| 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. |
- Benson, Barbara J., et al.
(författare)
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Extreme events, trends, and variability in Northern Hemisphere lake-ice phenology (1855-2005)
- 2012
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Ingår i: Climatic Change. - : Springer Science and Business Media LLC. - 0165-0009 .- 1573-1480. ; 112:2, s. 299-323
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Tidskriftsartikel (refereegranskat)abstract
- Often extreme events, more than changes in mean conditions, have the greatest impact on the environment and human well-being. Here we examine changes in the occurrence of extremes in the timing of the annual formation and disappearance of lake ice in the Northern Hemisphere. Both changes in the mean condition and in variability around the mean condition can alter the probability of extreme events. Using long-term ice phenology data covering two periods 1855-6 to 2004-5 and 1905-6 to 2004-5 for a total of 75 lakes, we examined patterns in long-term trends and variability in the context of understanding the occurrence of extreme events. We also examined patterns in trends for a 30-year subset (1975-6 to 2004-5) of the 100-year data set. Trends for ice variables in the recent 30-year period were steeper than those in the 100- and 150-year periods, and trends in the 150-year period were steeper than in the 100-year period. Ranges of rates of change (days per decade) among time periods based on linear regression were 0.3-1.6 later for freeze, 0.5-1.9 earlier for breakup, and 0.7-4.3 shorter for duration. Mostly, standard deviation did not change, or it decreased in the 150-year and 100-year periods. During the recent 50-year period, standard deviation calculated in 10-year windows increased for all ice measures. For the 150-year and 100-year periods changes in the mean ice dates rather than changes in variability most strongly influenced the significant increases in the frequency of extreme lake ice events associated with warmer conditions and decreases in the frequency of extreme events associated with cooler conditions.
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| 3. |
- Buhl, Rikke, et al.
(författare)
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Atrial fibrillatory rate as predictor of recurrence of atrial fibrillation in horses treated medically or with electrical cardioversion
- 2022
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Ingår i: Equine Veterinary Journal. - : Wiley. - 0425-1644 .- 2042-3306. ; 54:6, s. 1013-1022
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Tidskriftsartikel (refereegranskat)abstract
- Background: The recurrence rate of atrial fibrillation (AF) in horses after cardioversion to sinus rhythm (SR) is relatively high. Atrial fibrillatory rate (AFR) derived from surface ECG is considered a biomarker for electrical remodelling and could potentially be used for the prediction of successful AF cardioversion and AF recurrence. Objectives: Evaluate if AFR was associated with successful treatment and could predict AF recurrence in horses. Study design: Retrospective multicentre study. Methods: Electrocardiograms (ECG) from horses with persistent AF admitted for cardioversion with either medical treatment (quinidine) or transvenous electrical cardioversion (TVEC) were included. Bipolar surface ECG recordings were analysed by spatiotemporal cancellation of QRST complexes and calculation of AFR from the remaining atrial signal. Kaplan-Meier survival curve and Cox regression analyses were performed to assess the relationship between AFR and the risk of AF recurrence. Results: Of the 195 horses included, 74 received quinidine treatment and 121 were treated with TVEC. Ten horses did not cardiovert to SR after quinidine treatment and AFR was higher in these, compared with the horses that successfully cardioverted to SR (median [interquartile range]), (383 [367-422] vs 351 [332-389] fibrillations per minute (fpm), P <.01). Within the first 180 days following AF cardioversion, 12% of the quinidine and 34% of TVEC horses had AF recurrence. For the horses successfully cardioverted with TVEC, AFR above 380 fpm was significantly associated with AF recurrence (hazard ratio = 2.4, 95% confidence interval 1.2-4.8, P =.01). Main limitations: The treatment groups were different and not randomly allocated, therefore the two treatments cannot be compared. Medical records and the follow-up strategy varied between the centres. Conclusions: High AFR is associated with failure of quinidine cardioversion and AF recurrence after successful TVEC. As a noninvasive marker that can be retrieved from surface ECG, AFR can be clinically useful in predicting the probability of responding to quinidine treatment as well as maintaining SR after electrical cardioversion.
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| 4. |
- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 5. |
- Oliveros, Carl H., et al.
(författare)
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Earth history and the passerine superradiation
- 2019
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:16, s. 7916-7925
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Tidskriftsartikel (refereegranskat)abstract
- Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyper-diverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
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| 6. |
- Askri, Dalel, et al.
(författare)
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A blood test to monitor bee health across a European network of agricultural sites of different land-use by MALDI BeeTyping mass spectrometry
- 2024
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Ingår i: Science of the Total Environment. - 0048-9697 .- 1879-1026. ; 929
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Tidskriftsartikel (refereegranskat)abstract
- There are substantial concerns about impaired honey bee health and colony losses due to several poorly understood factors. We used MALDI profiling (MALDI BeeTyping®) analysis to investigate how some environmental and management factors under field conditions across Europe affected the honey bee haemolymph peptidome (all peptides in the circulatory fluid), as a profile of molecular markers representing the immune status of Apis mellifera. Honey bees were exposed to a range of environmental stressors in 128 agricultural sites across eight European countries in four biogeographic zones, with each country contributing eight sites each for two different cropping systems: oilseed rape (OSR) and apple (APP). The full haemolymph peptide profiles, including the presence and levels of three key immunity markers, namely the antimicrobial peptides (AMPs) Apidaecin, Abaecin and Defensin-1, allowed the honey bee responses to environmental variables to be discriminated by country, crop type and site. When considering just the AMPs, it was not possible to distinguish between countries by the prevalence of each AMP in the samples. However, it was possible to discriminate between countries on the amounts of the AMPs, with the Swedish samples in particular expressing high amounts of all AMPs. A machine learning model was developed to discriminate the haemolymphs of bees from APP and OSR sites. The model was 90.6 % accurate in identifying the crop type from the samples used to build the model. Overall, MALDI BeeTyping® of bee haemolymph represents a promising and cost-effective “blood test” for simultaneously monitoring dozens of peptide markers affected by environmental stressors at the landscape scale, thus providing policymakers with new diagnostic and regulatory tools for monitoring bee health.
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| 7. |
- Nicholson, Charlie C., et al.
(författare)
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Landscapes of risk : A comparative analysis of landscape metrics for the ecotoxicological assessment of pesticide risk to bees
- 2024
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Ingår i: Journal of Applied Ecology. - 0021-8901 .- 1365-2664.
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Tidskriftsartikel (refereegranskat)abstract
- Pesticide use in agricultural landscapes creates environmental contamination that is heterogenous in space and time. Mobile organisms, such as bees, are exposed to multiple contamination sources when visiting patches that vary in the amount, timing and toxicity of pesticides used. Yet, environmental risk assessments (ERA) typically fail to consider this heterogeneity, in part because of the complexities of estimating exposure to different pesticides, and subsequent risk at organism-relevant scales. We use pesticide assays of 269 bee-collected pollen samples to understand the spatiotemporal variability of risk across a network of 41 field sites in southern Sweden. Observed bee pesticide risk is calculated based on compound-specific residue quantifications in pollen and standardized toxicity data. We then compare the ability of three classes of landscape-scale variables to predict this risk: (1) landscape composition and configuration metrics, (2) landscape load based on national pesticide use data and (3) predictions from a newly developed bee pesticide exposure model. Based on use data, 10 crops account for 81% of the total risk. We detected 49 pesticide compounds in bee-collected pollen. Although herbicides and fungicides constitute the bulk of detected pesticides, both in frequency and amount quantified, unsurprisingly, insecticides contribute the most to risk. Landscape composition and configuration metrics did not predict observed pesticide risk, and interactions with bee species indicate taxa-dependency in predictions. Landscape load predicted observed risk consistently between taxa. Risk estimates from our exposure model were strongly predictive but only when considering realized risk (i.e., risk estimates based on prior pesticide use information). Synthesis and applications. Predicting pesticide risk based on landscape patterns could enable landscape-scale ERA. However, simple metrics of landscape pattern, such as proportion of agricultural land, are not sufficient. We found that risk observed in bee-collected pollen was best predicted when integrating spatialized pesticide use in the pesticide exposure model, underscoring the importance of such data for research, monitoring and mitigation. Further, we propose a guidance framework for future landscape ecotoxicological risk analyses that clarifies data needs relative to risk prediction goals.
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