| 1. |
- 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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| 2. |
- 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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| 3. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 4. |
- Cheng, Yu Ting, et al.
(författare)
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Tuning atom-field interaction via phase shaping
- 2024
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Ingår i: Physical Review A. - 2469-9934 .- 2469-9926. ; 109:2
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Tidskriftsartikel (refereegranskat)abstract
- A coherent electromagnetic field can be described by its amplitude, frequency, and phase. All these properties can influence the interaction between the field and an atom. Here we demonstrate the phase shaping of microwaves that are scattered by a superconducting artificial atom coupled to the end of a semi-infinite one-dimensional transmission line. In particular, we input a weak exponentially rising pulse with phase modulation to a transmon qubit. We observe that atom-field interaction can be tuned from a nearly full interaction (interaction efficiency, i.e., amount of the field energy interacting with the atom, of 94.5 %) to effectively no interaction (interaction efficiency of 3.5 %).
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| 5. |
- Harden, Jennifer W., et al.
(författare)
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Field information links permafrost carbon to physical vulnerabilities of thawing
- 2012
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Ingår i: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 39, s. L15704-
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Tidskriftsartikel (refereegranskat)abstract
- Deep soil profiles containing permafrost (Gelisols) were characterized for organic carbon (C) and total nitrogen (N) stocks to 3 m depths. Using the Community Climate System Model (CCSM4) we calculate cumulative distributions of active layer thickness (ALT) under current and future climates. The difference in cumulative ALT distributions over time was multiplied by C and N contents of soil horizons in Gelisol suborders to calculate newly thawed C and N. Thawing ranged from 147 PgC with 10 PgN by 2050 (representative concentration pathway RCP scenario 4.5) to 436 PgC with 29 PgN by 2100 (RCP 8.5). Organic horizons that thaw are vulnerable to combustion, and all horizon types are vulnerable to shifts in hydrology and decomposition. The rates and extent of such losses are unknown and can be further constrained by linking field and modelling approaches. These changes have the potential for strong additional loading to our atmosphere, water resources, and ecosystems. Citation: Harden, J. W., et al. (2012), Field information links permafrost carbon to physical vulnerabilities of thawing, Geophys. Res. Lett., 39, L15704, doi: 10.1029/2012GL051958.
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| 6. |
- Kuo, Ping Heng, et al.
(författare)
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An integrated edge and Fog system for future communication networks
- 2018
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Ingår i: 2018 IEEE Wireless Communications and Networking Conference Workshops (WCNCW). ; , s. 338-343
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Konferensbidrag (refereegranskat)abstract
- Put together, the edge and fog form a large diverse pool of computing and networking resources from different owners that can be leveraged towards low latency applications as well as for alleviating high traffic volume in future networks including 5G and beyond. This paper sets out a framework for the integration of edge and fog computing and networking leveraging on ongoing specifications by ETSI MEC ISG and the OpenFog Consortium. It also presents the technological gaps that need to be addressed before such an integrated solution can be developed. These noticeably include challenges relating to the volatility of resources, heterogeneity of underlying technologies, virtualization of devices, and security issues. The framework presented is a Launchpad for a complete solution under development by the 5G-CORAL consortium.
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| 7. |
- Lin, Wei Ju, et al.
(författare)
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Deterministic Loading of Microwaves onto an Artificial Atom Using a Time-Reversed Waveform
- 2022
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 22:20, s. 8137-8142
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Tidskriftsartikel (refereegranskat)abstract
- Loading quantum information deterministically onto a quantum node is an important step toward a quantum network. Here, we demonstrate that coherent-state microwave photons with an optimal temporal waveform can be efficiently loaded onto a single superconducting artificial atom in a semi-infinite one-dimensional (1D) transmission-line waveguide. Using a weak coherent state (the number of photons (N) contained in the pulse ≪1) with an exponentially rising waveform, whose time constant matches the decoherence time of the artificial atom, we demonstrate a loading efficiency of 94.2% ± 0.7% from 1D semifree space to the artificial atom. The high loading efficiency is due to time-reversal symmetry: the overlap between the incoming wave and the time-reversed emitted wave is up to 97.1% ± 0.4%. Our results open up promising applications in realizing quantum networks based on waveguide quantum electrodynamics.
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| 8. |
- Mishra, Umakant, et al.
(författare)
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Spatial heterogeneity and environmental predictors of permafrost region soil organic carbon stocks
- 2021
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:9
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Tidskriftsartikel (refereegranskat)abstract
- Large stocks of soil organic carbon (SOC) have accumulated in the Northern Hemisphere permafrost region, but their current amounts and future fate remain uncertain. By analyzing dataset combining >2700 soil profiles with environmental variables in a geospatial framework, we generated spatially explicit estimates of permafrost-region SOC stocks, quantified spatial heterogeneity, and identified key environmental predictors. We estimated that Pg C are stored in the top 3 m of permafrost region soils. The greatest uncertainties occurred in circumpolar toe-slope positions and in flat areas of the Tibetan region. We found that soil wetness index and elevation are the dominant topographic controllers and surface air temperature (circumpolar region) and precipitation (Tibetan region) are significant climatic controllers of SOC stocks. Our results provide first high-resolution geospatial assessment of permafrost region SOC stocks and their relationships with environmental factors, which are crucial for modeling the response of permafrost affected soils to changing climate.
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