Archaeological otoliths as environmental recorders: high resolution sampling of pacific cod (Gadus macrocephalus) otoliths from Kiska Island, Alaska

Archaeological fish otoliths have the potential to serve as proxies for both season of site occupation and palaeoclimate conditions. By sampling along the distinctive sub-annual seasonal bands of the otolith and completing a stable isotope (δ¹⁸O, δ¹³C) analysis, variations within the fish’s environment can be identified. Through the analysis of cod otoliths from two archaeological sites on Kiska Island, Gertrude Cove (KIS-010) and Witchcraft Point (KIS-005), this research evaluates a micromilling methodological approach to extracting climatic data from archaeological cod otoliths. In addition, δ¹⁸Ootolith data and radiocarbon dates frame a discussion of Pacific cod harvesting, site occupation, and changing climatic conditions on Kiska Island. To aid in the interpretation of the archaeological Pacific cod results, archaeological and modern Atlantic cod otoliths were also analyzed as a component of this study to develop. The Atlantic cod otoliths provided the methodological and interpretative framework for the study, and also served to assess the efficacy of this sampling strategy for archaeological materials and to add time-depth to existing datasets. The δ¹⁸Ootolith values successfully illustrate relative variation in ambient water temperature. The Pacific cod δ¹⁸O values demonstrate a weak seasonal signal identifiable up to year 3, followed by relatively stable values until year 6/7 when values continuously increase. Based on the δ¹⁸O values, the Pacific cod were exposed to the coldest water temperatures immediately prior to capture. The lack of a clear cycle of seasonal variation and the continued increase in values towards the otolith edge obscures the season of capture, and indicates that other behavioural, environmental, or methodological factors influenced the otolith δ¹⁸O values. It is suggested that Pacific cod would have been harvested throughout the year, and the presence of cod remains in Aleutian archaeological sites cannot be used as a reliable indicator of summer occupation. In addition, when the δ¹⁸O otolith values are integrated with radiocarbon dates and known climatic regimes, it is demonstrated that climatic conditions play an integral role in the pattern of occupation at Gertrude Cove. Initial site occupation coincides with the end of a neoglacial cooling period, and the most recent and continuous occupation coincides with the end of a localized warming period and the onset of the Little Ice Age (LIA).

High resolution study of narrow tailed radio galaxies in clusters

Clusters of galaxies are the most massive and large gravitationally bounded systems in the whole Universe. Their study is of fundamental importance to constrain cosmological parameters and to obtain informations regarding various kind of emission in different wavebands. In particular, in the radio domain, beside the diffuse emission, the study is focused on the radio galaxies emission. Radio galaxies in clusters can have peculiar morphology, since they interact with the intracluster medium (ICM) in which they are embedded. Particularly, in this thesis we focused our attention on the so-called Narrow-Angle Tailed radio galaxies (NAT), which present radio jets that are bent at extreme angle, up to 90 degrees, from their original orientation. Some NAT show a narrow extended structure and the two radio tails are not resolved even with high resolution radio observations. An example is provided by the source IC310, in the Perseus Cluster, whose structure has been recently interpreted as due to Doppler boosting effects of a relativistic jet oriented at a small angle with respect to the line of sight. If the structure is due to relativistic effects, this implies that the jets are relativistic at about 400 kpc from the core, but this is in contrast with unified models, which predict that for low-power radio source (NAT are classified as FRI radio galaxies) the jets decelerate to sub-relativistic speed within a few kpc from the core. To investigate this scientific topic, in this thesis we have analyzed the innermost structure of a sample of eleven radio galaxies showing a very narrow NAT structure. We can conclude that the structure of these radio galaxies is different from that of IC310. These radio galaxies are indeed strongly influenced by environmental effects and are similar to classical NAT sources.

Simultaneous high-resolution pH and spectrophotometric recordings of oxygen binding in native blood microvolumes, link to supplementary material

Oxygen equilibrium curves have been widely used to understand oxygen transport in numerous organisms. A major challenge has been to monitor oxygen binding characteristics and concomitant pH changes as they occur in vivo, in limited sample volumes. Here we report a technique allowing highly resolved and simultaneous monitoring of pH and blood pigment saturation in minute blood volumes. We equipped a gas diffusion chamber with a broad range fibre optic spectrophotometer and a micro-pH optode and recorded changes of pigment oxygenation along PO2 and pH gradients to test the setup. Oxygen binding parameters derived from measurements in only 15 µl of haemolymph from the cephalopod Octopus vulgaris showed low instrumental error (0.93%) and good agreement with published data. Broad range spectra, each resolving 2048 data points, provided detailed insight into the complex absorbance characteristics of diverse blood types. After consideration of photobleaching and intrinsic fluorescence, pH optodes yielded accurate recordings and resolved a sigmoidal shift of 0.03 pH units in response to changing PO2 from 0-21 kPa. Highly resolved continuous recordings along pH gradients conformed to stepwise measurements at low rates of pH changes. In this study we showed that a diffusion chamber upgraded with a broad range spectrophotometer and an optical pH sensor accurately characterizes oxygen binding with minimal sample consumption and manipulation. We conclude that the modified diffusion chamber is highly suitable for experimental biologists who demand high flexibility, detailed insight into oxygen binding as well as experimental and biological accuracy combined in a single set up.

High-resolution spatial-response measurements of optical nano-antennas in the visible

A few years ago, some of the authors of the paper demonstrated the resonance of optical antennas in the visible frequencies. The results of that paper were obtained using experimental techniques that were primarily developed for the measurement of antenna-coupled detectors in the infrared. In the present paper, we show the results of spatial-response mapping obtained by using a dedicated measurement station for the characterization of optical antennas in the visible. At the same time, the bottleneck in the spatial responsivity calculation represented by the beam characterization has been approached from a different perspective. The proposed technique uses a collection of knife edge measurements in order to avoid the use of any model of the laser beam irradiance. By taking all this into account we present the spatial responsivity of optical antennas measured with high spatial resolution in the visible.

Using high resolution tracer data to constrain water storage, flux and age estimates in a spatially distributed rainfall-runoff model

Acknowledgements The authors would like to thank Jonathan Dick, Josie Geris, Jason Lessels, and Claire Tunaley for data collection and Audrey Innes for lab sample preparation. We also thank Christian Birkel for discussions about the model structure and comments on an earlier draft of the paper. Climatic data were provided by Iain Malcolm and Marine Scotland Fisheries at the Freshwater Lab, Pitlochry. Additional precipitation data were provided by the UK Meteorological Office and the British Atmospheric Data Centre (BADC).We thank the European Research Council ERC (project GA 335910 VEWA) for funding the VeWa project.

Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish : Proof of concept for key components of the insulin-like growth factor axis

Acknowledgements This study was funded by a Natural Environment Research Council grant (NERC, project code: NBAF704). FML is funded by a NERC Doctoral Training Grant (Project Reference: NE/L50175X/1). RLS was an undergraduate student at the University of Aberdeen and benefitted from financial support from the School of Biological Sciences. DJM is indebted to Dr. Steven Weiss (University of Graz, Austria), Dr. Takashi Yada (National Research Institute of Fisheries Science, Japan), Dr. Robert Devlin (Fisheries and Oceans Canada, Canada), Prof. Samuel Martin (University of Aberdeen, UK), Mr. Neil Lincoln (Environment Agency, UK) and Prof. Colin Adams/Mr. Stuart Wilson (University of Glasgow, UK) for providing salmonid material or assisting with its sampling. We are grateful to staff at the Centre for Genomics Research (University of Liverpool, UK) (i.e. NERC Biomolecular Analysis Facility – Liverpool; NBAF-Liverpool) for performing sequence capture/Illumina sequencing and providing us with details on associated methods that were incorporated into the manuscript. Finally, we are grateful to the organizers of the Society of Experimental Biology Satellite meeting 'Genome-powered perspectives in integrative physiology and evolutionary biology' (held in Prague, July 2015) for inviting us to contribute to this special edition of Marine Genomics and hosting a really stimulating meeting.

High-Resolution In Situ Oxygen-Argon Studies of Surface Biological and Physical Processes in the Polar Oceans

The Arctic Ocean and Western Antarctic Peninsula (WAP) are the fastest warming regions on the planet and are undergoing rapid climate and ecosystem changes. Until we can fully resolve the coupling between biological and physical processes we cannot predict how warming will influence carbon cycling and ecosystem function and structure in these sensitive and climactically important regions. My dissertation centers on the use of high-resolution measurements of surface dissolved gases, primarily O2 and Ar, as tracers or physical and biological functioning that we measure underway using an optode and Equilibrator Inlet Mass Spectrometry (EIMS). Total O2 measurements are common throughout the historical and autonomous record but are influenced by biological (net metabolic balance) and physical (temperature, salinity, pressure changes, ice melt/freeze, mixing, bubbles and diffusive gas exchange) processes. We use Ar, an inert gas with similar solubility properties to O2, to devolve distinct records of biological (O2/Ar) and physical (Ar) oxygen. These high-resolution measurements that expose intersystem coupling and submesoscale variability were central to studies in the Arctic Ocean, WAP and open Southern Ocean that make up this dissertation.

Key findings of this work include the documentation of under ice and ice-edge blooms and basin scale net sea ice freeze/melt processes in the Arctic Ocean. In the WAP O2 and pCO2 are both biologically driven and net community production (NCP) variability is controlled by Fe and light availability tied to glacial and sea ice meltwater input. Further, we present a feasibility study that shows the ability to use modeled Ar to derive NCP from total O2 records. This approach has the potential to unlock critical carbon flux estimates from historical and autonomous O2 measurements in the global oceans.

The morphology of ordered block copolymer patterns as probed by high resolution imaging

The microphase separation of block copolymer (BCP) thin films can afford a simple and cost-effective means to studying nanopattern surfaces, and especially the fabrication of nanocircuitry. However, because of complex interface effects and other complications, their 3D morphology, which is often critical for application, can be more complex than first thought. Here, we describe how emerging microscopic methods may be used to study complex BCP patterns and reveal their rich detail. These methods include helium ion microscopy (HIM) and high resolution x-section transmission electron microscopy (XTEM), and complement conventional secondary electron and atomic force microscopies (SEM and TEM). These techniques reveal that these structures are quite different to what might be expected. We illustrate the advances in the understanding of BCP thin film morphology in several systems, which result from this characterization. The systems described include symmetric, lamellar forming polystyrene-b-polymethylmethacrylate (PS-b-PMMA), cylinder forming polystyrene-b-polydimethylsiloxane (PS-b-PDMS), as well as lamellar and cylinder forming patterns of polystyrene-b-polyethylene oxide (PS-b-PEO) and polystyrene-b-poly-4-vinylpyridine (PS-b-P4VP). Each of these systems exhibits more complex arrangements than might be first thought. Finding and developing techniques whereby complex morphologies, particularly at very small dimensions, can be determined is critical to the practical use of these materials in many applications. The importance of quantifying these complex morphologies has implications for their use in integrated circuit manufacture, where they are being explored as alternative pattern forming methods to conventional UV lithography.

Electron beam lithography assisted high-resolution pattern generation

This thesis details the top-down fabrication of nanostructures on Si and Ge substrates by electron beam lithography (EBL). Various polymeric resist materials were used to create nanopatterns by EBL and Chapter 1 discusses the development characteristics of these resists. Chapter 3 describes the processing parameters, resolution and topographical and structural changes of a new EBL resist known as ‘SML’. A comparison between SML and the standard resists PMMA and ZEP520A was undertaken to determine the suitability of SML as an EBL resist. It was established that SML is capable of high-resolution patterning and showed good pattern transfer capabilities. Germanium is a desirable material for use in microelectronic applications due to a number of superior qualities over silicon. EBL patterning of Ge with high-resolution hydrogen silsesquioxane (HSQ) resist is however difficult due to the presence of native surface oxides. Thus, to combat this problem a new technique for passivating Ge surfaces prior to EBL processes is detailed in Chapter 4. The surface passivation was carried out using simple acids like citric acid and acetic acid. The acids were gentle on the surface and enabled the formation of high-resolution arrays of Ge nanowires using HSQ resist. Chapter 5 details the directed self-assembly (DSA) of block copolymers (BCPs) on EBL patterned Si and, for the very first time, Ge surfaces. DSA of BCPs on template substrates is a promising technology for high volume and cost effective nanofabrication. The BCP employed for this study was poly (styrene-b-ethylene oxide) and the substrates were pre-defined by HSQ templates produced by EBL. The DSA technique resulted into pattern rectification (ordering in BCP) and in pattern multiplication within smaller areas.

Molecular composition of organic aerosols in central Amazonia: an ultra-high-resolution mass spectrometry study

The Amazon Basin plays key role in atmospheric chemistry, biodiversity and climate change. In this study we applied nanoelectrospray (nanoESI) ultra-high-resolution mass spectrometry (UHRMS) for the analysis of the organic fraction of PM2.5 aerosol samples collected during dry and wet seasons at a site in central Amazonia receiving background air masses, biomass burning and urban pollution. Comprehensive mass spectral data evaluation methods (e.g. Kendrick mass defect, Van Krevelen diagrams, carbon oxidation state and aromaticity equivalent) were used to identify compound classes and mass distributions of the detected species. Nitrogen- and/or sulfur-containing organic species contributed up to 60 % of the total identified number of formulae. A large number of molecular formulae in organic aerosol (OA) were attributed to later-generation nitrogen- and sulfur-containing oxidation products, suggesting that OA composition is affected by biomass burning and other, potentially anthropogenic, sources. Isoprene-derived organosulfate (IEPOX-OS) was found to be the most dominant ion in most of the analysed samples and strongly followed the concentration trends of the gas-phase anthropogenic tracers confirming its mixed anthropogenic–biogenic origin. The presence of oxidised aromatic and nitro-aromatic compounds in the samples suggested a strong influence from biomass burning especially during the dry period. Aerosol samples from the dry period and under enhanced biomass burning conditions contained a large number of molecules with high carbon oxidation state and an increased number of aromatic compounds compared to that from the wet period. The results of this work demonstrate that the studied site is influenced not only by biogenic emissions from the forest but also by biomass burning and potentially other anthropogenic emissions from the neighbouring urban environments.

Elemental Analysis of Biological Matrices by Laser Ablation High Resolution Inductively Coupled Plasma Mass Spectrometry (LA-HR-ICP-MS) and High Resolution Inductively Coupled Plasma Mass Spectrometry (HR-ICP-MS)

The need for elemental analysis of biological matrices such as bone, teeth, and plant matter for sourcing purposes has emerged within the forensic and geochemical laboratories. Trace elemental analyses for the comparison of aterials such as glass by inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS has been shown to offer a high degree of discrimination between different manufacturing sources. Unit resolution ICP-MS instruments may suffer from some polyatomic interferences including 40Ar16O+, 40Ar16O1H+, and 40Ca16O+ that affect iron measurement at trace levels. Iron is an important element in the analysis of glass and also of interest for the analysis of several biological matrices. A comparison of the nalytical performance of two different ICP-MS systems for iron analysis in glass for determining the method detection limits (MDLs), accuracy, and precision of the measurement is presented. Acid digestion and laser ablation methods are also compared. Iron polyatomic interferences were reduced or resolved by using dynamic reaction cell and high resolution ICP-MS. MDLs as low as 0.03 ìg g-1 and 0.14 ìg g-1 for laser ablation and solution based analyses respectively were achieved. The use of helium as a carrier gas demonstrated improvement in the detection limits of both iron isotopes (56Fe and 57Fe) in medium resolution for the HR-ICP-MS and with a dynamic reaction cell (DRC) coupled to a quadrupole ICP-MS system. The development and application of robust analytical methods for the quantification of trace elements in biological matrices has lead to a better understanding of the potential utility of these measurements in forensic chemical analyses. Standard reference materials (SRMs) were used in the development of an analytical method using HR-ICP-MS and LA-HR-ICP-MS that was subsequently applied on the analysis of real samples. Bone, teeth and ashed marijuana samples were analyzed with the developed method. Elemental analysis of bone samples from 12 different individuals provided discrimination between individuals, when femur and humerus bones were considered separately. Discrimination of 14 teeth samples based on elemental composition was achieved with the exception of one case where samples from the same individual were not associated with each other. The discrimination of 49 different ashed plant (cannabis)samples was achieved using the developed method.