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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Manry, Jérémy, et al.
(författare)
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The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies.
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 1091-6490. ; 119:21
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Tidskriftsartikel (refereegranskat)abstract
- Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection fatality rate (IFR) doubles with every 5 y of age from childhood onward. Circulating autoantibodies neutralizing IFN-α, IFN-ω, and/or IFN-β are found in ∼20% of deceased patients across age groups, and in ∼1% of individuals aged <70 y and in >4% of those >70 y old in the general population. With a sample of 1,261 unvaccinated deceased patients and 34,159 individuals of the general population sampled before the pandemic, we estimated both IFR and relative risk of death (RRD) across age groups for individuals carrying autoantibodies neutralizing type I IFNs, relative to noncarriers. The RRD associated with any combination of autoantibodies was higher in subjects under 70 y old. For autoantibodies neutralizing IFN-α2 or IFN-ω, the RRDs were 17.0 (95% CI: 11.7 to 24.7) and 5.8 (4.5 to 7.4) for individuals <70 y and ≥70 y old, respectively, whereas, for autoantibodies neutralizing both molecules, the RRDs were 188.3 (44.8 to 774.4) and 7.2 (5.0 to 10.3), respectively. In contrast, IFRs increased with age, ranging from 0.17% (0.12 to 0.31) for individuals <40 y old to 26.7% (20.3 to 35.2) for those ≥80 y old for autoantibodies neutralizing IFN-α2 or IFN-ω, and from 0.84% (0.31 to 8.28) to 40.5% (27.82 to 61.20) for autoantibodies neutralizing both. Autoantibodies against type I IFNs increase IFRs, and are associated with high RRDs, especially when neutralizing both IFN-α2 and IFN-ω. Remarkably, IFRs increase with age, whereas RRDs decrease with age. Autoimmunity to type I IFNs is a strong and common predictor of COVID-19 death.
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| 5. |
- Paul, Jan, et al.
(författare)
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Ab initio calculations of electron distributions in heme-CO models
- 1983
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Ingår i: Biochimica et Biophysica Acta - Bioenergetics. - : Elsevier BV. - 0005-2728 .- 1879-2650. ; 722:1, s. 209-213
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Tidskriftsartikel (refereegranskat)abstract
- We have, by the use of ab initio calculations, found a back-bonding state of π symmetry close to the Fermi level for CO bound to FeN5C14. We thus find it likely that small shifts of the redox potential ¦EF - Ev¦ will cause relatively large changes of the CO vibrational frequency. The separation of Fe 3d orbitals in our heme model is found to agree with what is predicted by ligand field theory for Oh symmetry. This paper presents nonrelativistic Hartree-Fock-Slater calculations of the 5σ bonding and 2π back-bonding between CO and Fe. The effects of up to 19 additional atoms are discussed for models of heme (COFe to COFeN5C14). The filled back-bonding state is found to be strongly influenced by second nearest neighbor atoms. By use of symmetry orbitals we have resolved the Fe 3d orbitals into the T2g and Eg representations of the Oh point group and find the former states to be occupied whereas the latter are unoccupied. The difference in occupancy is reduced when the CO ligand is removed which also causes an increased density of states at the Fermi level, i.e., the highest occupied and lowest unoccupied orbitals. Possible correlations between our data and experimental results are discussed for heme proteins as well as for metal surfaces.
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| 6. |
- Schmidt-May, Alice F., 1988-, et al.
(författare)
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State-resolved mutual neutralization of 16O+ with 1H− and 2H− at collision energies below 100 meV
- 2024
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - 2469-9926 .- 2469-9934. ; 109:5
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Tidskriftsartikel (refereegranskat)abstract
- We measured the product-state distribution and its dependence on the hydrogen isotope for the mutual neutralization between 16O+ and 1,2H− at the double electrostatic ion-beam storage ring DESIREE for center-of-mass collision energies below 100 meV. We find at least six product channels into ground-state hydrogen and oxygen in different excited states. The majority of oxygen products populate terms corresponding to 2?22?3(4?∘)4? with 5S∘ as the main reaction product. We also observe product channels into terms corresponding to 2?22?3(4?)3?. Collisions with the heavier hydrogen isotope yield a branching into these lower excited states smaller than collisions with 1H−. The observed reaction products agree with the theoretical predictions. The detailed branching fractions, however, differ between the theoretical results, and none of them fully agree with the experiment.
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| 7. |
- Wang, Li-San, et al.
(författare)
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Rarity of the Alzheimer Disease-Protective APP A673T Variant in the United States.
- 2015
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Ingår i: JAMA neurology. - : American Medical Association (AMA). - 2168-6157 .- 2168-6149. ; 72:2
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Tidskriftsartikel (refereegranskat)abstract
- Recently, a rare variant in the amyloid precursor protein gene (APP) was described in a population from Iceland. This variant, in which alanine is replaced by threonine at position 673 (A673T), appears to protect against late-onset Alzheimer disease (AD). We evaluated the frequency of this variant in AD cases and cognitively normal controls to determine whether this variant will significantly contribute to risk assessment in individuals in the United States.
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| 8. |
- Zhou, XP, et al.
(författare)
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Non-coding variability at the APOE locus contributes to the Alzheimer's risk
- 2019
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 3310-
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Tidskriftsartikel (refereegranskat)abstract
- Alzheimer’s disease (AD) is a leading cause of mortality in the elderly. While the coding change of APOE-ε4 is a key risk factor for late-onset AD and has been believed to be the only risk factor in the APOE locus, it does not fully explain the risk effect conferred by the locus. Here, we report the identification of AD causal variants in PVRL2 and APOC1 regions in proximity to APOE and define common risk haplotypes independent of APOE-ε4 coding change. These risk haplotypes are associated with changes of AD-related endophenotypes including cognitive performance, and altered expression of APOE and its nearby genes in the human brain and blood. High-throughput genome-wide chromosome conformation capture analysis further supports the roles of these risk haplotypes in modulating chromatin states and gene expression in the brain. Our findings provide compelling evidence for additional risk factors in the APOE locus that contribute to AD pathogenesis.
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| 9. |
- Bakhit, Babak, 1983-
(författare)
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Multifunctional Transition-metal Diboride Coatings Synthesized by Magnetron sputtering with Synchronized Metal-ion Irradiation
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Refractory transition-metal diborides (TMB2), classified as ultra-high temperature ceramics, are promising materials for extreme thermal and chemical environments. There is a growing demand for employing TMB2 in high-temperature electrodes, advanced nuclear fission reactors, molten metal containment, refractory crucibles, thermocouple protection tubes in steel baths and aluminum reduction cells, reinforcement fibers, solar power, aerospace, and armor applications. Magnetron-sputter-deposited TMB2 have recently received increasing attention as the next class of hard ceramic protective thin films. These layers usually crystallize in a hexagonal AlB2 crystal structure (P6/mmm, SG-191) in which B atoms form graphite-like honeycomb sheets between hexagonal-close-packed TM layers. The strong covalent bonding between TM and B atoms as well as within the honeycomb B sheets provides high melting temperature, hardness, and stiffness, while metallic bonding within TM layers results in good electrical and thermal conductivities. However, sputter-deposited TMB2 films suffer from several critical issues such as boron overstoichiometry, high brittleness, and low oxidation resistance. All of these aspects are addressed in the thesis.In Paper 1, the common issue with sputter-deposited diboride thin films, i.e. the presence of excess B, is resolved by using high power impulse magnetron sputtering (HiPIMS). The B/Ti ratio in TiBx films, used as a model materials system, is controllably varied from 2.08 to 1.83 by adjusting the HiPIMS pulse length ton, while maintaining the average power and pulse frequency constant. As a result, the peak current density increases from 0.27 to 0.88 A/cm2, which leads to an increased gas rarefaction and, hence, higher metal-ion densities in the plasma. Film growth becomes then increasingly controlled by ionized target atoms, rather than neutral species. Since sputter-ejected Ti atoms have a higher probability of being ionized than B atoms, due to their lower first-ionization potential and larger ionization cross-section, the B/Ti ratio in the films decreases a function of target peak current.While TM diborides are inherently hard, that alone is not sufficient to prevent failure in applications involving high stresses, as hardness is typically accompanied by brittleness. In order to avoid brittle cracking, thin films must be both hard and relatively ductile, which is referred to as high toughness. In Paper 2, it is demonstrated that Zr1-xTaxBy thin films grown by hybrid high-power impulse and DC magnetron co-sputtering (Ta-HiPIMS/ZrB2-DCMS) with x ≥ 0.2 are not only hard, but also tough. The films with x ≥ 0.2 show a self-organized columnar core/shell nanostructure (see Paper 3), in which crystalline hexagonal Zr-rich stoichiometric Zr1-xTaxB2 cores are surrounded by narrow dense, disordered Ta-rich shells that are B-deficient.The disordered shells have the structural characteristics of metallic-glass thin films, which exhibit both high strength and toughness. Hence, such a nanostructure combines the benefits of crystalline diboride nanocolumns, providing the high hardness, with the dense metallic-glasslike shells, which give rise to enhanced toughness.The mechanical properties of Zr1-xTaxBy thin films annealed in Ar atmosphere are studied as a function of annealing temperature Ta up to 1200 °C in Paper 4. In-situ and ex-situ nanoindentation analyses reveal that all films undergo age hardening up to Ta = 800 °C, with the highest hardness achieved for Zr0.8Ta0.2B1.8 (45.5±1.0 GPa). The age hardening, which occurs without any phase separation or decomposition, can be explained by point-defect recovery that enhances chemical bond density. Although hardness decreases at Ta > 800 °C due mainly to recrystallization, column coarsening, and planar defect annihilation, all layers show hardness values above 34 GPa over the entire Ta range.The oxidation resistance of TiBx thin films is addressed in Paper 5. In general, TMB2 suffer from rapid high-temperature oxidation, which is a critical issue for many applications. In this study, it is demonstrated that alloying the films with Al significantly increases the oxidation resistance with only a slight decrease in hardness. Contrary to bulk TiB2 synthesized by powder metallurgy processes, the oxidation products of TiB2 thin films do not contain the B2O3 oxide scale, which is usually observed below 1000 °C in air, and merely consists of a TiO2 phase. The enhanced oxidation resistance is attributed to the formation of a dense, protective Al-containing oxide scale, which considerably decreases the oxygen diffusion rate by suppressing the oxidecrystallites coarsening.To realize the goal of fully multifunctional diborides, Zr1-xCrxBy thin films grown by hybrid Cr-HiPIMS/ZrB2-DCMS co-sputtering are studied in Paper 6. These layers exhibit a unique combination of high hardness, toughness, wear, oxidation, and corrosion resistance.The last paper (Paper 7) addresses the issue of efficient energy and resource consumption in industrial processes, which United Nations defines as one of the sustainable development goals. The idea here is to replace the conventionally used thermal-energy flux from resistive heaters with the irradiation by high mass metal ions (Hf+), which results in more efficient energy transfer to the deposited layer. We deposited Ti0.67Hf0.33B1.7 films using hybrid HfB2-HiPIMS/TiB2-DCMS co-sputtering at substrate temperature not exceeding 100 °C. Results reveal that dense layers can be achieved with high hardness values (> 40 GPa) even though no external substrate heating was used during the process.
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| 10. |
- Barklem, Paul, et al.
(författare)
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Mutual Neutralization in Li++H−/D− and Na++H−/D− Collisions : Implications of Experimental Results for Non-LTE Modeling of Stellar Spectra
- 2021
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 908:2
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Tidskriftsartikel (refereegranskat)abstract
- Advances in merged-beams instruments have allowed experimental studies of the mutual neutralization (MN) processes in collisions of both Li+ and Na+ ions with D− at energies below 1 eV. These experimental results place constraints on theoretical predictions of MN processes of Li+ and Na+ with H−, important for non-LTE modeling of Li and Na spectra in late-type stars. We compare experimental results with calculations for methods typically used to calculate MN processes, namely the full quantum (FQ) approach, and asymptotic model approaches based on the linear combination of atomic orbitals (LCAO) and semiempirical (SE) methods for deriving couplings. It is found that FQ calculations compare best overall with the experiments, followed by the LCAO, and the SE approaches. The experimental results together with the theoretical calculations, allow us to investigate the effects on modeled spectra and derived abundances and their uncertainties arising from uncertainties in the MN rates. Numerical experiments in a large grid of 1D model atmospheres, and a smaller set of 3D models, indicate that neglect of MN can lead to abundance errors of up to 0.1 dex (26%) for Li at low metallicity, and 0.2 dex (58%) for Na at high metallicity, while the uncertainties in the relevant MN rates as constrained by experiments correspond to uncertainties in abundances of much less than 0.01 dex (2%). This agreement for simple atoms gives confidence in the FQ, LCAO, and SE model approaches to be able to predict MN with the accuracy required for non-LTE modeling in stellar atmospheres.
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