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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. |
- Huang, Ningdong, et al.
(författare)
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Microscopic Probing of the Size Dependence in Hydrophobic Solvation
- 2012
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 136:7, s. 074507-
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Tidskriftsartikel (refereegranskat)abstract
- A dependence on solute size of the hydrophobic effect has been proposed based on theory and simulations, such that small apolar solutes leave the hydrogen (H-) bonding network in water intact or even strengthened, whereas hydration of larger, nanometer-sized apolar solutes breaks hydrogen bonds and creates a liquid-vapor-like interface around the solutes. Here we report the direct experimental microscopic observation of the small-to-large crossover behavior of hydrophobic effects in aqueous solutions of amphiphilic tetraalkyl-ammonium (CnH2n+1)4N + (TAA) cations with increased side chain length by probing the H-bonding network in water through O K-edge x-ray absorption spectroscopy and the solute-solute interaction using small angle x-ray scattering. These results open for unique experimental opportunities to investigate hydrophobic effects for a range of important processes in chemistry and biology.We report small angle x-ray scattering data demonstrating the direct experimental microscopic observation of the small-to-large crossover behavior of hydrophobic effects in hydrophobic solvation. By increasing the side chain length of amphiphilic tetraalkyl-ammonium (CnH2n+1)4N+ (R4N+) cations in aqueous solution we observe diffraction peaks indicating association between cations at a solute size between 4.4 and 5 Å, which show temperature dependence dominated by hydrophobic attraction. Using O K-edge x-ray absorption we show that small solutes affect hydrogen bonding in water similar to a temperature decrease, while large solutes affect water similar to a temperature increase. Molecular dynamics simulations support, and provide further insight into, the origin of the experimental observations.
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| 4. |
- Huang, Ningdong, et al.
(författare)
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X-ray Raman scattering provides evidence for interfacial acetonitrile-water dipole interactions in aqueous solutions
- 2011
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 135:16, s. 164509-
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Tidskriftsartikel (refereegranskat)abstract
- Aqueous solutions of acetonitrile (MeCN) have been studied with oxygen K-edge x-ray Raman scattering (XRS) which is found to be sensitive to the interaction between water and MeCN. The changes in the XRS spectra can be attributed to water directly interacting with MeCN and are reproduced by density functional theory calculations on small clusters of water and MeCN. The dominant structural arrangement features dipole interaction instead of H-bonds between the two species as revealed by the XRS spectra combined with spectrum calculations. Small-angle x-ray scattering shows the largest heterogeneity for a MeCN to water ratio of 0.4 in agreement with earlier small-angle neutron scattering data.
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| 5. |
- Chen, Chen, et al.
(författare)
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Long-range ion-water and ion-ion interactions in aqueous solutions
- 2015
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 17:13, s. 8427-8430
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Tidskriftsartikel (refereegranskat)abstract
- Using small-angle X-ray scattering (SAXS), we obtained direct experimental evidence on the structure of hydrated polyatomic anions, with hydration effects starkly different from those of cations (J. Chem. Phys., 2011, 134, 064513). We propose that the size and charge density of the naked ions do not sufficiently account for the differences in the SAXS curves. For cations, the ion-ion contribution gives a prominent first-order diffraction peak, whereas for anions, the low-Q enhancement in the SAXS curves indicates density inhomogeneities as a result of ion-water interactions.
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| 6. |
- Chen, Chen, et al.
(författare)
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Solvation structures of protons and hydroxide ions in water
- 2013
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 138:15, s. 154506-
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Tidskriftsartikel (refereegranskat)abstract
- X-ray Raman spectroscopy (XRS) combined with small-angle x-ray scattering (SAXS) were used to study aqueous solutions of HCl and NaOH. Hydrated structures of H+ and OH- are not simple mirror images of each other. While both ions have been shown to strengthen local hydrogen bonds in the hydration shell as indicated by XRS, SAXS suggests that H+ and OH- have qualitatively different long-range effects. The SAXS structure factor of HCl (aq) closely resembles that of pure water, while NaOH (aq) behaves similar to NaF (aq). We propose that protons only locally enhance hydrogen bonds while hydroxide ions induce tetrahedrality in the overall hydrogen bond network of water.
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| 7. |
- Cheng, Anying, et al.
(författare)
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Diagnostic performance of initial blood urea nitrogen combined with D-dimer levels for predicting in-hospital mortality in COVID-19 patients
- 2020
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Ingår i: International Journal of Antimicrobial Agents. - : ELSEVIER. - 0924-8579 .- 1872-7913. ; 56:3
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Tidskriftsartikel (refereegranskat)abstract
- The crude mortality rate in critical pneumonia cases with coronavirus disease 2019 (COVID-19) reaches 49%. This study aimed to test whether levels of blood urea nitrogen (BUN) in combination with D-dimer were predictors of in-hospital mortality in COVID-19 patients. The clinical characteristics of 305 COVID19 patients were analysed and were compared between the survivor and non-survivor groups. Of the 305 patients, 85 (27.9%) died and 220 (72.1%) were discharged from hospital. Compared with discharged cases, non-survivor cases were older and their BUN and D-dimer levels were significantly higher ( P < 0.0 0 01). Least absolute shrinkage and selection operator (LASSO) and multivariable Cox regression analyses identified BUN and D-dimer levels as independent risk factors for poor prognosis. Kaplan-Meier analysis showed that elevated levels of BUN and D-dimer were associated with increased mortality (logrank, P 0.0 0 01). The area under the curve for BUN combined with D-dimer was 0.94 (95% CI 0.90-0.97), with a sensitivity of 85% and specificity of 91%. Based on BUN and D-dimer levels on admission, a nomogram model was developed that showed good discrimination, with a concordance index of 0.94. Together, initial BUN and D-dimer levels were associated with mortality in COVID-19 patients. The combination of BUN 4.6 mmol/L and D-dimer > 0.845 mu g/mL appears to identify patients at high risk of in-hospital mortality, therefore it may prove to be a powerful risk assessment tool for severe COVID-19 patients. (c) 2020 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.
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| 8. |
- Huang, Congcong, et al.
(författare)
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Increasing correlation length in bulk supercooled H2O, D2O and NaCl solution determined from small angle x-ray scattering
- 2010
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 133:13, s. 134504-
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Tidskriftsartikel (refereegranskat)abstract
- Using small angle x-ray scattering, we find that the correlation length of bulk liq. water shows a steep increase as temp. decreases at subzero temps. (supercooling) and that it can, similar to the thermodn. response functions, be fitted to a power law. This indicates that the anomalous properties of water are attributable to fluctuations between low- and high-d. regions with rapidly growing av. size upon supercooling. The substitution of H2O with D2O, as well as the addn. of NaCl salt, leads to substantial changes of the power law behavior of the correlation length. Our results are consistent with the proposed existence of a liq.-liq. crit. point in the deeply supercooled region but do not exclude a singularity-free model
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| 9. |
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| 10. |
- Huang, Congcong, et al.
(författare)
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Wide-angle X-ray diffraction and molecular dynamics study of medium-range order in ambient and hot water
- 2011
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 13:44, s. 19997-20007
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Tidskriftsartikel (refereegranskat)abstract
- We have developed wide-angle X-ray diffraction measurements with high energy-resolution and accuracy to study water structure at three different temperatures (7, 25 and 66 degrees C) under normal pressure. Using a spherically curved Ge crystal an energy resolution better than 15 eV has been achieved which eliminates influence from Compton scattering. The high quality of the data allows for a reliable Fourier transform of the experimental data resolving shell structure out to similar to 12 angstrom, i.e. 5 hydration shells. Large-scale molecular dynamics (MD) simulations using the TIP4P/2005 force-field reproduce excellently the experimental shell-structure in the range 4-12 angstrom although less agreement is seen for the first peak in the intermolecular pair-correlation function (PCF). The Shiratani-Sasai Local Structure Index [J. Chem. Phys. 104, 7671 (1996)] identifies a tetrahedral minority giving the intermediate-range oscillations in the O-O PCF and a disordered majority providing a more featureless background in this range. The current study supports the proposal that the structure of liquid water, even at high temperatures, can be described in terms of a two-state fluctuation model involving local structures related to the high-density and low-density forms of liquid water postulated in the liquid-liquid phase transition hypothesis.
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