Nanobody-aided structural study of the activity- regulated cytoskeleton-associated protein (Arc) using synchrotron radiation and cryo-EM

Masteroppgave i biomedisinBMED395MAMD-MEDB

Comparing Efficiency of Lysis Buffer Solutions and Sample Preparation Methods for Liquid Chromatography–Mass Spectrometry Analysis of Human Cells and Plasma

The use of a proper sample processing methodology for maximum proteome coverage and high-quality quantitative data is an important choice to make before initiating a liquid chromatography–mass spectrometry (LC–MS)-based proteomics study. Popular sample processing workflows for proteomics involve in-solution proteome digestion and single-pot, solid-phaseenhanced sample preparation (SP3). We tested them on both HeLa cells and human plasma samples, using lysis buffers containing SDS, or guanidinium hydrochloride. We also studied the effect of using commercially available depletion mini spin columns before SP3, to increase proteome coverage in human plasma samples. Our results show that the SP3 protocol, using either buffer, achieves the highest number of quantified proteins in both the HeLa cells and plasma samples. Moreover, the use of depletion mini spin columns before SP3 results in a two-fold increase of quantified plasma proteins. With additional fractionation, we quantified nearly 1400 proteins, and examined lower-abundance proteins involved in neurodegenerative pathways and mitochondrial metabolism. Therefore, we recommend the use of the SP3 methodology for biological sample processing, including those after depletion of high-abundance plasma proteins.Research Council of Norway 29591

Comparing Efficiency of Lysis Buffer Solutions and Sample Preparation Methods for Liquid Chromatography–Mass Spectrometry Analysis of Human Cells and Plasma

The use of a proper sample processing methodology for maximum proteome coverage and high-quality quantitative data is an important choice to make before initiating a liquid chromatography–mass spectrometry (LC–MS)-based proteomics study. Popular sample processing workflows for proteomics involve in-solution proteome digestion and single-pot, solid-phase-enhanced sample preparation (SP3). We tested them on both HeLa cells and human plasma samples, using lysis buffers containing SDS, or guanidinium hydrochloride. We also studied the effect of using commercially available depletion mini spin columns before SP3, to increase proteome coverage in human plasma samples. Our results show that the SP3 protocol, using either buffer, achieves the highest number of quantified proteins in both the HeLa cells and plasma samples. Moreover, the use of depletion mini spin columns before SP3 results in a two-fold increase of quantified plasma proteins. With additional fractionation, we quantified nearly 1400 proteins, and examined lower-abundance proteins involved in neurodegenerative pathways and mitochondrial metabolism. Therefore, we recommend the use of the SP3 methodology for biological sample processing, including those after depletion of high-abundance plasma proteins.publishedVersio

Comparing Efficiency of Lysis Buffer Solutions and Sample Preparation Methods for Liquid Chromatography–Mass Spectrometry Analysis of Human Cells and Plasma

The use of a proper sample processing methodology for maximum proteome coverage and high-quality quantitative data is an important choice to make before initiating a liquid chromatography–mass spectrometry (LC–MS)-based proteomics study. Popular sample processing workflows for proteomics involve in-solution proteome digestion and single-pot, solid-phase-enhanced sample preparation (SP3). We tested them on both HeLa cells and human plasma samples, using lysis buffers containing SDS, or guanidinium hydrochloride. We also studied the effect of using commercially available depletion mini spin columns before SP3, to increase proteome coverage in human plasma samples. Our results show that the SP3 protocol, using either buffer, achieves the highest number of quantified proteins in both the HeLa cells and plasma samples. Moreover, the use of depletion mini spin columns before SP3 results in a two-fold increase of quantified plasma proteins. With additional fractionation, we quantified nearly 1400 proteins, and examined lower-abundance proteins involved in neurodegenerative pathways and mitochondrial metabolism. Therefore, we recommend the use of the SP3 methodology for biological sample processing, including those after depletion of high-abundance plasma proteins

Lateral straggling of implanted aluminum in 4H-SiC

The implantation of aluminum into 4H-SiC is studied using secondary ion mass spectrometry. In particular, two-dimensional concentration profiles are obtained, which allow the investigation of lateral straggling and its dependence on the crystallographic orientation. A high dose, medium energy aluminum implantation is studied in great detail. It shows an asymmetric distribution due to the 4°-off axis growth of the epitaxial layer. The lateral straggling is found to be in the range of several micrometers for a concentration of 1×1015 cm−3, which is contrary to the expectation given by most simulation studies. Implantations performed at different orientations support the idea that lateral straggling highly depends on the particular channeling opening. The Research Council of Norway is acknowledged for the support to the Norwegian Micro- and Nano-Fabrication Facility, NorFab, Project No. 245963

Lateral straggling of implanted aluminum in 4H-SiC

The implantation of aluminum into 4H-SiC is studied using secondary ion mass spectrometry. In particular, two-dimensional concentration profiles are obtained, which allow the investigation of lateral straggling and its dependence on the crystallographic orientation. A high dose, medium energy aluminum implantation is studied in great detail. It shows an asymmetric distribution due to the 4°-off axis growth of the epitaxial layer. The lateral straggling is found to be in the range of several micrometers for a concentration of 1×1015 cm−3, which is contrary to the expectation given by most simulation studies. Implantations performed at different orientations support the idea that lateral straggling highly depends on the particular channeling opening.ISSN:0003-6951ISSN:1077-311

Gallium diffusion in zinc oxide via the paired dopant-vacancy mechanism

Isochronal and isothermal diffusion experiments of gallium (Ga) in zinc oxide (ZnO) have been performed in the temperature range of 900–1050 °C. The samples used consisted of a sputter-deposited and highly Ga-doped ZnO film at the surface of a single-crystal bulk material. We use a novel reaction diffusion (RD) approach to demonstrate that the diffusion behavior of Ga in ZnO is consistent with zinc vacancy (VZn) mediation via the formation and dissociation of GaZnVZn complexes. In the RD modeling, experimental diffusion data are fitted utilizing recent density-functional-theory estimates of the VZn formation energy and the binding energy of GaZnVZn. From the RD modeling, a migration energy of 2.3 eV is deduced for GaZnVZn, and a total/effective activation energy of 3.0 eV is obtained for the Ga diffusion. Furthermore, and for comparison, employing the so-called Fair model, a total/effective activation energy of 2.7 eV is obtained for the Ga diffusion, reasonably close to the total value extracted from the RD-modeling. © 2018 AIP Publishin

The interaction between lithium acceptors and gallium donors in zinc oxide

Diffusion of lithium (Li) in uniformly gallium (Ga)-doped monocrystalline bulk Zinc Oxide (ZnO) is studied over a wide temperature range (500 − 1150◦C) and is demonstrated to be dictated by the distribution of Ga. Below 800◦C, the indiffusion of Li from a Li-doped ZnO sputtered film into a n + ZnO bulk yields an abrupt and compensated Li-doped box region with the Li concentration matching the free-electron concentration, in accordance with several previous experimental and theoretical reports. However, experimental observations of Li-diffusion at higher temperatures have not previously been reported. In this study we give a detailed description of a dissociative diffusion mechanism for Li up to 1150◦C. By employing a reaction-diffusion model that accounts for the presence of both Li and Ga, a dissociation energy of 4.6 eV with an attempt frequency of 5×1015s −1 is obtained from the experimental Li diffusion data. This is in excellent agreement with theoretical results for the dissociation of (LiZnGaZn) 0 (4.8 eV) into Li+ i and (GaZnVZn) −, and strongly suggest that this neutral and stable acceptor-donor pair prevails in Li- and Ga-doped ZnO

Influence of annealing atmosphere on formation of electrically-active defects in rutile TiO2

Electronic states in the upper part of the bandgap of reduced and/or hydrogenated n-type rutile TiO2 single crystals have been studied by means of thermal admittance and deep-level transient spectroscopy measurements. The studies were performed at sample temperatures between 28 and 300 K. The results reveal limited charge carrier freeze-out even at 28 K and evidence the existence of dominant shallow donors with ionization energies below 25 meV. Interstitial atomic hydrogen is considered to be a major contributor to these shallow donors, substantiated by infrared absorption measurements. Three defect energy levels with positions of about 70 meV, 95 meV, and 120 meV below the conduction band edge occur in all the studied samples, irrespective of the sample production batch and the post-growth heat treatment used. The origin of these levels is discussed in terms of electron polarons, intrinsic point defects, and/or common residual impurities, where especially interstitial titanium atoms, oxygen vacancies, and complexes involving Al atoms appear as likely candidates. In contrast, no common deep-level defect, exhibiting a charge state transition in the 200–700 meV range below the conduction band edge, is found in different samples. This may possibly indicate a strong influence on deep-level defects by the post-growth heat treatments employed