Experimental Investigation Of Thermal Maturation Processes Of Bakken Formation And Their Impact On Organic Matter And Mechanical Properties

Early development of the Bakken Petroleum System recognized the significance of source rock maturation and the onset of oil generation in determining the geographic limits of production. This research project aims to confirm the role of thermal maturation as the dominant mechanism in controlling the oil generation of the Bakken Shale. Additionally, the purpose ofthis research is to test the influence of thermal maturation on the geochemical and mechanical properties of the Bakken Shale. To conduct these investigations, samples from 2-BRENDEN 9-33 1-M, a well in the North Dakota part of the Williston Basin that has experienced the least thermal stress were heated at 340 ℃ for 3, 6, 12, 24, and 48 hours to induce maturity. Bitumen was removed from the experimental samples using the Dean-Stark method. Source rock analysis was used to test the level of maturation and document the changes in the geochemical properties of the untreated and extracted experimental samples. Nonisothermal kinetic experiments using an extended kinetic method were included to better evaluate the point that oil generation begins. To characterize the experimental samples, thin sections prepared from the experimental reaction products were examined under UV light visible fluorescence before and after extraction of bitumen. The changes in the mineralogical composition during maturation were studied through x-ray diffraction (XRD) analysis. Fluid reaction products were evaluated (hydrocarbon composition) using gas chromatography (GC). Scanning electron microscopy (SEM) was used to determine changes in the microstructure as a function of experimentally induced thermal maturation. Finally, the atomic force microscopy (AFM) technique was used to map the mechanical properties of the natural and experimentally matured samples at a nanometer resolution. Data shows that the point of oil generation can be estimated by locating the boundary between a linear, low-gradient maturation series (non-generating) and a nonlinear one (generating). The broadening of reactant temperatures under geologically reasonable subsidence rates further suggests that the reactivity of the Bakken changes throughout oil generation, necessitating the generation of new, immobile, reactive products during catagenesis. Fluorescence shows that amorphous organic matter (AOM) is lost and even more in extracted samples, and solid bitumen is gained because of AOM transformation. Tasmanites alginite is more resistant to transformation than AOM. XRD shows that increased heating time caused more dissolution of calcite than dolomite and textural changes. The results and analyses using the PFQNM approach show a decrease in mechanical properties with an increase in thermal maturation (increased heating time). These research findings show consistency with what is seen in nature and offer an additional metric that can be used to better define the point that marks the beginning of oil generation

Multispectral Imaging for Determination of Astaxanthin Concentration in Salmonids

Multispectral imaging has been evaluated for characterization of the concentration of a specific cartenoid pigment; astaxanthin. 59 fillets of rainbow trout, Oncorhynchus mykiss, were filleted and imaged using a rapid multispectral imaging device for quantitative analysis. The multispectral imaging device captures reflection properties in 19 distinct wavelength bands, prior to determination of the true concentration of astaxanthin. The samples ranged from 0.20 to 4.34 g per g fish. A PLSR model was calibrated to predict astaxanthin concentration from novel images, and showed good results with a RMSEP of 0.27. For comparison a similar model were built for normal color images, which yielded a RMSEP of 0.45. The acquisition speed of the multispectral imaging system and the accuracy of the PLSR model obtained suggest this method as a promising technique for rapid in-line estimation of astaxanthin concentration in rainbow trout fillets

A fast genetically encoded fluorescent sensor for faithful in vivo acetylcholine detection in mice, fish, worms and flies

Here we design and optimize a genetically encoded fluorescent indicator, iAChSnFR, for the ubiquitous neurotransmitter acetylcholine, based on a bacterial periplasmic binding protein. iAChSnFR shows large fluorescence changes, rapid rise and decay kinetics, and insensitivity to most cholinergic drugs. iAChSnFR revealed large transients in a variety of slice and in vivo preparations in mouse, fish, fly and worm. iAChSnFR will be useful for the study of acetylcholine in all organisms

Probes, hardware and software for next-generation super-resolution microscopy

Super-resolution microscopy enables optical imaging using fluorescence probes below the diffraction limit. In stochastic super-resolution microscopy, molecules are „switched“ between non-fluorescent dark-state (OFF-state) and fluorescent bright-state (ON-state) in order to pinpoint their position with sub-diffraction precision. The most prominent techniques of localization-based super-resolution microscopy are photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM). Here, the switching between dark- and bright-state is accomplished using photophysical or photochemical processes. A recently introduced super-resolution microscopy method called DNA-PAINT (deoxyribonucleic acid - point accumulation for imaging in nanoscale topography) is based on DNA-DNA interaction. In contrast to STORM or PALM, the fluorescence molecules do not switch between dark and bright states. The so-called „blinking“ in DNA-PAINT is created by transient hybridization of short fluorescent DNA strands (imagers) to their targets. The work in this dissertation focuses on three different advancements in the technological aspect of super-resolution microscopy. Probes In the first project of this thesis, I demonstrate the combination of single-molecule Förster resonance energy transfer (FRET) with DNA-PAINT imaging to overcome some current limitations of the DNA-based super-resolution microscopy. I evaluate the novel probe design with in vitro experiments using DNA nanostructures and prove the performance of the FRET-based probes in a cellular context. Hardware In the second project, I describe a cost-efficient single-molecule microscope platform, which is an order of magnitude more affordable, while still yielding high-performance imaging capacity. Using two-dimensional (2D) and three-dimensional (3D) super-resolution in vitro experiments using DNA nanostructures, I asses the performance of the microscopy platform. Finally, I present exemplary experiments for multiplexed cellular imaging. Software In the last project, I present a software package that is developed to assist during super-resolution data analysis. It is based on the deep learning concept of the artificial neural network (ANN) and designed to automate the classification of nano-scaled patterns found in super-resolution images. I evaluate the performance of the software package using super-resolution in vitro experiments of DNA nanostructures as well as targets in cellular samples.Die superauflösende Mikroskopie ermöglicht die optische Abbildung mittels Fluoreszenzsonden unterhalb der Beugungsgrenze. In stochastischen Superauflösungsmikroskopie werden Moleküle zwischen dem nicht-fluoreszierenden Zustand (OFF-Zustand) und dem fluoreszierenden Zustand (ON-Zusstand) “geschaltet“, um ihre Position präziser als die Beugungsgrenze zu bestimmen. Die bekanntesten Mikroskopietechniken der lokalisationsbasierten Superauflösungsmikroskopie sind photo-activated localization microscopy (PALM) und stochastic optical reconstruction microscopy (STORM). Hier wird die Umschaltung zwischen Dunkel- und Hellzustand mithilfe photophysikalischer oder photochemischer Prozesse durchgeführt. Eine kürzlich eingeführte Methode der Superauflösungsmikroskopie namens DNA-PAINT (deoxyribonucleic acid - point accumulation for imaging in nanoscale topography) basiert auf der DNA-DNA Wechselwirkung. Im Vergleich zu STORM oder PALM wechseln die Fluoreszenzmoleküle nicht zwischen dem dunklen und dem hellen Zustand. Das sogenannte “Blinken“ in DNA-PAINT wird durch transiente Hybridisierung kurzer fluoreszierender DNA Stränge (Imager) an ihre Ziele erzeugt. Die Arbeiten in dieser Dissertation konzentriert sich auf drei unterschiedliche Fortschritte im technologischen Aspekt der Superauflösungsmikroskopie. Sonden Im ersten Projekt dieser Arbeit zeige ich die Kombination von Einzelmolekül-Förster-Resonanzenergietransfer (englisch Förster resonance energy transfer (FRET)) mit DNA-PAINT Mikroskopie, um einige aktuelle Einschränkungen der DNA basierten Superauflösungsmikroskopie zu überwinden. Ich evaluiere das neuartige Sondendesign mithilfe von in vitro Experimenten mit DNA nanostructure und zeige die Leistungsfähigkeit der FRET-basierten Sonden im zellulären Kontext. Hardware Im zweiten Projekt beschreibe ich eine kosteneffiziente Mikroskop-Plattform für Einzelmolekülstudien, die um eine Größenordnung erschwinglicher ist und dennoch eine leistungsstarke Abbildungsfähigkeit bietet. Unter Verwendung von zweidimensionalen (2D) und dreidimensionalen (3D) in vitro Superauflösungsexperimenten von DNA Nanostrukturen bewerte ich die Leistung der Mikroskopie-Plattform. Schließlich zeige ich exemplarische Experimente für die zelluläre Bildgebung in mehreren Farben. Software Im letzten Projekt stelle ich ein Softwarepaket vor, das zur Unterstützung der Analyse von Daten in Superauflösungsmikroskopie entwickelt wurde. Es basiert auf dem Konzept des tiefen Lernens (englisch deep learning) mithilfe von künstlichen neuronalen Netzen und wurde entwickelt, um die Klassifikation von nanoskaligen Mustern zu automatisieren, die in superaufgelösten Bildern zu finden sind. Ich evaluiere die Leistung des Softwarepakets anhand von in vitro Superauflösungsexperimenten von DNA Nanostrukturen sowie von in Zellproben

Internationalisation of Innovation: Why Chip Design Moving to Asia

This paper will appear in International Journal of Innovation Management, special issue in honor of Keith Pavitt, (Peter Augsdoerfer, Jonathan Sapsed, and James Utterback, guest editors), forthcoming. Among Keith Pavitt's many contributions to the study of innovation is the proposition that physical proximity is advantageous for innovative activities that involve highly complex technological knowledge But chip design, a process that creates the greatest value in the electronics industry and that requires highly complex knowledge, is experiencing a massive dispersion to leading Asian electronics exporting countries. To explain why chip design is moving to Asia, the paper draws on interviews with 60 companies and 15 research institutions that are doing leading-edge chip design in Asia. I demonstrate that "pull" and "policy" factors explain what attracts design to particular locations. But to get to the root causes that shift the balance in favor of geographical decentralization, I examine "push" factors, i.e. changes in design methodology ("system-on-chip design") and organization ("vertical specialization" within global design networks). The resultant increase in knowledge mobility explains why chip design - that, in Pavitt's framework is not supposed to move - is moving from the traditional centers to a few new specialized design clusters in Asia. A completely revised and updated version has been published as: " Complexity and Internationalisation of Innovation: Why is Chip Design Moving to Asia?," in International Journal of Innovation Management, special issue in honour of Keith Pavitt, Vol. 9,1: 47-73.

3.46 Ga Apex chert 'microfossils' reinterpreted as mineral artefacts produced during phyllosilicate exfoliation

We acknowledge the facilities, scientific and technical assistance of the Australian Microscopy & Microanalysis Research Facility at: Centre for Microscopy Characterisation and Analysis, The University of Western Australia; Electron Microscopy Unit, The University of New South Wales. These facilities are funded by the Universities, State and Commonwealth Governments. DW was funded by the European Commission and the Australian Research Council (FT140100321). This is ARC CCFS paper number XXX. We acknowledge Martin van Kranendonk, Owen Green, Cris Stoakes, Nicola McLoughlin, the late John Lindsay and the Geological Survey of Western Australia for fieldwork assistance, Thomas Becker for assistance with Raman microspectroscopy, Anthony Burgess from FEI for the preparation of one of the TEM wafers, and Russell Garwood, Tom Davies, Imran Rahman & Stephan Lautenschlager for training and advice on the SPIERS and AVIZO software suites. We thank Chris Fedo and an anonymous reviewer for comments that improved the manuscript.Peer reviewedPostprin

Evidence for the Inhibition of Dengue Virus Binding in the Presence of Silver Nanoparticles

Dengue is an emerging hemorrhagic fever virus and widely considered the most important arbovirus in the world. Dengue virus (DENV) is a positive-sense RNA virus that exists in 4, potentially 5, antigenic serotypes. Currently, no vaccines or treatments are approved for DENV infections. Unsuccessful vaccine trials open the door for non-traditional treatments such as silver nanoparticles. Silver nanoparticles (AgNP) are known to inhibit viral replication of numerous viruses but have never before been tested for inhibition of dengue virus type 2 (DENV2, ATCC® VR-1584TM). For the first time, this research presents up to a 96% reduction in DENV2 binding to Vero cells following pretreatment with AgNP (6-10nm, 25µg/mL). These results suggest that similarly to other viruses, DENV2 can be inhibited at the first stage of the virus replication cycle, binding & entry

Probes, hardware and software for next-generation super-resolution microscopy

Super-resolution microscopy enables optical imaging using fluorescence probes below the diffraction limit. In stochastic super-resolution microscopy, molecules are „switched“ between non-fluorescent dark-state (OFF-state) and fluorescent bright-state (ON-state) in order to pinpoint their position with sub-diffraction precision. The most prominent techniques of localization-based super-resolution microscopy are photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM). Here, the switching between dark- and bright-state is accomplished using photophysical or photochemical processes. A recently introduced super-resolution microscopy method called DNA-PAINT (deoxyribonucleic acid - point accumulation for imaging in nanoscale topography) is based on DNA-DNA interaction. In contrast to STORM or PALM, the fluorescence molecules do not switch between dark and bright states. The so-called „blinking“ in DNA-PAINT is created by transient hybridization of short fluorescent DNA strands (imagers) to their targets. The work in this dissertation focuses on three different advancements in the technological aspect of super-resolution microscopy. Probes In the first project of this thesis, I demonstrate the combination of single-molecule Förster resonance energy transfer (FRET) with DNA-PAINT imaging to overcome some current limitations of the DNA-based super-resolution microscopy. I evaluate the novel probe design with in vitro experiments using DNA nanostructures and prove the performance of the FRET-based probes in a cellular context. Hardware In the second project, I describe a cost-efficient single-molecule microscope platform, which is an order of magnitude more affordable, while still yielding high-performance imaging capacity. Using two-dimensional (2D) and three-dimensional (3D) super-resolution in vitro experiments using DNA nanostructures, I asses the performance of the microscopy platform. Finally, I present exemplary experiments for multiplexed cellular imaging. Software In the last project, I present a software package that is developed to assist during super-resolution data analysis. It is based on the deep learning concept of the artificial neural network (ANN) and designed to automate the classification of nano-scaled patterns found in super-resolution images. I evaluate the performance of the software package using super-resolution in vitro experiments of DNA nanostructures as well as targets in cellular samples.Die superauflösende Mikroskopie ermöglicht die optische Abbildung mittels Fluoreszenzsonden unterhalb der Beugungsgrenze. In stochastischen Superauflösungsmikroskopie werden Moleküle zwischen dem nicht-fluoreszierenden Zustand (OFF-Zustand) und dem fluoreszierenden Zustand (ON-Zusstand) “geschaltet“, um ihre Position präziser als die Beugungsgrenze zu bestimmen. Die bekanntesten Mikroskopietechniken der lokalisationsbasierten Superauflösungsmikroskopie sind photo-activated localization microscopy (PALM) und stochastic optical reconstruction microscopy (STORM). Hier wird die Umschaltung zwischen Dunkel- und Hellzustand mithilfe photophysikalischer oder photochemischer Prozesse durchgeführt. Eine kürzlich eingeführte Methode der Superauflösungsmikroskopie namens DNA-PAINT (deoxyribonucleic acid - point accumulation for imaging in nanoscale topography) basiert auf der DNA-DNA Wechselwirkung. Im Vergleich zu STORM oder PALM wechseln die Fluoreszenzmoleküle nicht zwischen dem dunklen und dem hellen Zustand. Das sogenannte “Blinken“ in DNA-PAINT wird durch transiente Hybridisierung kurzer fluoreszierender DNA Stränge (Imager) an ihre Ziele erzeugt. Die Arbeiten in dieser Dissertation konzentriert sich auf drei unterschiedliche Fortschritte im technologischen Aspekt der Superauflösungsmikroskopie. Sonden Im ersten Projekt dieser Arbeit zeige ich die Kombination von Einzelmolekül-Förster-Resonanzenergietransfer (englisch Förster resonance energy transfer (FRET)) mit DNA-PAINT Mikroskopie, um einige aktuelle Einschränkungen der DNA basierten Superauflösungsmikroskopie zu überwinden. Ich evaluiere das neuartige Sondendesign mithilfe von in vitro Experimenten mit DNA nanostructure und zeige die Leistungsfähigkeit der FRET-basierten Sonden im zellulären Kontext. Hardware Im zweiten Projekt beschreibe ich eine kosteneffiziente Mikroskop-Plattform für Einzelmolekülstudien, die um eine Größenordnung erschwinglicher ist und dennoch eine leistungsstarke Abbildungsfähigkeit bietet. Unter Verwendung von zweidimensionalen (2D) und dreidimensionalen (3D) in vitro Superauflösungsexperimenten von DNA Nanostrukturen bewerte ich die Leistung der Mikroskopie-Plattform. Schließlich zeige ich exemplarische Experimente für die zelluläre Bildgebung in mehreren Farben. Software Im letzten Projekt stelle ich ein Softwarepaket vor, das zur Unterstützung der Analyse von Daten in Superauflösungsmikroskopie entwickelt wurde. Es basiert auf dem Konzept des tiefen Lernens (englisch deep learning) mithilfe von künstlichen neuronalen Netzen und wurde entwickelt, um die Klassifikation von nanoskaligen Mustern zu automatisieren, die in superaufgelösten Bildern zu finden sind. Ich evaluiere die Leistung des Softwarepakets anhand von in vitro Superauflösungsexperimenten von DNA Nanostrukturen sowie von in Zellproben