Field-based measurement of hydrodynamics associated with engineered in-channel structures: the example of fish pass assessment

The construction of fish passes has been a longstanding measure to improve river ecosystem status by ensuring the passability of weirs, dams and other in- channel structures for migratory fish. Many fish passes have a low biological effectiveness because of unsuitable hydrodynamic conditions hindering fish to rapidly detect the pass entrance. There has been a need for techniques to quantify the hydrodynamics surrounding fish pass entrances in order to identify those passes that require enhancement and to improve the design of new passes. This PhD thesis presents the development of a methodology for the rapid, spatially continuous quantification of near-pass hydrodynamics in the field. The methodology involves moving-vessel Acoustic Doppler Current Profiler (ADCP) measurements in order to quantify the 3-dimensional water velocity distribution around fish pass entrances. The approach presented in this thesis is novel because it integrates a set of techniques to make ADCP data robust against errors associated with the environmental conditions near engineered in-channel structures. These techniques provide solutions to (i) ADCP compass errors from magnetic interference, (ii) bias in water velocity data caused by spatial flow heterogeneity, (iii) the accurate ADCP positioning in locales with constrained line of sight to navigation satellites, and (iv) the accurate and cost-effective sensor deployment following pre-defined sampling strategies. The effectiveness and transferability of the methodology were evaluated at three fish pass sites covering conditions of low, medium and high discharge. The methodology outputs enabled a detailed quantitative characterisation of the fish pass attraction flow and its interaction with other hydrodynamic features. The outputs are suitable to formulate novel indicators of hydrodynamic fish pass attractiveness and they revealed the need to refine traditional fish pass design guidelines

Automated identification of river hydromorphological features using UAV high resolution aerial imagery

European legislation is driving the development of methods for river ecosystem protection in light of concerns over water quality and ecology. Key to their success is the accurate and rapid characterisation of physical features (i.e., hydromorphology) along the river. Image pattern recognition techniques have been successfully used for this purpose. The reliability of the methodology depends on both the quality of the aerial imagery and the pattern recognition technique used. Recent studies have proved the potential of Unmanned Aerial Vehicles (UAVs) to increase the quality of the imagery by capturing high resolution photography. Similarly, Artificial Neural Networks (ANN) have been shown to be a high precision tool for automated recognition of environmental patterns. This paper presents a UAV based framework for the identification of hydromorphological features from high resolution RGB aerial imagery using a novel classification technique based on ANNs. The framework is developed for a 1.4 km river reach along the river Dee in Wales, United Kingdom. For this purpose, a Falcon 8 octocopter was used to gather 2.5 cm resolution imagery. The results show that the accuracy of the framework is above 81%, performing particularly well at recognising vegetation. These results leverage the use of UAVs for environmental policy implementation and demonstrate the potential of ANNs and RGB imagery for high precision river monitoring and river management

Reticulons 3 and 6 interact with viral movement proteins

Funding; This research was funded by the Science and Technology Facilities Council Programme (grant no. 14230008), a British Biotechnology and Biological Sciences Research Council (grant no. BB/J004987/1 to Professor Chris Hawes), and a Vice-Chancellors Research Fellowship to V.K. Parts of this work were funded by the U.K. Biotechnology and Biomedical Sciences Research Council (BBSRC) grant BB/M007200/1 to J.T. Work in J.T.'s laboratory is supported by the Scottish Government's Rural and Environment Science and Analytical Services Division (RESAS).Plant reticulon (RTN) proteins are capable of constricting membranes and are vital for creating and maintaining tubules in the endoplasmic reticulum (ER), making them prime candidates for the formation of the desmotubule in plasmodesmata (PD). RTN3 and RTN6 have previously been detected in an Arabidopsis PD proteome and have been shown to be present in primary PD at cytokinesis. It has been suggested that RTN proteins form protein complexes with proteins in the PD plasma membrane and desmotubule to stabilize the desmotubule constriction and regulate PD aperture. Viral movement proteins (vMPs) enable the transport of viruses through PD and can be ER-integral membrane proteins or interact with the ER. Some vMPs can themselves constrict ER membranes or localize to RTN-containing tubules; RTN proteins and vMPs could be functionally linked or potentially interact. Here we show that different vMPs are capable of interacting with RTN3 and RTN6 in a membrane yeast two-hybrid assay, coimmunoprecipitation, and Förster resonance energy transfer measured by donor excited-state fluorescence lifetime imaging microscopy. Furthermore, coexpression of the vMP CMV-3a and RTN3 results in either the vMP or the RTN changing subcellular localization and reduces the ability of CMV-3a to open PD, further indicating interactions between the two proteins.Publisher PDFPeer reviewe

Defining the dance: Quantification and classification of ER dynamics

The availability of quantification methods for sub-cellular organelle dynamic analysis has increased rapidly over the last 20 years. The application of these techniques to contiguous sub-cellular structures that exhibit dynamic re-modelling over a range of scales and orientations is challenging as quantification of ‘movement’ rarely corresponds to traditional, qualitative classifications of types of organelle movement. The plant endoplasmic reticulum represents a particular challenge for dynamic quantification as it itself is an entirely contiguous organelle that is in a constant state of flux and gross remodelling, controlled by the actinomyosin cytoskeleton

The plant endoplasmic reticulum: An organized chaos of tubules and sheets with multiple functions

The endoplasmic reticulum (ER) is a fascinating organelle at the core of the secretory pathway. It is responsible for the synthesis of one third of the cellular proteome and, in plant cells, it produces receptors and transporters of hormones as well as the proteins responsible for the biosynthesis of critical components of a cellulosic cell wall. The ER structure resembles a spider-web network of interconnected tubules and cisternae that pervades the cell. The study of the dynamics and interaction of this organelles with other cellular structures such as the plasma membrane, the Golgi apparatus and the cytoskeleton, have been permitted by the implementation of fluorescent protein and advanced confocal imaging. In this review, we report on the findings that contributed toward the understanding of the ER morphology and function with the aid of fluorescent proteins, focusing on the contributions provided by pioneering work from the lab of the late Professor Chris Hawes

Labeling the ER for Light and Fluorescence Microscopy

The ER is a highly dynamic network of tubules and membrane sheets. Hence imaging this organelle in its native and mobile state is of great importance. Here we describe methods of labeling the native ER using fluorescent proteins and lipid dyes as well as methods for immunolabeling on plant tissue

Analyse der Knochendeformation und Muskelkräfte der menschlichen Tibia

Für die Erforschung des Weltraums durch den Menschen, aber auch für die Gesundheit auf der Erde allgemein, ist ein grundlegendes Verständnis über die Adaption des Knochens essentiell. Die Regulierung des Auf- und Abbaus des Knochens wird über seine Deformation gesteuert, welche wiederum aus der mechanischen Belastung dessen resultiert. Diese Zusammenhänge zu verstehen, die Auswirkungen von verschiedenen Aktivitäten auf die Deformation des Knochens zu kennen und in Relation setzten zu können, ist der Schlüssel zu dem gesuchten, grundlegenden Verständnis. Im Zuge dieser Arbeit wurde hierfür eine Methode entwickelt, diese Zusammenhänge qualitativ und quantitativ herzuleiten. Basierend auf in vivo Messungen an der Tibia wurde ein Algorithmus zur in silico Analyse der vorliegenden Daten entwickelt. Dieser macht sich die Konsequenzen des Hookeschen Gesetzes in Form des Superpositionsprinzips zu Nutze, um quasi-invers aus der gemessenen Deformationsbewegung die dafür notwendigen Kräfte zu bestimmen. Diese können in einer Finite Elemente Analyse (FEA) mit den rekonstruierten Tibia-Knochen verwendet werden, um deren Spannungs-Dehnungs-Zustand zu bestimmen. Zur Validierung der Annahmen und Randbedingungen des Algorithmus wurde ein biomechanischer Messstand konstruiert. In diesem konnten in replica und ex vivo Untersuchungen durchgeführt werden. Zu diesem Zweck wurden Tibia-Replikate aus Komposite-Material bzw. Leichenbeine künstlich über Aktuatoren mit Kräften beaufschlagt und über eine spezielle Anwendung von Motion Capturing die Deformationsbewegung des Knochens gemessen. Die Auswertung der in vivo Daten mittels der in silico Analyse lieferte quantitative Ergebnisse zur Dehnung in der Tibia für diverse alltägliche Aktivitäten. Diese Ergebnisse sind, im Gegensatz zur bisherigen gängigen Methode, jedoch nicht auf einen singulären Messpunkt limitiert, sondern decken den kompletten rekonstruierten Bereich der Tibia ab. Dies führte zur Feststellung, dass die aktuell angenommenen Werte zu niedrig angesetzt sind. Hinzu kommt, dass die Analyse eine zeitliche und örtliche Varianz der Peak-Dehnungen im Knochen über den Ablauf einer Aktivität aufzeigt. Diese Ergebnisse verändern das bisherige Verständnis über die Knochenadaption und deren Regulierungsmechanismen

Das Aufführungsformat Festival unter besonderer Berücksichtigung der Neuen Musik in Österreich

In der vorliegenden Arbeit wird das Phänomen Festival als wichtiges Aufführungsformat in der Musik, insbesondere unter Betrachtung des Genres der Neuen Musik, behandelt. Anhand wichtiger Beispiele aus dem deutschsprachigen Raum wird auf die Geschichte des Musikfestivals eingegangen sowie die Rolle der Neuen Musik im Festivalbetrieb diskutiert und bedeutende Institutionen und Merkmale beschrieben. Einen weiteren wichtigen Aspekt stellt der Aufführungskontext des (Musik-)Festivals dar, der durch einen geschichtlichen Abriss des Wandels des Konzertwesens veranschaulicht wird. Vor diesem Hintergrund wird zudem auf wichtige Elemente, wie etwa die Programmgestaltung und das Publikum sowie auch auf Kulturpolitik und Musikvermittlung näher eingegangen. Abschließend porträtiert ein umfassendes Resümee dreier ausgewählter Neue Musik-Festivals stellvertretend die österreichische Festivalsituation und stellt diese im Kontext der zuvor genannten Punkte dar. Schlussfolgernd lässt sich ein deutlicher Trend zum Veranstalten von Festivals erkennen, der auch Aspekte wie die zunehmende Eventisierung beinhaltet