Establishing a Biochemical System for the Purification and ATPase activity of GST-Dbp5

The export of mRNA out of the nucleus is a crucial step for eukaryotic gene expression. The export of mRNA transcripts is aided by Mex67, which allows export through the nuclear pore complex doorways in the nuclear envelope. Once out of the nucleus, a protein known as Dbp5, bound to ATP, Gle1, and Nup42 aids in the directionality of mRNA export by helping remove Mex67 from the mRNA strand. Following interaction with RNA, Dbp5 then hydrolyzes ATP so that it unbinds the mRNA, allowing for enzyme recycling. Previous efforts worked towards the purification of Dbp5, but the attempts were unsuccessful due to low expression of recombinant protein in E.coli. In this project, I am focusing on enhancing the bacterial induction in order to establish robust purification of recombinant Dbp5. This will help in developing ATPase assays involving Dbp5, Nup42, and Gle1. These ATPase assays will aid in better understanding the effects of Nup42 and Gle1 on Dbp5’s ATPase activity and will allow for future study on Dbp5’s ATPase activity. In order to enhance the bacterial induction, E. coli cells were transformed with a GST-Dbp5 plasmid and were induced with varying amounts of IPTG to determine the best procedure for bacterial induction. Results from the bacterial induction have indicated that alternative methods for bacterial induction should be explored. Future experiments will look into further enhancing the bacterial induction of Dbp5 in order to establish a biochemical system analyzing the ATPase activity of GST-Dbp5

Assessing the number of users who are excluded by domestic heating controls

This is the pre-print version of the Article. This Article is also referred to as: "Assessing the 'Design Exclusion' of Heating Controls at a Low-Cost, Low-Carbon Housing Development". - Copyright @ 2011 Taylor & FrancisSpace heating accounts for almost 60% of the energy delivered to housing which in turn accounts for nearly 27% of the total UK's carbon emissions. This study was conducted to investigate the influence of heating control design on the degree of ‘user exclusion’. This was calculated using the Design Exclusion Calculator, developed by the Engineering Design Centre at the University of Cambridge. To elucidate the capability requirements of the system, a detailed hierarchical task analysis was produced, due to the complexity of the overall task. The Exclusion Calculation found that the current design placed excessive demands upon the capabilities of at least 9.5% of the UK population over 16 years old, particularly in terms of ‘vision’, ‘thinking’ and ‘dexterity’ requirements. This increased to 20.7% for users over 60 years old. The method does not account for the level of numeracy and literacy and so the true exclusion may be higher. Usability testing was conducted to help validate the results which indicated that 66% of users at a low-carbon housing development could not programme their controls as desired. Therefore, more detailed analysis of the cognitive demands placed upon the users is required to understand where problems within the programming process occur. Further research focusing on this cognitive interaction will work towards a solution that may allow users to behave easily in a more sustainable manner

Determining anion-quadrupole interactions among protein, DNA, and ligand molecules

Background An extensive search through the Protein Databank (about 4500 nonredundant structures) was previously completed within our lab to analyze the energetic and geometric characteristics of an understudied molecular interaction known as an anion-quadrupole (AQ) interaction. Such an interaction occurs when the positively charged edge of an aromatic ring, resulting from a quadruple moment (i.e., a dual dipole moment), renders the aromatic molecule noncovalently bound to a nearby anionic molecule. The study considered a very limited scenario of molecules that can participate in AQ interactions, consisting of the phenyl group of a phenylalanine (phe) amino acid as the aromatic participant and the carboxylate group of an aspartate (asp) or glutamate (glu) amino acid as the anionic participant. The results revealed anion-quadrupole pairs to be prevalent within most of the protein structures. It was also observed that the interaction energy for AQ pairs was heavily dependent on the angle between the anion and plane of the aromatic ring, favoring a more planar interaction. In light of these critical observations being made from such a limited scenario, only phe-glu and phe-asp pairs and in a reduced sample set of the PDB, we are now continuing this work of identifying AQ interactions using a greatly expanded strategy. We are following these four aims: 1. Optimizing the AQ-search program to run in a semi-parallel fashion and on a large cluster of processors in order to handle larger analyses, 2. Adding to our search additional anionic participants which will include non-protein structures such as DNA and small ligands, 3. Studying a subset of the AQ pairs with molecular dynamics simulations in buried and solvent exposed environments to observe non-static behavioral traits as well as the reproducibility of AQ interactions by force field parameters. 4. Building an online database for public access to our data and search program. Acknowledgments We would like to acknowledge the NSF-IGERT traineeship, Scalable Computing and Leading Edge Innovative Technologies (SCALE-IT), for providing the resources for this project

Thermal Liability of Hyaloclastite in the Krafla Geothermal Reservoir, Iceland:The Impact of Phyllosilicates on Permeability and Rock Strength

Geothermal fields are prone to temperature fluctuations from natural hydrothermal activity, anthropogenic drilling practices, and magmatic intrusions. These fluctuations may elicit a response from the rocks in terms of their mineralogical, physical (i.e., porosity and permeability), and mechanical properties. Hyaloclastites are a highly variable volcaniclastic rock predominantly formed of glass clasts that are produced during nonexplosive quench-induced fragmentation, in both subaqueous and subglacial eruptive environments. They are common in high-latitude geothermal fields as both weak, highly permeable reservoir rocks and compacted impermeable cap rocks. Basaltic glass is altered through interactions with external water into a clay-dominated matrix, termed palagonite, which acts to cement the bulk rock. The abundant, hydrous phyllosilicate minerals within the palagonite can dehydrate at elevated temperatures, potentially resulting in thermal liability of the bulk rock. Using surficial samples collected from Krafla, northeast Iceland, and a range of petrographic, mineralogical, and mechanical analyses, we find that smectite dehydration occurs at temperatures commonly experienced within geothermal fields. Dehydration events at 130, 185, and 600°C result in progressive mass loss and contraction. This evolution results in a positive correlation between treatment temperature, porosity gain, and permeability increase. Gas permeability measured at 1 MPa confining pressure shows a 3-fold increase following thermal treatment at 600°C. Furthermore, strength measurements show that brittle failure is dependent on porosity and therefore the degree of thermal treatment. Following thermal treatment at 600°C, the indirect tensile strength, uniaxial compressive strength, and triaxial compressive strength (at 5 MPa confining pressure) decrease by up to 68% (1.1 MPa), 63% (7.3 MPa), and 25% (7.9 MPa), respectively. These results are compared with hyaloclastite taken from several depths within the Krafla reservoir, through which the palagonite transitions from smectite-to chlorite-dominated. We discuss how temperature-induced changes to the geomechanical properties of hyaloclastite may impact fluid flow in hydrothermal reservoirs and consider the potential implications for hyaloclastite-hosted intrusions. Ultimately, we show that phyllosilicate-bearing rocks are susceptible to temperature fluctuations in geothermal fields. © 2020 Josh Weaver et al

The Origin and Evolution of Magnetic Fabrics in Mafic Sills

Studying extinct volcanoes where erosion has exposed dykes and sills provides direct access to the fossil remnants of magma movement, however, linking crystallized magma to emplacement dynamics is challenging. This study investigates how magma flow varies across the thickness of a thin (6 m thick) mafic sill. We use a high-resolution sampling regime to measure micro-scale variations in magnetic anisotropy, which is associated with the orientation of the magnetic particles present within the crystalline rock. Fieldwork was conducted on exposed sills of the British and Irish Palaeogene Igneous Province, Isle of Skye, Scotland. Here Jurassic sedimentary rocks have been intruded by a series of sills, of picrite to crinanite composition, from the Little Minch Sill Complex (c.60 Ma). Anisotropy of magnetic susceptibility (AMS) and anisotropy of anhysteretic remanent magnetization (AARM) signals have been used to separate a crinanite sill into distinct magnetic groupings. We identified two AMS groups (the upper and lower sill margins, and the central region) and four AARM groups (the lower margin, the middle region, a region just below the upper margin, and the upper margin). Both AMS and AARM signals originate from titanomagnetite of multi-domain or vortex-state to single-domain sized grains, respectively. The AMS and AARM fabrics are aligned with each other in the margin regions preserving a history of magma flow toward the North during initial emplacement. However, in the sill interior the magnetic fabrics are oblique to each other, thus reflecting multiple origins. We suggest the AMS fabrics have recorded magma flow during sill growth, and AARM fabrics have recorded melt percolation flow as the interstitial melt migrated upward through a solidifying crystal mush. We demonstrate that when AMS and AARM are used in combination they enable a detailed understanding of magma flow and solidification dynamics to be obtained, from initial emplacement to solidification. Overall, our detailed sampling and analysis indicates that magnetic fabrics can be highly variable over small distances, supporting the suggestion of horizontal flow restriction and propagation path migration within growing sills, and that previous reports of magma flow and solidification dynamics based on under-sampled bodies may require reconsideration

Strike-slip influenced stratigraphic and structural development of the Foula Sandstone Group, Shetland: implications for offshore Devonian basin development on the northern UK continental shelf

The island of Foula, located 25 km SW of Shetland, preserves a gently folded, 1.6 km thick sequence of Middle Devonian sandstones spectacularly exposed in kilometre-long cliff sections >350 m high. These rocks unconformably overlie likely Precambrian-age amphibolite facies basement rocks that are intruded by sheeted granites. The onshore succession is similar in age to the nearby Lower Clair Group offshore to the west. New mapping, incorporating the use of drone imagery in the inaccessible cliff sections, uses down-plunge projections to show that growth folding and faulting on Foula were contemporaneous with sedimentation during basin filling. The large-scale structural geometry is consistent with the regional constrictional strain due to the sinistral transtension associated with movements along the Walls Boundary–Great Glen fault zone system during the Mid-Devonian. Detrital zircon provenance studies indicate that the Devonian sequences of Foula (and nearby Melby in western Shetland) show similarities with the Clair Group and Orkney successions. We suggest that NE–SW transtensional fold development contemporaneous with regional subsidence in the Devonian basins of Scotland may be more widespread than previously realized. Large, kilometre-scale folds previously interpreted to be related to Permo-Carboniferous inversion may therefore have initiated earlier in the basin evolution sequence than previously realized

Compaction of Hyaloclastite from the Active Geothermal System at Krafla Volcano, Iceland

Hyaloclastites commonly form high-quality reservoir rocks in volcanic geothermal provinces. Here, we investigated the effects of confinement due to burial following prolonged accumulation of eruptive products on the physical and mechanical evolution of surficial and subsurface (depths of 70 m, 556 m, and 732 m) hyaloclastites from Krafla volcano, Iceland. Upon loading in a hydrostatic cell, the porosity and permeability of the surficial hyaloclastite decreased linearly with mean effective stress, as pores and cracks closed due to elastic (recoverable) compaction up to 22-24 MPa (equivalent to ~1.3 km depth in the reservoir). Beyond this mean effective stress, denoted as P∗, we observed accelerated porosity and permeability reduction with increasing confinement, as the rock underwent permanent inelastic compaction. In comparison, the porosity and permeability of the subsurface core samples were less sensitive to mean effective stress, decreasing linearly with increasing confinement as the samples compacted elastically within the conditions tested (to 40 MPa). Although the surficial material underwent permanent, destructive compaction, it maintained higher porosity and permeability than the subsurface hyaloclastites throughout the experiments. We constrained the evolution of yield curves of the hyaloclastites, subjected to different effective mean stresses in a triaxial press. Surficial hyaloclastites underwent a brittle-ductile transition at an effective mean stress of ~10.5 MPa, and peak strength (differential stress) reached 13 MPa. When loaded to effective mean stresses of 33 and 40 MPa, the rocks compacted, producing new yield curves with a brittle-ductile transition at ~12.5 and ~19 MPa, respectively, but showed limited strength increase. In comparison, the subsurface samples were found to be much stronger, displaying higher strengths and brittle-ductile transitions at higher effective mean stresses (i.e., 37.5 MPa for 70 m sample, >75 MPa for 556 m, and 68.5 MPa for 732 m) that correspond to their lower porosities and permeabilities. Thus, we conclude that compaction upon burial alone is insufficient to explain the physical and mechanical properties of the subsurface hyaloclastites present in the reservoir at Krafla volcano. Mineralogical alteration, quantified using SEM-EDS, is invoked to explain the further reduction of porosity and increase in strength of the hyaloclastite in the active geothermal system at Krafla

Frictional melt homogenisation during fault slip: Geochemical, textural and rheological fingerprints

info:eu-repo/semantics/publishe

Empirical Validation of the RCDC and RCDE Semantic Complexity Metrics for Object-Oriented Software

The Relative Class Domain Complexity (RCDC) and Relative Class Definition Entropy (RCDE) semantic metrics have been proposed for use as complexity metrics for object-oriented software. These semantic metrics are calculated on a knowledge-based representation of software, following a knowledge-based program understanding examination of the software. The metrics have great potential because they can be applied during the software design phase whereas most complexity metrics cannot be applied until after development is complete. In this paper, we present the results of a study to empirically validate the RCDC and RCDE metrics. We show that the metrics compare favorably with the findings of human experts and also that they correlate well with the results of conventional complexity metrics