| 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. |
- Yang, Kunpeng, et al.
(författare)
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North Atlantic Ocean–Originated Multicentennial Oscillation of the AMOC : A Coupled Model Study
- 2024
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Ingår i: Journal of Climate. - 0894-8755 .- 1520-0442. ; 37:9, s. 2789-2807
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Tidskriftsartikel (refereegranskat)abstract
- Using a CESM1 control simulation, we conduct a follow-up study to advance our earlier theoretical research on the multicentennial oscillation (MCO) of the Atlantic meridional overturning circulation (AMOC). The modeled AMOC MCO primarily arises from internal oceanic processes in the North Atlantic, potentially representing a North Atlantic Ocean–originated mode of AMOC multicentennial variability (MCV) in reality. Specifically, this AMOC MCO is mainly driven by salinity variation in the subpolar upper North Atlantic, which dominates local density variation. Salinity anomaly in the subpolar upper ocean is enhanced by the well-known positive salinity advection feedback that is realized through anomalous advection in the subtropical to subpolar upper ocean. Meanwhile, mean advection moves salinity anomaly in the subtropical intermediate ocean northward, weakening the subpolar upper salinity anomaly and leading to its phase change. The salinity anomalies have a clear three-dimensional life cycle around the North Atlantic. The mechanism and time scale of the modeled AMOC MCO are consistent with our earlier theoretical studies. In the theoretical model, artificially deactivating either the anomalous or mean advection in the AMOC upper branch prevents it from exhibiting AMOC MCO, underscoring the indispensability of both the anomalous and mean advections in this North Atlantic Ocean–originated AMOC MCO. In our coupled model simulation, the South Atlantic and Southern Oceans do not exhibit variabilities synchronous with the AMOC MCO; the Arctic Ocean’s contribution to the subpolar upper salinity anomaly is much weaker than the North Atlantic. Hence, this North Atlantic Ocean–originated AMOC MCO is distinct from the previously proposed Southern Ocean–originated and Arctic Ocean–originated AMOC MCOs.
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| 3. |
- Li, Cai, et al.
(författare)
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Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment
- 2014
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Ingår i: GigaScience. - 2047-217X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adelie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. Results: Phylogenetic dating suggests that early penguins arose similar to 60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from similar to 1 million years ago to similar to 100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. Conclusions: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
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| 4. |
- Yang, Haijun, et al.
(författare)
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多百年际气候变率 : 观测、理论与模拟研究 [Multi-centennial climate variability: Observational, theoretical and modeling studies]
- 2023
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Ingår i: Chinese Science Bulletin. - 0023-074X .- 2095-9419. ; 68:16, s. 2037-2045
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Tidskriftsartikel (refereegranskat)abstract
- Research using long-term proxy data suggests the existence of multi-centennial climate variability in the Earth’s climate system. Its origin and mechanism have been bewildering for climatologists and archaeologists for a long time. Considering that the variation of external forcing of the Earth’ climate was relatively small from the mid-Holocene to the pre-industrial time, it is important to investigate the role of internal natural oscillation of the climate system during this period. The Atlantic meridional overturning circulation (AMOC) is thought to be the first candidate for such multi-centennial timescale variability. It is thus critical to investigate systematically the connection between the AMOC and the Earth climate system at this timescale. From the mid-Holocene to the pre-industrial time, the human civilization experienced rapid development. Historical documents in China suggest that in the past 2000 years, the historical climate in China had a low-frequency variation with 200–300 year period, which might have affected the ancient Chinese civilization. The multi-centennial variability of the AMOC may have played a role in the vax and vane of the human civilization.Currently, there is a lack of in-depth studies on the multi-centennial variability of the AMOC. This is mainly due to the following factors. First, the time period of modern instrumental observations is less than 200 years, which is not long enough to confirm the existence of the multi-centennial climate variability. Second, there is a lack of a well-recognized theory that can account for the multi-centennial variability of the AMOC. Third, it is much easier for a researcher to study the Earth climate change due to external forcing than to study the internal variability of the Earth climate system under a stable external forcing, particularly at this long timescale.Several coupled Earth climate system models have simulated the multi-centennial variability of the AMOC. However, the results from both coupled models and proxy data include comprehensive factors. To fundamentally understand the multi-centennial climate variability, a simple theoretical model is needed. Unfortunately, there is a lack of theoretical studies on the internal multi-centennial variability under the background of stable climate.In this work, we systematically review the current studies on multi-centennial climate variability from observational, theoretical and coupled modeling aspects. We hope that by proposing innovative theory and creative climate modeling approach, we can identify the intrinsic mode of multi-centennial climate variability, picture its spatial pattern, decipher the origin of its timescale, and reveal its internal mechanism. The outcome of these studies will help us understand deeply the wax and wane of the human civilization during the past several thousand years. It will also be of great significance for a better prediction of the long-term trend of future climate change.
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| 5. |
- Zhang, Zebin, et al.
(författare)
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Whole-genome resequencing reveals signatures of selection and timing of duck domestication
- 2018
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Ingår i: GigaScience. - : OXFORD UNIV PRESS. - 2047-217X. ; 7:4
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Tidskriftsartikel (refereegranskat)abstract
- Background: The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change. Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual. Results: Our population and demographic analyses indicate a complex history of domestication, with early selection for separate meat and egg lineages. Genomic comparison of wild to domesticated populations suggests that genes that affect brain and neuronal development have undergone strong positive selection during domestication. Our F-ST analysis also indicates that the duck white plumage is the result of selection at the melanogenesis-associated transcription factor locus. Conclusions: Our results advance the understanding of animal domestication and selection for complex phenotypic traits.
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| 6. |
- Döscher, Ralf, et al.
(författare)
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The EC-Earth3 Earth system model for the Coupled Model Intercomparison Project 6
- 2022
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Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 15:7, s. 2973-3020
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Tidskriftsartikel (refereegranskat)abstract
- The Earth system model EC-Earth3 for contributions to CMIP6 is documented here, with its flexible coupling framework, major model configurations, a methodology for ensuring the simulations are comparable across different high-performance computing (HPC) systems, and with the physical performance of base configurations over the historical period. The variety of possible configurations and sub-models reflects the broad interests in the EC-Earth community. EC-Earth3 key performance metrics demonstrate physical behavior and biases well within the frame known from recent CMIP models. With improved physical and dynamic features, new Earth system model (ESM) components, community tools, and largely improved physical performance compared to the CMIP5 version, EC-Earth3 represents a clear step forward for the only European community ESM. We demonstrate here that EC-Earth3 is suited for a range of tasks in CMIP6 and beyond.
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| 7. |
- Gravgaard Askjær, Thomas, et al.
(författare)
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Multi-centennial Holocene climate variability in proxy records and transient model simulations
- 2022
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Ingår i: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 296
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Tidskriftsartikel (refereegranskat)abstract
- Variability on centennial to multi-centennial timescales is mentioned as a feature in reconstructions of the Holocene climate. As more long transient model simulations with complex climate models become available and efforts have been made to compile large proxy databases, there is now a unique opportunity to study multi-centennial variability with greater detail and a large amount of data than earlier. This paper presents a spectral analysis of transient Holocene simulations from 9 models and 120 proxy records to find the common signals related to oscillation periods and geographic dependencies and discuss the implications for the potential driving mechanisms. Multi-centennial variability is significant in most proxy records, with the dominant oscillation periods around 120–130 years and an average of 240 years. Spectra of model-based global mean temperature (GMT) agree well with proxy evidence with significant multi-centennial variability in all simulations with the dominant oscillation periods around 120–150 years. It indicates a comparatively good agreement between model and proxy data. A lack of latitudinal dependencies in terms of oscillation period is found in both the model and proxy data. However, all model simulations have the highest spectral density distributed over the Northern hemisphere high latitudes, which could indicate a particular variability sensitivity or potential driving mechanisms in this region. Five models also have differentiated forcings simulations with various combinations of forcing agents. Significant multi-centennial variability with oscillation periods between 100 and 200 years is found in all forcing scenarios, including those with only orbital forcing. The different forcings induce some variability in the system. Yet, none appear to be the predominant driver based on the spectral analysis. Solar irradiance has long been hypothesized to be a primary driver of multi-centennial variability. However, all the simulations without this forcing have shown significant multi-centennial variability. The results then indicate that internal mechanisms operate on multi-centennial timescales, and the North Atlantic-Arctic is a region of interest for this aspect.
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| 8. |
- Cao, Ning, 1987-, et al.
(författare)
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The role of internal feedbacks in sustaining multi-centennial variability of the Atlantic Meridional Overturning Circulation revealed by EC-Earth3-LR simulations
- 2023
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Ingår i: Earth and Planetary Science Letters. - 0012-821X .- 1385-013X. ; 621
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Tidskriftsartikel (refereegranskat)abstract
- A significant multi-centennial climate variability with a distinct peak at approximately 200 years is observed in a pre-industrial (PI) control simulation using the EC-Earth3-LR climate model. This oscillation originates predominately from the North Atlantic and displays a strong association with the Atlantic Meridional Overturning Circulation (AMOC). Our study identifies the interplay between salinity advection feedback and vertical mixing in the subpolar North Atlantic as key roles in providing the continues internal energy source to maintain this multi-centennial oscillation. The perturbation flow of mean subtropical-subpolar salinity gradients serves as positive feedback to sustain the AMOC anomaly, while the mean advection of salinity anomalies and the vertical mixing or convection acts as negative feedback, constraining the AMOC anomaly. Notably, this low-frequency variability persists even in a warmer climate with weakened AMOC, emphasizing the robustness of the salinity advection feedback mechanism.
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| 9. |
- Brierley, Chris M., et al.
(författare)
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Large-scale features and evaluation of the PMIP4-CMIP6 midHolocene simulations
- 2020
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Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 16:5, s. 1847-1872
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Tidskriftsartikel (refereegranskat)abstract
- The mid-Holocene (6000 years ago) is a standard time period for the evaluation of the simulated response of global climate models using palaeoclimate reconstructions. The latest mid-Holocene simulations are a palaeoclimate entry card for the Palaeoclimate Model Intercomparison Project (PMIP4) component of the current phase of the Coupled Model Intercomparison Project (CMIP6) - hereafter referred to as PMIP4-CMIP6. Here we provide an initial analysis and evaluation of the results of the experiment for the mid-Holocene. We show that state-of-the-art models produce climate changes that are broadly consistent with theory and observations, including increased summer warming of the Northern Hemisphere and associated shifts in tropical rainfall. Many features of the PMIP4-CMIP6 simulations were present in the previous generation (PMIP3-CMIP5) of simulations. The PMIP4-CMIP6 ensemble for the mid-Holocene has a global mean temperature change of -0.3 K, which is -0.2K cooler than the PMIP3-CMIP5 simulations predominantly as a result of the prescription of realistic greenhouse gas concentrations in PMIP4-CMIP6. Biases in the magnitude and the sign of regional responses identified in PMIP3-CMIP5, such as the amplification of the northern African monsoon, precipitation changes over Europe, and simulated aridity in mid-Eurasia, are still present in the PMIP4-CMIP6 simulations. Despite these issues, PMIP4-CMIP6 and the mid-Holocene provide an opportunity both for quantitative evaluation and derivation of emergent constraints on the hydrological cycle, feedback strength, and potentially climate sensitivity.
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| 10. |
- Chen, Qiman, et al.
(författare)
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Flexible Service Chain Mapping in Server-Centric Optical Datacenter Networks
- 2018
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Ingår i: 2018 ASIA COMMUNICATIONS AND PHOTONICS CONFERENCE (ACP). - : IEEE. - 9781538661581
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Konferensbidrag (refereegranskat)abstract
- We investigate flexible service chain mapping in server-centric optical terconnects, handling virtual network function (VNF) dependency operly. Blocking probability decreases by a factor of 10 when signing multiple VNFs in the same server is allowed.
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