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.

Molecular composition of biogenic secondary organic aerosols using ultrahigh resolution mass spectrometry: comparing laboratory and field studies

Numerous laboratory experiments have been performed in an attempt to mimic atmospheric secondary organic aerosol (SOA) formation. However, it is still unclear how close the aerosol particles generated in laboratory experiments resemble atmospheric SOA with respect to their detailed chemical composition. In this study, we generated SOA in a simulation chamber from the ozonolysis of α-pinene and a biogenic volatile organic compound (BVOC) mixture containing α- and β-pinene, Δ3-carene, and isoprene. The detailed molecular composition of laboratory-generated SOA was compared with that of background ambient aerosol collected at a boreal forest site (Hyytiälä, Finland) and an urban location (Cork, Ireland) using direct infusion nanoelectrospray ultrahigh resolution mass spectrometry. Kendrick Mass Defect and Van Krevelen approaches were used to identify and compare compound classes and distributions of the detected species. The laboratory-generated SOA contained a distinguishable group of dimers that was not observed in the ambient samples. The presence of dimers was found to be less pronounced in the SOA from the VOC mixtures when compared to the one component precursor system. The elemental composition of the compounds identified in the monomeric region from the ozonolysis of both α-pinene and VOC mixtures represented the ambient organic composition of particles collected at the boreal forest site reasonably well, with about 70% of common molecular formulae. In contrast, large differences were found between the laboratory-generated BVOC samples and the ambient urban sample. To our knowledge this is the first direct comparison of molecular composition of laboratory-generated SOA from BVOC mixtures and ambient samples.

Human intestinal microbiota and metabolites they produce in relation to host health

The aim of this thesis was to identify selected potential probiotic characteristics of Bifidobacterium longum strains isolated from human sources, and to examine these characteristics in detail using genomic and phenotypic techniques. One strain in particular Bifidobacterium longum DPC 6315 was the main focus of the thesis and this strain was used in both the manufacture of yoghurt and an animal study. In total, 38 B. longum strains, obtained from infants and adults, were assessed in vitro for the selected probiotic traits using a combined phenotypic and molecular approach. Differentiation of the 38 strains using amplified ribosomal DNA restriction analysis (ARDRA) into subspecies indicated that of the 38 bifidobacterial strains tested, 34 were designated B. longum subsp. longum and four B. longum subsp. infantis.

Citizenship education in Irish secondary schools: the influence of curriculum content, school culture and stakeholder perspectives

This research interrogates the status of citizenship education in Irish secondary schools. The following questions are examined: How does school culture impact on citizenship education? What value is accorded to the subjects, Civic, Social and Political Education (CSPE) and Social, Personal and Health Education (SPHE)? To what extent are the subjects of both the cognitive and non-cognitive curricula affirmed? The importance of these factors in supporting the social, ethical, personal, political and emotional development of students is explored. The concept of citizenship is dynamic and constantly evolving in response to societal change. Society is increasingly concerned with issues such as: globalisation; cosmopolitanism; the threat of global risk; environment sustainability; socio-economic inequality; and recognition/misrecognition of new identities and group rights. The pedagogical philosophy of Paulo Freire which seeks to educate for the conscientisation and humanisation of the student is central to this research. Using a mixed methods approach, data on the insights of students, parents, teachers and school Principals was collected. In relation to Irish secondary school education, the study reached three main conclusions. (1) The educational stakeholders rate the subjects of the non-cognitive curriculum poorly. (2) The subjects Civic, Social and Political education (CSPE), and Social, Personal and Health Education (SPHE) command a low status in the secondary school setting. (3) The day-to-day school climate is influenced by an educational philosophy that is instrumentalist in character. Elements of school culture such as: the ethic of care; the informal curriculum; education for life after school; and affirmation of teachers, are not sufficiently prioritised in supporting education for citizenship. The research concludes that the approach to education for citizenship needs to be more robust within the overall curriculum, and culture and ethos of the Irish education system.

Platinum(II)-catalyzed intermolecular hydroamination of monosubstituted allenes with secondary alkylamines.

A 1:1 mixture of (dppf)PtCl(2) and AgOTf (5 mol%) catalyzed the intermolecular hydroamination of monosubstituted allenes with secondary alkylamines at 80 degrees C to form allylic amines in good yield with selective formation of the E-diastereomer.

Acute eosinophilic pneumonia secondary to daptomycin: a report of three cases.

We describe 3 cases of daptomycin-induced pulmonary toxic effects that are consistent with drug-induced acute eosinophilic pneumonia. Patients presented similarly with dyspnea, cough, hypoxia, and diffuse ground-glass opacities at chest computed tomography. Clinical suspicion for this adverse drug event and cessation of daptomycin until definitive diagnosis can be made is crucial.

Using sediment flocculation to reduce the impacts of Chesapeake Bay Microcystis aeruginosa harmful algal blooms

Gemstone Team BREATHE (Bay Revitalization Efforts Against the Hypoxic Environment)

Biomarkers of PTA

© Springer Science+Business Media New York 2015.Prognostic biomarkers may indicate the likelihood of disease development and speed of progression or may serve as predictive indicators of responsiveness to treatment. Joint injuries, particularly severe injuries, may result in post-traumatic osteoarthritis (PTOA), and pre- and post-injury prognostic biomarkers are needed to enhance primary and secondary prevention approaches for PTOA. Several macromolecules from joint structures found in serum, urine, and synovial fluid are promising biochemical markers for monitoring joint metabolism and health before and after joint injury. The use of metabolic profiling (analysis of small molecules) as a predictive tool for osteoarthritis (OA) has increased in the past decade. Although there is some question as to whether PTOA and idiopathic OA are comparable conditions, there is some evidence to suggest that components of their pathogenesis are similar. Potentially, biomarkers important to the high-risk PTOA profile translate to idiopathic OA. Further work is needed to confirm the utility of macromolecules and metabolites as biomarkers for PTOA, particularly focusing on those strongly correlated to clinical efficacy measures important to the patient (e.g., symptoms, physical function, and quality of life) and the causal pathway of PTOA.

Efecto de la inoculación algal suplementada con fertilización química, sobre propiedades del suelo

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Basic components in the scienctific didactical training of the secondary school mathematics teachers

Secondary mathematics teacher training in Spain is currently the subject of a heated revision debate. The speed of social, cultural, scientific and economic changes have left a hundred years old teacher training model well behind. However, academical inertia and professional interests are impeding a real new training of the mathematics teacher as an autonomous mathematical educator. Teachers of Didactic of Mathematics and the Spanish Associations of mathematics teachers have recently been discussing the issue. Their conclusions are included here.

Grammar acquisition and processing instruction: Secondary and cumulative effects

Research on Processing Instruction has so far investigated the primary effects of Processing Instruction. In this book, the results of a series of experimental studies investigating possible secondary and cumulative effects of Processing Instruction on the acquisition of French, Italian and English as a second language will be presented. The results of the three experiments have demonstrated that Processing Instruction not only provides learners the direct or primary benefit of learning to process and produce the morphological form on which they received instruction, but also a secondary benefit in that they transferred that training to processing and producing another morphological form on which they had received no instruction.