Pelagic deep-sea metazoan biodiversity and ecology revealed by environmental DNA analysis in combination with other censuses

The deep sea (> 200 m) not only represents the largest habitat on earth, but also has the highest faunal biomasses and greatest number of individual organisms. While the deep sea provides humans with substantial services, its ecosystems remain poorly studied. Logistical and technical challenges to sample deep-sea ecosystems as well as organisms’ avoidance behavior to underwater gear stress the need for alternative techniques. In this thesis, I focused on a relatively novel tool in deep-sea biology; environmental DNA (eDNA) analysis. Environmental DNA is genetic material that organisms shed into their environment. This eDNA can be assigned to a specific taxon and provides information on species presence, diversity and distribution without the need to encounter or capture the source animal. The first objective of this thesis was to develop a pipeline to collect diversity and distribution data on deep-sea cephalopods with eDNA analysis from water and sediment samples. The second objective was to establish biodiversity baselines and distribution patterns of key organisms in the deep sea and to put these patterns into an ecological context. The third objective of this thesis was to identify cephalopod and fish taxa that potentially contribute to the vertical transport of carbon. This thesis showed that eDNA can be used successfully in the assessment and monitoring of deep-sea pelagic metazoans in hotspots of diversity and climate change. Especially when eDNA analysis is analyzed in different kinds of samples and used in combination with other techniques, it can help to answer ecological questions and ultimately contribute to aid in conservation of deep-sea habitats

Generation and Characterisation of Novel Monoclonal Antibodies towards Ovarian Tumour Stem Cells

Tumour stem cells (TSCs) are hypothesised to be a rare population of tumour cells which possess stem cell-like properties and are resistant to conventional therapy. Although cell surface markers have been widely used to characterise TSCs, previous literature suggests that no specific marker has been found for ovarian TSCs. We aimed to identify and characterise novel antibodies specific to ovarian epithelial TSCs, particularly towards populations with Hoechst efflux (Side Population, SP) and aldehyde dehydrogenase activity which are associated with a stem cell phenotype and drug resistance. Putative TSC subpopulations from ovarian tumour cell lines isolated by fluorescence activated cell sorting (FACS) using differential Hoechst dye uptake and Aldefluor activity assays displayed stem cell-like characteristics, including the upregulation of stem cell markers, increased anchorage-independent growth and increased invasive properties. A panel of monoclonal antibodies (mAbs) was then generated by injecting Aldefluor-positive ovarian tumour IGROV1 cells into female BALB/c mice. 34 antibodies were found to be specific to Aldefluor-positive cells and 2 of these enriched for SP cells. The 2 mAbs demonstrated cross-reactivity on human embryonic stem cells but no cross-reactivity to normal ovarian cell lines. Subpopulations of ovarian cell lines positive for the mAbs displayed stem cell-like characteristics, including upregulation of stem cell markers - CD133, ABCB1 and ALDH1A1. Sorted mAb populations were injected into non-obese diabetic/severe combined (NOD/SCID) mice and differential in vivo tumour formation was observed. Finally, the target antigen which both mAbs recognised was identified by mass spectrometry to be clathrin heavy chain (CHC1). We conclude that rare subpopulations with tumour-sustaining capability and stem cell-like characteristics can be identified in ovarian cancer using the 2 novel antibodies generated. Both mAbs target CHC1 on tumour-sustaining populations which are enriched for multiple stem cell markers and are therefore potential novel diagnostic markers and/or therapeutic agents

Computational Methods for the Analysis of Genomic Data and Biological Processes

In recent decades, new technologies have made remarkable progress in helping to understand biological systems. Rapid advances in genomic profiling techniques such as microarrays or high-performance sequencing have brought new opportunities and challenges in the fields of computational biology and bioinformatics. Such genetic sequencing techniques allow large amounts of data to be produced, whose analysis and cross-integration could provide a complete view of organisms. As a result, it is necessary to develop new techniques and algorithms that carry out an analysis of these data with reliability and efficiency. This Special Issue collected the latest advances in the field of computational methods for the analysis of gene expression data, and, in particular, the modeling of biological processes. Here we present eleven works selected to be published in this Special Issue due to their interest, quality, and originality

Generation and Characterisation of Novel Monoclonal Antibodies towards Ovarian Tumour Stem Cells

Tumour stem cells (TSCs) are hypothesised to be a rare population of tumour cells which possess stem cell-like properties and are resistant to conventional therapy. Although cell surface markers have been widely used to characterise TSCs, previous literature suggests that no specific marker has been found for ovarian TSCs. We aimed to identify and characterise novel antibodies specific to ovarian epithelial TSCs, particularly towards populations with Hoechst efflux (Side Population, SP) and aldehyde dehydrogenase activity which are associated with a stem cell phenotype and drug resistance. Putative TSC subpopulations from ovarian tumour cell lines isolated by fluorescence activated cell sorting (FACS) using differential Hoechst dye uptake and Aldefluor activity assays displayed stem cell-like characteristics, including the upregulation of stem cell markers, increased anchorage-independent growth and increased invasive properties. A panel of monoclonal antibodies (mAbs) was then generated by injecting Aldefluor-positive ovarian tumour IGROV1 cells into female BALB/c mice. 34 antibodies were found to be specific to Aldefluor-positive cells and 2 of these enriched for SP cells. The 2 mAbs demonstrated cross-reactivity on human embryonic stem cells but no cross-reactivity to normal ovarian cell lines. Subpopulations of ovarian cell lines positive for the mAbs displayed stem cell-like characteristics, including upregulation of stem cell markers - CD133, ABCB1 and ALDH1A1. Sorted mAb populations were injected into non-obese diabetic/severe combined (NOD/SCID) mice and differential in vivo tumour formation was observed. Finally, the target antigen which both mAbs recognised was identified by mass spectrometry to be clathrin heavy chain (CHC1). We conclude that rare subpopulations with tumour-sustaining capability and stem cell-like characteristics can be identified in ovarian cancer using the 2 novel antibodies generated. Both mAbs target CHC1 on tumour-sustaining populations which are enriched for multiple stem cell markers and are therefore potential novel diagnostic markers and/or therapeutic agents

Handbook of Marine Model Organisms in Experimental Biology

"The importance of molecular approaches for comparative biology and the rapid development of new molecular tools is unprecedented. The extraordinary molecular progress belies the need for understanding the development and basic biology of whole organisms. Vigorous international efforts to train the next-generation of experimental biologists must combine both levels – next generation molecular approaches and traditional organismal biology. This book provides cutting-edge chapters regarding the growing list of marine model organisms. Access to and practical advice on these model organisms have become aconditio sine qua non for a modern education of advanced undergraduate students, graduate students and postdocs working on marine model systems. Model organisms are not only tools they are also bridges between fields – from behavior, development and physiology to functional genomics. Key Features Offers deep insights into cutting-edge model system science Provides in-depth overviews of all prominent marine model organisms Illustrates challenging experimental approaches to model system research Serves as a reference book also for next-generation functional genomics applications Fills an urgent need for students Related Titles Jarret, R. L. & K. McCluskey, eds. The Biological Resources of Model Organisms (ISBN 978-1-1382-9461-5) Kim, S.-K. Healthcare Using Marine Organisms (ISBN 978-1-1382-9538-4) Mudher, A. & T. Newman, eds. Drosophila: A Toolbox for the Study of Neurodegenerative Disease (ISBN 978-0-4154-1185-1) Green, S. L. The Laboratory Xenopus sp. (ISBN 978-1-4200-9109-0)

The First Global Integrated Marine Assessment: World Ocean Assessment I

We used satellite-derived sea-surface-temperature (SST) data along with in-situ data collected along a meridional transect between 18.85 and 20.25°N along 69.2°E to describe the evolution of an SST filament and front during 25 November to 1 December in the northeastern Arabian Sea (NEAS). Both features were ∼ 100 km long, lasted about a week and were associated with weak temperature gradients (∼ 0.07°C km⁻¹). The in-situ data were collected first using a suite of surface sensors during a north–south mapping of this transect and showed the existence of a chlorophyll maximum within the filament. This surface data acquisition was followed by a high-resolution south–north CTD (conductivity–temperature–depth) sampling along the transect. In the two days that elapsed between the two in-situ measurements, the filament had shrunk in size and moved northward. In general, the current direction was northwestward and advected these mesoscale features. The CTD data also showed an SST front towards the northern end of the transect. In both these features, the chlorophyll concentration was higher than in the surrounding waters. The temperature and salinity data from the CTD suggest upward mixing or pumping of water from the base of the mixed layer, where a chlorophyll maximum was present, into the mixed layer that was about 60 m thick. A striking diurnal cycle was evident in the chlorophyll concentration, with higher values tending to occur closer to the surface during the night. The in-situ data from both surface sensors and CTD, and so also satellite-derived chlorophyll data, showed higher chlorophyll concentration, particularly at sub-surface levels, between the filament and the front, but there was no corresponding signature in the temperature and salinity data. Analysis of the SST fronts in the satellite data shows that fronts weaker than those associated with the filament and the front had crossed the transect in this region a day or two preceding the sampling of the front