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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- 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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| 4. |
- Jin, Ying-Hui, et al.
(författare)
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Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
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Ingår i: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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| 5. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.
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| 6. |
- Deng, Min, et al.
(författare)
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Genome-wide association analyses in Han Chinese identify two new susceptibility loci for amyotrophic lateral sclerosis
- 2013
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 45:6, s. 697-
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Tidskriftsartikel (refereegranskat)abstract
- To identify susceptibility genes for amyotrophic lateral sclerosis (ALS), we conducted a genome-wide association study (GWAS) in 506 individuals with sporadic ALS and 1,859 controls of Han Chinese ancestry. Ninety top SNPs suggested by the current GWAS and 6 SNPs identified by previous GWAS were analyzed in an independent cohort of 706 individuals with ALS and 1,777 controls of Han Chinese ancestry. We discovered two new susceptibility loci for ALS at 1q32 (CAMK1G, rs6703183, P-combined = 2.92 x 10(-8), odds ratio (OR) = 1.31) and 22p11 (CABIN1 and SUSD2, rs8141797, P-combined = 2.35 x 10(-9), OR = 1.52). These two loci explain 12.48% of the overall variance in disease risk in the Han Chinese population. We found no association evidence for the previously reported loci in the Han Chinese population, suggesting genetic heterogeneity of disease susceptibility for ALS between ancestry groups. Our study identifies two new susceptibility loci and suggests new pathogenic mechanisms of ALS.
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| 7. |
- Li, Qian, et al.
(författare)
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Genome-wide identification of resistance genes and cellular analysis of key gene knockout strain under 5-hydroxymethylfurfural stress in Saccharomyces cerevisiae
- 2023
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Ingår i: BMC Microbiology. - 1471-2180. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- In bioethanol production, the main by-product, 5-hydroxymethylfurfural (HMF), significantly hinders microbial fermentation. Therefore, it is crucial to explore genes related to HMF tolerance in Saccharomyces cerevisiae for enhancing the tolerance of ethanol fermentation strains. A comprehensive analysis was conducted using genome-wide deletion library scanning and SGAtools, resulting in the identification of 294 genes associated with HMF tolerance in S. cerevisiae. Further KEGG and GO enrichment analysis revealed the involvement of genes OCA1 and SIW14 in the protein phosphorylation pathway, underscoring their role in HMF tolerance. Spot test validation and subcellular structure observation demonstrated that, following a 3-h treatment with 60mM HMF, the SIW14 gene knockout strain exhibited a 12.68% increase in cells with abnormal endoplasmic reticulum (ER) and a 22.41% increase in the accumulation of reactive oxygen species compared to the BY4741 strain. These findings indicate that the SIW14 gene contributes to the protection of the ER structure within the cell and facilitates the clearance of reactive oxygen species, thereby confirming its significance as a key gene for HMF tolerance in S. cerevisiae.
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| 8. |
- Liu, Tao, et al.
(författare)
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16% efficiency all-polymer organic solar cells enabled by a finely tuned morphology via the design of ternary blend
- 2021
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Ingår i: Joule. - : CELL PRESS. - 2542-4351. ; 5:4, s. 914-930
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Tidskriftsartikel (refereegranskat)abstract
- A SUMMARY There is an urgent demand for all-polymer organic solar cells (AP-OSCs) to gain higher efficiency. Here, we successfully improve the performance to 16.09% by introducing a small amount of BN-T, a B <- N-type polymer acceptor, into the PM6:PY-IT blend. It has been found that BN-T makes the active layer, based on the PM6:PY-IT:BN-T ternary blend, more crystalline but meanwhile slightly reduces the phase separation, leading to enhancement of both exciton harvesting and charge transport. From a thermodynamic viewpoint, BN-T prefers to reside between PM6 and PY-IT, and the fraction of this fine-tunes the morphology. Besides, a significantly reduced nonradiative energy loss occurs in the ternary blend, along with the coexistence of energy and charge transfer between the two acceptors. The progressive performance facilitated by these improved properties demonstrates that AP-OSCs can possibly comparably efficient with those based on small molecule acceptors, further enhancing the competitiveness of this device type.
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| 9. |
- Lu, Xiao-Gang, et al.
(författare)
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Calculations of thermophysical properties of cubic carbides and nitrides using Debye-Grüneisen model
- 2007
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Ingår i: Acta Materialia. - : Elsevier BV. - 1359-6454 .- 1873-2453. ; 55:4, s. 1215-1226
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Tidskriftsartikel (refereegranskat)abstract
- The thermal expansivities and heat capacities of NIX (M = Ti, Zr, Hf, V, Nb, Ta; X = C, N) carbides and nitrides with NaCl structure were calculated using the Debye-Gruneisen model combined with ab initio calculations. Two different approximations for the Gruneisen parameter gamma were used in the Debye-Gruneisen model, i.e. the expressions proposed by Slater and by Dugdale and MacDonald. The thermal electronic contribution was evaluated from ab initio calculations of the electronic density of states. The calculated results were compared with CALPHAD assessments and experimental data. It was found that the calculations using the Dugdale-MacDonald gamma can account for most of the experimental data. By fitting experimental heat capacity and thermal expansivity data below the Debye temperatures, an estimation of Poisson's ratio was obtained and Young's and shear moduli were evaluated. In order to reach a reasonable agreement with experimental data, it was necessary to use the logarithmic averaged mass of the constituent atoms. The agreements between the calculated and the experimental values for the bulk and Young's moduli are generally better than the agreement for shear modulus.
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| 10. |
- Lu, Xiao-Gang, 1970-
(författare)
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Theoretical modeling of molar volume and thermal expansion
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Combination of the Calphad method and theoretical calculations provides new possibilities for the study of materials science. This work is a part of the efforts within the CCT project (Centre of Computational Thermodynamics) to combine these methods to facilitate modeling and to extend the thermodynamic databases with critically assessed volume data. In this work, the theoretical calculations refer to first-principles and Debye-Grüneisen calculations. The first-principles (i.e. ab initio) electronic structure calculations, based on the Density- Functional Theory (DFT), are capable of predicting various physical properties at 0 K, such as formation energy, volume and bulk modulus. The ab initio simulation software, VASP, was used to calculate the binding curves (i.e. equation of state at 0 K) of metallic elements, cubic carbides and nitrides. From the binding curves, the equilibrium volumes at 0 K were calculated for several metastable structures as well as stable structures. The vibrational contribution to the free energy was calculated using the Debye-Grüneisen model combined with first-principles calculations. Two different approximations for the Grüneisen parameter, γ, were used in the Debye-Grüneisen model, i.e. Slater’s and Dugdale-MacDonald’s expressions. The thermal electronic contribution was evaluated from the calculated electronic density of states. The calculated thermal expansivities for metallic elements, cubic carbides and nitrides were compared with Calphad assessments. It was found that the experimental data are within the limits of the calculations using the two approximations for γ. By fitting experimental heat capacity and thermal expansivity around Debye temperatures, we obtained optimal Poisson’s ratio values and used them to evaluate Young’s and Shear moduli. In order to reach a reasonable agreement with the experiments, it is necessary to use the logarithmic averaged mass of the constitutional atoms. The agreements between the calculations and experiments are generally better for bulk modulus and Young’s modulus than that for shear modulus. A new model describing thermodynamic properties at high pressures was implemented in Thermo-Calc. The model is based on an empirical relation between volume and isothermal bulk modulus. Pure Fe and solid MgO were assessed using this model. Solution phases will be considered in a future work to check the model for compositional dependence.
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