| 1. |
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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. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 5. |
- Palmer, Nicholette D, et al.
(författare)
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A genome-wide association search for type 2 diabetes genes in African Americans.
- 2012
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Ingår i: PloS one. - San Francisco : Public Library of Science (PLoS). - 1932-6203. ; 7:1, s. e29202-
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Tidskriftsartikel (refereegranskat)abstract
- African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.
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| 6. |
- Wang, Haidong, et al.
(författare)
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Global, regional, and national life expectancy, all-cause mortality, and cause-specific mortality for 249 causes of death, 1980-2015 : a systematic analysis for the Global Burden of Disease Study 2015
- 2016
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Ingår i: The Lancet. - 0140-6736 .- 1474-547X. ; 388:10053, s. 1459-1544
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Improving survival and extending the longevity of life for all populations requires timely, robust evidence on local mortality levels and trends. The Global Burden of Disease 2015 Study (GBD 2015) provides a comprehensive assessment of all-cause and cause-specific mortality for 249 causes in 195 countries and territories from 1980 to 2015. These results informed an in-depth investigation of observed and expected mortality patterns based on sociodemographic measures.METHODS: We estimated all-cause mortality by age, sex, geography, and year using an improved analytical approach originally developed for GBD 2013 and GBD 2010. Improvements included refinements to the estimation of child and adult mortality and corresponding uncertainty, parameter selection for under-5 mortality synthesis by spatiotemporal Gaussian process regression, and sibling history data processing. We also expanded the database of vital registration, survey, and census data to 14 294 geography-year datapoints. For GBD 2015, eight causes, including Ebola virus disease, were added to the previous GBD cause list for mortality. We used six modelling approaches to assess cause-specific mortality, with the Cause of Death Ensemble Model (CODEm) generating estimates for most causes. We used a series of novel analyses to systematically quantify the drivers of trends in mortality across geographies. First, we assessed observed and expected levels and trends of cause-specific mortality as they relate to the Socio-demographic Index (SDI), a summary indicator derived from measures of income per capita, educational attainment, and fertility. Second, we examined factors affecting total mortality patterns through a series of counterfactual scenarios, testing the magnitude by which population growth, population age structures, and epidemiological changes contributed to shifts in mortality. Finally, we attributed changes in life expectancy to changes in cause of death. We documented each step of the GBD 2015 estimation processes, as well as data sources, in accordance with Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER).FINDINGS: Globally, life expectancy from birth increased from 61·7 years (95% uncertainty interval 61·4-61·9) in 1980 to 71·8 years (71·5-72·2) in 2015. Several countries in sub-Saharan Africa had very large gains in life expectancy from 2005 to 2015, rebounding from an era of exceedingly high loss of life due to HIV/AIDS. At the same time, many geographies saw life expectancy stagnate or decline, particularly for men and in countries with rising mortality from war or interpersonal violence. From 2005 to 2015, male life expectancy in Syria dropped by 11·3 years (3·7-17·4), to 62·6 years (56·5-70·2). Total deaths increased by 4·1% (2·6-5·6) from 2005 to 2015, rising to 55·8 million (54·9 million to 56·6 million) in 2015, but age-standardised death rates fell by 17·0% (15·8-18·1) during this time, underscoring changes in population growth and shifts in global age structures. The result was similar for non-communicable diseases (NCDs), with total deaths from these causes increasing by 14·1% (12·6-16·0) to 39·8 million (39·2 million to 40·5 million) in 2015, whereas age-standardised rates decreased by 13·1% (11·9-14·3). Globally, this mortality pattern emerged for several NCDs, including several types of cancer, ischaemic heart disease, cirrhosis, and Alzheimer's disease and other dementias. By contrast, both total deaths and age-standardised death rates due to communicable, maternal, neonatal, and nutritional conditions significantly declined from 2005 to 2015, gains largely attributable to decreases in mortality rates due to HIV/AIDS (42·1%, 39·1-44·6), malaria (43·1%, 34·7-51·8), neonatal preterm birth complications (29·8%, 24·8-34·9), and maternal disorders (29·1%, 19·3-37·1). Progress was slower for several causes, such as lower respiratory infections and nutritional deficiencies, whereas deaths increased for others, including dengue and drug use disorders. Age-standardised death rates due to injuries significantly declined from 2005 to 2015, yet interpersonal violence and war claimed increasingly more lives in some regions, particularly in the Middle East. In 2015, rotaviral enteritis (rotavirus) was the leading cause of under-5 deaths due to diarrhoea (146 000 deaths, 118 000-183 000) and pneumococcal pneumonia was the leading cause of under-5 deaths due to lower respiratory infections (393 000 deaths, 228 000-532 000), although pathogen-specific mortality varied by region. Globally, the effects of population growth, ageing, and changes in age-standardised death rates substantially differed by cause. Our analyses on the expected associations between cause-specific mortality and SDI show the regular shifts in cause of death composition and population age structure with rising SDI. Country patterns of premature mortality (measured as years of life lost [YLLs]) and how they differ from the level expected on the basis of SDI alone revealed distinct but highly heterogeneous patterns by region and country or territory. Ischaemic heart disease, stroke, and diabetes were among the leading causes of YLLs in most regions, but in many cases, intraregional results sharply diverged for ratios of observed and expected YLLs based on SDI. Communicable, maternal, neonatal, and nutritional diseases caused the most YLLs throughout sub-Saharan Africa, with observed YLLs far exceeding expected YLLs for countries in which malaria or HIV/AIDS remained the leading causes of early death.INTERPRETATION: At the global scale, age-specific mortality has steadily improved over the past 35 years; this pattern of general progress continued in the past decade. Progress has been faster in most countries than expected on the basis of development measured by the SDI. Against this background of progress, some countries have seen falls in life expectancy, and age-standardised death rates for some causes are increasing. Despite progress in reducing age-standardised death rates, population growth and ageing mean that the number of deaths from most non-communicable causes are increasing in most countries, putting increased demands on health systems.
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| 7. |
- Borodkina, I., et al.
(författare)
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An analytical expression for ion velocities at the wall including the sheath electric field and surface biasing for erosion modeling at JET ILW
- 2017
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Ingår i: Nuclear Materials and Energy. - : Elsevier. - 2352-1791. ; 12, s. 341-345
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Tidskriftsartikel (refereegranskat)abstract
- For simulation of plasma-facing component erosion in fusion experiments, an analytical expression for the ion velocity just before the surface impact including the local electric field and an optional surface biasing effect is suggested. Energy and angular impact distributions and the resulting effective sputtering yields were produced for several experimental scenarios at JET ILW mostly involving PFCs exposed to an oblique magnetic field. The analytic solution has been applied as an improvement to earlier ERO modelling of localized, Be outer limiter, RF-enhanced erosion, modulated by toggling of a remote, however magnetically connected ICRH antenna. The effective W sputtering yields due to D and Be ion impact in Type-I and Type-III ELMs and inter-ELM conditions were also estimated using the analytical approach and benchmarked by spectroscopy. The intra-ELM W sputtering flux increases almost 10 times in comparison to the inter-ELM flux.
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| 8. |
- Chankina, A. V., et al.
(författare)
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Possible influence of near SOL plasma on the H-mode power threshold
- 2017
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Ingår i: Nuclear Materials and Energy. - : Elsevier. - 2352-1791. ; 12, s. 273-277
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Tidskriftsartikel (refereegranskat)abstract
- A strong effect of divertor configuration on the threshold power for the L-H transition (P-LH) was observed in recent JET experiments in the new ITER-like Wall (ILW) [1-3]. Following a series of EDGE2D-EIRENE code simulations with Be impurity and drifts a possible mechanism for the P-LH variation with the divertor geometry is proposed. Both experiment and code simulations show that in the configuration with lower neutral recycling near the outer strike point (OSP), electron temperature (T-e) peaks near the OSP prior to the L-H transition, while in the configuration with higher OSP recycling T-e peaks further out in the scrape-offlayer (SOL) and the plasma stays in the L-mode at the same input power. Code results show large positive radial electric field (E-r) in the near SOL under lower recycling conditions leading to a large E x B shear across the separatrix which may trigger earlier (at lower input power) edge turbulence suppression and lower P-LH. Suppressed T-e's at OSP in configurations with strike points on vertical targets (VT) were observed earlier and explained by a geometrical effect of neutral recycling near this particular position, whereas in configurations with strike points on horizontal targets (HT) the OSP appears to be more open for neutrals (see e.g. review paper [4]).
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| 9. |
- Eich, T., et al.
(författare)
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ELM divertor peak energy fluence scaling to ITER with data from JET, MAST and ASDEX upgrade
- 2017
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Ingår i: Nuclear Materials and Energy. - : Elsevier. - 2352-1791. ; 12, s. 84-90
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Tidskriftsartikel (refereegranskat)abstract
- A newly established scaling of the ELM energy fluence using dedicated data sets from JET operation with CFC & ILW plasma facing components (PFCs), ASDEX Upgrade (AUG) operation with both CFC and full-W PFCs and MAST with CFC walls has been generated. The scaling reveals an approximately linear dependence of the peak ELM energy with the pedestal top electron pressure and with the minor radius; a square root dependence is seen on the relative ELM loss energy. The result of this scaling gives a range in parallel peak ELM energy fluence of 10-30 MJm(-2) for ITER Q = 10 operation and 2.5-7.5 MJm(-2) for intermediate ITER operation at 7.5 MA and 2.65 T. These latter numbers are calculated using a numerical regression (epsilon(II) = 0.28 MJ/m(2) n(e)(0.75) T-e(1) Delta E-ELM(0.5) R-1(geo)). A simple model for ELM induced thermal load is introduced, resulting in an expression for the ELM energy fluence of epsilon(II) congruent to 6 pi p(e) R-geo q(edge). The relative ELM loss energy in the data is between 2-10% and the ELM energy fluence varies within a range of 10(0.5) similar to 3 consistently for each individual device. The so far analysed power load database for ELM mitigation experiments from JET-EFCC and Kicks, MAST-RMP and AUG-RMP operation are found to be consistent with both the scaling and the introduced model, ie not showing a further reduction with respect to their pedestal pressure. The extrapolated ELM energy fluencies are compared to material limits in ITER and found to be of concern.
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| 10. |
- Guillemaut, C., et al.
(författare)
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Main chamber wall plasma loads in JET-ITER-like wall at high radiated fraction
- 2017
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Ingår i: Nuclear Materials and Energy. - : Elsevier. - 2352-1791. ; 12, s. 234-240
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Tidskriftsartikel (refereegranskat)abstract
- Future tokamak reactors of conventional design will require high levels of exhaust power dissipation (more than 90% of the input power) if power densities at the divertor targets are to remain compatible with active cooling. Impurity seeded H-mode discharges in JET-ITER-like Wall (ILW) have reached a maximum radiative fraction (F-rad) of similar to 75%. Divertor Langmuir probe (LP) measurements in these discharges indicate, however, that less than similar to 3% of the thermal plasma power reaches the targets, suggesting a missing channel for power loss. This paper presents experimental evidence from limiter LP for enhanced cross-field particle fluxes on the main chamber walls at high F-rad. In H-mode nitrogen-seeded discharges with F-rad increasing from similar to 30% to up to similar to 75%, the main chamber wall particle fluence rises by a factor similar to 3 while the divertor plasma fluence drops by one order of magnitude. Contribution of main chamber wall particle losses to detachment, as suggested by EDGE2D-EIRENE modeling, is not sufficient to explain the magnitude of the observed divertor fluence reduction. An intermediate detached case obtained at F-rad similar to 60% with neon seeding is also presented. Heat loads were measured using the main chamber wall thermocouples. Comparison between thermocouple and bolometry measurements shows that the fraction of the input power transported to the main chamber wall remains below similar to 5%, whatever the divertor detachment state is. Main chamber sputtering of beryllium by deuterium is reduced in detached conditions only on the low field side. If the fraction of power exhaust dissipated to the main chamber wall by cross-field transport in future reactors is similar to the JET-ILW levels, wall plasma power loading should not be an issue. However, other contributions such as charge exchange may be a problem.
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