy coastlines and have received little attention. This work aimed to assess the physicochemical and ecological status of three lagoons, Cuskinny, Farranamanagh and Toormore, on the southwest coast of Ireland. Baseline salinity, nutrient and biological conditions were determined in order to provide reference conditions to detect perturbations, and to inform future maintenance of ecosystem health. Accumulation of organic matter is an increasing pressure in coastal lagoon habitats worldwide, often compounding existing eutrophication problems. This research also aimed to investigate the in situ decomposition process in a lagoon habitat together with exploring the associated invertebrate assemblages. Re-classification of the lagoons, under the guidelines of the Venice system for the classifications of marine waters according to salinity, was completed by taking spatial and temporal changes in salinity regimes into consideration. Based on the results of this study, Cuskinny, Farranamanagh and Toormore lagoons are now classified as mesohaline (5 ppt – 18 ppt), oligohaline (0.5 ppt – 5 ppt) and polyhaline (18 ppt – 30 ppt), respectively. Varying vertical, longitudinal and transverse salinity patterns were observed in the three lagoons. Strong correlations between salinity and cumulative rainfall highlighted the important role of precipitation in controlling the lagoon environment. Maximum effect of precipitation on the salinity of the lagoon was observed between four and fourteen days later depending on catchment area geology, indicating the uniqueness of each lagoon system. Seasonal nutrient patterns were evident in the lagoons. Nutrient concentrations were found to be reflective of the catchment area and the magnitude of the freshwater inflow. Assessment based on the Redfield molar ratio indicated a trend towards phosphorus, rather than nitrogen, limitation in Irish lagoons. Investigation of the decomposition process in Cuskinny Lagoon revealed that greatest biomass loss occurred in the winter season. Lowest biomass loss occurred in spring, possibly due to the high density of invertebrates feeding on the thick microbial layer rather than the decomposing litter. It has been reported that the decomposition of plant biomass is highest in the preferential distribution area of the plant species; however, no similar trend was observed in this study with the most active zones of decomposition varying spatially throughout the seasons. Macroinvertebrate analysis revealed low species diversity but high abundance, indicating the dominance of a small number of species. Invertebrate assemblages within the lagoon varied significantly from communities in the adjacent freshwater or marine environments. Although carried out in coastal lagoons on the southwest coast of Ireland, it is envisaged that the overall findings of this study have relevance throughout the entire island of Ireland and possibly to many North Atlantic coastal lagoon ecosystems elsewhere.

Migration and fishing in Indonesian coastal villages.

The coastal ecosystems in Southeast Asia are under increased pressure from local and global change. This paper examines human migration and the use of marine resources in coastal villages in the Minahasa district of North Sulawesi, Indonesia. Primary data were collected through interviews with village leaders, focus groups, and a sample survey of 600 fishing households. Migration is responsible for at least one quarter of the total growth during the past decade. All groups of fishermen report falling productivity of the nearshore fisheries. Econometric analysis is used to examine the weekly fish catch of the artisanal fishing sector. Migration status and socioeconomic variables seem to have no systematic effect, while fishing effort (labor, boat, and gear), the degree of specialization, and the remoteness of villages are found to be positively related to weekly fish catches.

The Effects of Geography, Environment and Phylogeny on Community Assembly and Gene Flow Dynamics

It is increasingly evident that evolutionary processes play a role in how ecological communities are assembled. However the extend to which evolution influences how plants respond to spatial and environmental gradients and interact with each other is less clear. In this dissertation I leverage evolutionary tools and thinking to understand how space and environment affect community composition and patterns of gene flow in a unique system of Atlantic rainforest and restinga (sandy coastal plains) habitats in Southeastern Brazil.

In chapter one I investigate how space and environment affect the population genetic structure and gene flow of Aechmea nudicaulis, a bromeliad species that co-occurs in forest and restinga habitats. I genotyped seven microsatellite loci and sequenced one chloroplast DNA region for individuals collected in 7 pairs of forest / restinga sites. Bayesian genetic clustering analyses show that populations of A. nudicaulis are geographically structured in northern and southern populations, a pattern consistent with broader scale phylogeographic dynamics of the Atlantic rainforest. On the other hand, explicit migration models based on the coalescent estimate that inter-habitat gene flow is less common than gene flow between populations in the same habitat type, despite their geographic discontinuity. I conclude that there is evidence for repeated colonization of the restingas from forest populations even though the steep environmental gradient between habitats is a stronger barrier to gene flow than geographic distance.

In chapter two I use data on 2800 individual plants finely mapped in a restinga plot and on first-year survival of 500 seedlings to understand the roles of phylogeny, functional traits and abiotic conditions in the spatial structuring of that community. I demonstrate that phylogeny is a poor predictor of functional traits in and that convergence in these traits is pervasive. In general, the community is not phylogenetically structured, with at best 14% of the plots deviating significantly from the null model. The functional traits SLA, leaf dry matter content (LDMC), and maximum height also showed no clear pattern of spatial structuring. On the other hand, leaf area is strongly overdispersed across all spatial scales. Although leaf area overdispersion would be generally taken as evidence of competition, I argue that interpretation is probably misleading. Finally, I show that seedling survival is dramatically increased when they grow shaded by an adult individual, suggesting that seedlings are being facilitated. Phylogenetic distance to their adult neighbor has no influence on rates of survival though. Taken together, these results indicate that phylogeny has very limited influence on the fine scale assembly of restinga communities.

Dramatic variability of the carbonate system at a temperate coastal ocean site (Beaufort, North Carolina, USA) is regulated by physical and biogeochemical processes on multiple timescales.

Increasing atmospheric carbon dioxide (CO2) from anthropogenic sources is acidifying marine environments resulting in potentially dramatic consequences for the physical, chemical and biological functioning of these ecosystems. If current trends continue, mean ocean pH is expected to decrease by ~0.2 units over the next ~50 years. Yet, there is also substantial temporal variability in pH and other carbon system parameters in the ocean resulting in regions that already experience change that exceeds long-term projected trends in pH. This points to short-term dynamics as an important layer of complexity on top of long-term trends. Thus, in order to predict future climate change impacts, there is a critical need to characterize the natural range and dynamics of the marine carbonate system and the mechanisms responsible for observed variability. Here, we present pH and dissolved inorganic carbon (DIC) at time intervals spanning 1 hour to >1 year from a dynamic, coastal, temperate marine system (Beaufort Inlet, Beaufort NC USA) to characterize the carbonate system at multiple time scales. Daily and seasonal variation of the carbonate system is largely driven by temperature, alkalinity and the balance between primary production and respiration, but high frequency change (hours to days) is further influenced by water mass movement (e.g. tides) and stochastic events (e.g. storms). Both annual (~0.3 units) and diurnal (~0.1 units) variability in coastal ocean acidity are similar in magnitude to 50 year projections of ocean acidity associated with increasing atmospheric CO2. The environmental variables driving these changes highlight the importance of characterizing the complete carbonate system rather than just pH. Short-term dynamics of ocean carbon parameters may already exert significant pressure on some coastal marine ecosystems with implications for ecology, biogeochemistry and evolution and this shorter term variability layers additive effects and complexity, including extreme values, on top of long-term trends in ocean acidification.

Paleoenvironmental reconstruction of the coastal Monte Léon and Santa Cruz formations (Early Miocene) at Rincón del Buque, Southern Patagonia: A revisited locality

© 2015 Elsevier Ltd.Sedimentological, ichnological and paleontological analyses of the Early Miocene uppermost Monte León Formation and the lower part of the Santa Cruz Formation were carried out in Rincón del Buque (RDB), a fossiliferous locality north of Río Coyle in Santa Cruz Province, Patagonia, Argentina. This locality is of special importance because it contains the basal contact between the Monte Léon (MLF) and the Santa Cruz (SCF) formations and because it preserves a rich fossil assemblage of marine invertebrates and marine trace fossils, and terrestrial vertebrates and plants, which has not been extensively studied. A ~90m-thick section of the MLF and the SCF that crops out at RDB was selected for this study. Eleven facies associations (FA) are described, which are, from base to top: subtidal-intertidal deposits with Crassotrea orbignyi and bioturbation of the Skolithos-Cruziana ichnofacies (FA1); tidal creek deposits with terrestrial fossil mammals and Ophiomorpha isp. burrows (FA2); tidal flat deposits with Glossifungites ichnofacies (FA3); deposits of tidal channels (FA4) and tidal sand flats (FA5) both with and impoverish Skolithos ichnofacies associated; marsh deposits (FA6); tidal point bar deposits recording a depauperate mixture of both the Skolithos and Cruziana ichnofacies (FA7); fluvial channel deposits (FA8); fluvial point bar deposits (FA9); floodplain deposits (FA10); and pyroclastic and volcaniclastic deposits of the floodplain where terrestrial fossil mammal remains occur (FA11).The transition of the MLF-SCF at RDB reflects a changing depositional environment from the outer part of an estuary (FA1) through the central (FA2-6) to inner part of a tide-dominated estuary (FA7). Finally a fluvial system occurs with single channels of relatively low energy and low sinuosity enclosed by a broad, low-energy floodplain dominated by partially edaphized ash-fall, sheet-flood, and overbank deposits (FA8-11). Pyroclastic and volcaniclastic materials throughout the succession must have been deposited as ash-fall distal facies in a fluvial setting and also were carried by fluvial streams and redeposited in both estuarine and fluvial settings. These materials preserve most of the analyzed terrestrial fossil mammals that characterize the Santacrucian age of the RDB's succession. Episodic sedimentation under volcanic influence, high sedimentation rates and a relatively warm and seasonal climate are inferred for the MLF and SCF section.Lateral continuity of the marker horizons at RDB serve for correlation with other coastal localities such as the lower part of the coastal SCF south of Río Coyle (~17.6-17.4Ma) belonging to the Estancia La Costa Member of the SCF.

Facilitation shifts paradigms and can amplify coastal Restoration efforts

Restoration has been elevated as an important strategy to reverse the decline of coastal wetlands worldwide. Current practice in restoration science emphasizes minimizing competition between outplanted propagules to maximize planting success. This paradigm persists despite the fact that foundational theory in ecology demonstrates that positive species interactions are key to organism success under high physical stress, such as recolonization of bare substrate. As evidence of how entrenched this restoration paradigm is, our survey of 25 restoration organizations in 14 states in the United States revealed that >95% of these agencies assume minimizing negative interactions (i.e., competition) between outplants will maximize propagule growth. Restoration experiments in both Western and Eastern Atlantic salt marshes demonstrate, however, that a simple change in planting configuration (placing propagules next to, rather than at a distance from, each other) results in harnessing facilitation and increased yields by 107% on average. Thus, small adjustments in restoration design may catalyze untapped positive species interactions, resulting in significantly higher restoration success with no added cost. As positive interactions between organisms commonly occur in coastal ecosystems (especially in more physically stressful areas like uncolonized substrate) and conservation resources are limited, transformation of the coastal restoration paradigm to incorporate facilitation theory may enhance conservation efforts, shoreline defense, and provisioning of ecosystem services such as fisheries production.

Drug Delivery through the Blood-Brain Barrier through Use of Vascular Cell Adhesion Molecule 1- Targeted Nanoparticles

The blood brain barrier (BBB) is a semi-permeable membrane separating the brain from the bloodstream, preventing many drugs that treat neurological diseases, such as Alzheimer’s and Parkinson’s, from reaching the brain. Our project aimed to create a novel drug delivery system targeting the brain during neural inflammation. We developed a cationic solid lipid nanoparticle (CSLN) complex composed of cationic nanoparticles, biotin, streptavidin, and anti-vascular cell adhesion molecule-1 (anti- VCAM-1) antibodies. The anti-VCAM-1 antibody is used to target VCAM-1, a cell adhesion protein found on the BBB endothelium. VCAM-1 expression is elevated in the presence of inflammatory molecules, such as tumor necrosis factor-alpha (TNF- α). Through the use of a simple BBB model, results showed that our novel drug delivery system experienced some level of success in targeting the brain inflammation due to increasing TNF-α concentrations. This is promising for drug delivery research and provides support for VCAM-1 targeting using more robust and complex BBB models.

A volume of fluid numerical model for wave impacts at coastal structures

The first stages in the development of a new design tool, to be used by coastal engineers to improve the efficiency, analysis, design, management and operation of a wide range of coastal and harbour structures, are described. The tool is based on a two-dimensional numerical model, NEWMOTICS-2D, using the volume of fluid (VOF) method, which permits the rapid calculation of wave hydrodynamics at impermeable natural and man-made structures. The critical hydrodynamic flow processes and forces are identified together with the equations that describe these key processes. The different possible numerical approaches for the solution of these equations, and the types of numerical models currently available, are examined and assessed. Preliminary tests of the model, using comparisons with results from a series of hydraulic model test cases, are described. The results of these tests demonstrate that the VOF approach is particularly appropriate for the simulation of the dynamics of waves at coastal structures because of its flexibility in representing the complex free surfaces encountered during wave impact and breaking. The further programme of work, required to develop the existing model into a tool for use in routine engineering design, is outlined.

Birth-death processes with an instantaneous reflection barrier

A new structure with the special property that an instantaneous reflection barrier is imposed on the ordinary birth-death processes is considered. An easy-checking criterion for the existence of such Markov processes is first obtained. The uniqueness criterion is then established. In the nonunique case, all the honest processes are explicitly constructed. Ergodicity properties for these processes are investigated. It is proved that honest processes are always ergodic without necessarily imposing any extra conditions. Equilibrium distributions for all these ergodic processes are established. Several examples are provided to illustrate our results.

Guide to the coastal and surface zooplankton of the south-western Indian Ocean. Occasional Publication of the Marine Biological Association 15

A guide compiled as an aid to researchers in the identification of the coastal and shallow water, south-western Indian Ocean pelagic zooplankton, as much of the identification literature covering this area of amazing biodiversity is currently spread through the scientific literature and not accessible without extensive library resources. Most zooplankton groups, except fish larvae and eggs, have been covered, but some specialist groups have not yet been dealt with in great detail. However, a selection of representative members of most groups have been given, so that organisms can at least be assigned to perhaps a particular genus within the main group. The species list is based on zooplankton sampling carried out round the coastal areas of the islands of Mahé and Aldabra (Seychelles), Rodrigues (Mauritius), Madagascar and from a sampling transect between Seychelles and Rodrigues. The guide therefore includes a high proportion of the island-coastal and surface water zooplankton of the whole Indian Ocean. The location where a particular species has been sampled has been noted and some species that have not been sampled, but are known to occur in the region, have been included. Comprehensive taxonomic information has not been presented, but sufficient information should be given to identify each species. Keys have not yet been included for genera, as further species will be added. A bibliography of relevant plankton references has also been included.