Novel DNA carrier structures for protein detection and analysis in a nanopore sensing system

The continued development of diagnostic and therapeutic techniques for biological samples requires robust single-molecule detection techniques. Protein assays that are currently commonly used, such as ELISA, do not fit the specificity and sensitivity requirements, and also involve significant sample processing. In short, they do not provide what is needed for biomarker qualification and quantification. One technique that has the potential to offer improved single-molecule detection is nanopore sensing. Nanopore sensing uses electrical voltage to drive molecules across a small pore, one that is either biological or solid state. For this research, as solid state pore at the end of a pipette, a nanopipette, is used. In this technique, the current is continuously monitored and as specific molecules, usually DNAs or proteins, cross through the pore (translocate) the current changes. As nanopore sensing is a single-molecule technique, it easily fulfils the sensitivity requirements. Unfortunately, on its own, it is not able to select for specific molecules, and this limitation, in addition to difficulties that are encountered with protein translocations, leads to the necessity of DNA carriers. DNA carriers are typically double-stranded DNAs that has been modified to bind specifically to certain proteins. The translocations of these DNA tethered protein molecules then look significantly different compared to DNA on its own, such that it is possible to select for them specifically. The distinguishing figure for these events is typically another peak inside these events, or rather a subpeak. This research investigates two DNA carriers, a DNA dendrimer and a DNA plasmid carrier. The DNA dendrimer has great potential due to its customisability and ability to perform multiplexed sensing. To form the dendrimer, Y-shaped DNAs, each made of three oligonucleotides, was combined in stoichiometric ratios. For the first generation (G1) dendrimer, four Y-shaped DNAs were combined. This G1 could have three protein binding sites or be combined with another six Y-shaped DNAs to form a second generation (G2) with six protein binding sites. However, unfortunately, at the low concentrations required for the nanopore, the binding of the oligonucleotides was not strong enough. Many of the dendrimer structures simply fell apart or could not stay in a reliable shape with the required salt conditions. Therefore, there were few translocation events recorded and it was established that the dendrimers were not feasible DNA carriers. 3 The plasmid, like the dendrimer, is completely customisable and has the potential to perform multiplexed protein sensing. A 10 Kbp plasmid was modified such that a short single-stranded section was replaced with a sequence including both the original sequence as well as a biotin. Theoretically, any aptamer could be used in place of the biotin, but the biotin-streptavidin bond was used for the proof of concept. The plasmid was also linearised. Successful modification of the plasmid so that it could bind to streptavidin was confirmed. Several protein binding curves with both monovalent streptavidin and quadrivalent streptavidin were performed, and events with subpeaks were regularly identified. Additionally, a binding curve for a biotinylated phosphatase bound to quadrivalent streptavidin was performed. This allowed for an investigation of a sandwichlike assay as it moved through the nanopore. While there was a significant difference in the binding curve for this sandwich-like assay, individual events did not have as many differences as was expected. This plasmid carrier has a lot of potential, as it overcomes the issue of introducing selectivity into the nanopore platform without diminishing its sensitivity. The long term goal for this plasmid carrier is for it to be used to identify specific proteins, ideally with multiplexed sensing capabilities, at extremely low concentrations.Open Acces

Retrofit of Corn Ethanol Plant to Produce Biobutanol through Fermentation

The depletion of natural gas resources coupled with the improved technologies for biofuel production present a favorable scenario for entry into the biobutanol market. This process aims to produce butanol at a competitive price to oil and natural gas produced from petrochemical processes. As such, the proposed design takes an existing 40MM gpy corn ethanol plant and retrofits the plant to produce butanol via continuous fermentation of corn using a genetically engineered strain of Clostridia. The proposed design consumes 14.5 million bushels of corn per year and produces acetone, butanol and ethanol at a mass ratio of 12:58:1, respectively. The corn is undergoes traditional wet mill processing upstream, and is then fed as a slurry to the fermenters. The liquid fermentation products pass through liquid-liquid extraction followed by distillation to recover the butanol and acetone. The solids pass through a DDGS separation section and the vapor phase leaving the fermenters is combusted. This process intends to produce butanol, acetone, and DDGS for sale in the market. The plant has the capacity to operate 330 days per year and to produce 21.7MM gpy of butanol at 99.5% purity, 2.8MM gpy of acetone at 93.2% purity and 182,509 metric tons of DDGS per year. The plant is located in the Midwest United States in the Corn Belt. It has a return on investment of 12.07%

Solution Strategy mit der Methode 635 als Cross Plattform App

Ausgangslage: Die papiergestützte Methode 635 ist eine Kreativitäts- und Brainwriting-Technik, welche die Entwicklung von neuen, ungewöhnlichen Ideen für Problemlösungen in der Gruppe fördert. Nach unserem Wissensstand existiert für die Methode 635 noch keine mobile Applikation. Ergebnis: Aus der vorliegenden Bachelorarbeit ist eine Cross-Plattform Applikation für iOS und Android hervorgegangen. Diese Applikation erlaubt es Benutzern, die Methode 635 gemeinsam auf ihrem Smartphones oder Tablets zu verwenden. Zusätzlich zur Eingabe von Ideen via Text ist es möglich, Skizzen als Lösungsvorschlag zu zeichnen oder aus einer Liste von vordefinierten Microservice API Patterns (MAP) ein passendes Pattern auszuwählen. Erarbeitete Brainstormings können im Markdown-Format exportiert werden. Die Möglichkeit, Skizzen zu zeichnen und Patterns aus der vordefinierten Patternsprache zu verwenden, kommt gerade (aber nicht ausschliesslich) Software-Architekten zugute. So können sie diese Funktionen beispielsweise im Zuge der Entwurfsphase Solution Strategy nutzen, um kollaborativ und kreativ an einer allfälligen Lösung zu arbeiten. Als Teil der Dokumentation beschreiben wir zudem die Herausforderungen, die während der Umsetzung aufgetreten sind. So können andere Entwickler in ähnlichen Cross-Plattform-Vorhaben von unseren Erfahrungen profitieren und die Projektrisiken verringern. Als mögliche Erweiterung dieser Applikation wäre es denkbar, weitere Ideen-Typen zu integrieren oder den Fokus etwas zu weiten und andere Brainstorming-Methoden oder Konzepte wie z.B. ein Mitglied der World-Cafe-Methodenfamilie zu integrieren

Pollution from Aircraft Emissions in the North Atlantic Flight Corridor: Overview on the POLINAT Projects

The Pollution From Aircraft Emissions in the North Atlantic Flight Corridor (POLINAT) projects were undertaken to investigate the impact of aircraft engine exhaust emissions on the state of the atmosphere in the North Atlantic flight corridor. Changes in the composition of the lower stratosphere and upper troposphere from aircraft emissions are identified from combined measurements and model analyses. Measurements were performed using the Deutsches Zentrum für Luft- und Raumfahrt Falcon research aircraft and a Swissair B-747 over the North Atlantic covering the altitude range 6 to 13 km in November 1994 and June/July 1995 and from August to November 1997. The measurements include those of nitrogen oxides, nitrous and nitric acids, sulfur dioxide, sulfuric acid, acetone, carbon dioxide, ozone, water vapor, carbon monoxide, aerosols, and meteorological parameters. The atmospheric composition was found to be highly variable, and emissions from sources at the surface or from lightning discharges also contribute strongly to the nitrogen oxides abundance and ozone formation. Contributions from aircraft emissions have been measured and identified in single and multiple plumes of several hours ages, and accumulation of such nitrogen oxides and particles emissions can be identified under certain conditions in and downstream of the flight corridor region. Acetone was found at high mixing ratios. The global and regional models predict ozone increases of 3 to 6% by current air traffic at the flight corridor altitude north of 30°N, in agreement with previous model analyses but too small to be measurable. In autumn, the upper troposphere is often humid with water vapor concentration far above ice saturation, providing conditions for persistent contrails

Data composites of airborne observations of tropospheric ozone and its precursors

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