| 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. |
- Li, W., et al.
(författare)
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Interrelationships between tetracyclines and nitrogen cycling processes mediated by microorganisms : A review
- 2021
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Ingår i: Bioresource Technology. - : Elsevier BV. - 0960-8524 .- 1873-2976. ; 319
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Forskningsöversikt (refereegranskat)abstract
- Due to their broad-spectrum antibacterial activity and low cost, tetracyclines (TCs) are a class of antibiotics widely used for human and veterinary medical purposes and as a growth-promoting agent for aquaculture. Interrelationships between TCs and nitrogen cycling have attracted scientific attention due to the complicated processes mediated by microorganisms. TCs negatively impact the nitrogen cycling; however, simultaneous degradation of TCs during nitrogen cycling mediated by microorganisms can be achieved. This review encapsulates the background and distribution of TCs in the environment. Additionally, the main nitrogen cycling process mediated by microorganisms were retrospectively examined. Furthermore, effects of TCs on the nitrogen cycling processes, namely nitrification, denitrification, and anammox, have been summarized. Finally, the pathway and microbial mechanism of degradation of TCs accompanied by nitrogen cycling processes were reviewed, along with the scope for prospective studies. © 2020
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| 3. |
- Arndt, D. S., et al.
(författare)
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STATE OF THE CLIMATE IN 2017
- 2018
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 99:8, s. S1-S310
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Forskningsöversikt (refereegranskat)
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| 4. |
- Cousin, C., et al.
(författare)
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Protein-serine/threonine/tyrosine kinases in bacterial signaling and regulation
- 2013
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 1574-6968 .- 0378-1097. ; 346:1, s. 11-19
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Forskningsöversikt (refereegranskat)abstract
- In this review, we address some recent developments in the field of bacterial protein phosphorylation, focusing specifically on serine/threonine and tyrosine kinases. We present an overview of recent studies outlining the scope of physiological processes that are regulated by phosphorylation, ranging from cell cycle, growth, cell morphology, to metabolism, developmental phenomena, and virulence. Specific emphasis is placed on Mycobacterium tuberculosis as a showcase organism for serine/threonine kinases, and Bacillus subtilis to illustrate the importance of protein phosphorylation in developmental processes. We argue that bacterial serine/threonine and tyrosine kinases have a distinctive feature of phosphorylating multiple substrates and might thus represent integration nodes in the signaling network. Some open questions regarding the evolutionary benefits of relaxed substrate selectivity of these kinases are treated, as well as the notion of nonfunctional background' phosphorylation of cellular proteins. We also argue that phosphorylation events for which an immediate regulatory effect is not clearly established should not be dismissed as unimportant, as they may have a role in cross-talk with other post-translational modifications. Finally, recently developed methods for studying protein phosphorylation networks in bacteria are briefly discussed.
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| 5. |
- Gavelli, Francesco, et al.
(författare)
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Extravascular lung water levels are associated with mortality : a systematic review and meta-analysis
- 2022
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Ingår i: Critical Care. - : BMC. - 1364-8535 .- 1466-609X. ; 26:1
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Forskningsöversikt (refereegranskat)abstract
- Background The prognostic value of extravascular lung water (EVLW) measured by transpulmonary thermodilution (TPTD) in critically ill patients is debated. We performed a systematic review and meta-analysis of studies assessing the effects of TPTD-estimated EVLW on mortality in critically ill patients. Methods Cohort studies published in English from Embase, MEDLINE, and the Cochrane Database of Systematic Reviews from 1960 to 1 June 2021 were systematically searched. From eligible studies, the values of the odds ratio (OR) of EVLW as a risk factor for mortality, and the value of EVLW in survivors and non-survivors were extracted. Pooled OR were calculated from available studies. Mean differences and standard deviation of the EVLW between survivors and non-survivors were calculated. A random effects model was computed on the weighted mean differences across the two groups to estimate the pooled size effect. Subgroup analyses were performed to explore the possible sources of heterogeneity. Results Of the 18 studies included (1296 patients), OR could be extracted from 11 studies including 905 patients (464 survivors vs. 441 non-survivors), and 17 studies reported EVLW values of survivors and non-survivors, including 1246 patients (680 survivors vs. 566 non-survivors). The pooled OR of EVLW for mortality from eleven studies was 1.69 (95% confidence interval (CI) [1.22; 2.34], p < 0.0015). EVLW was significantly lower in survivors than non-survivors, with a mean difference of -4.97 mL/kg (95% CI [-6.54; -3.41], p < 0.001). The results regarding OR and mean differences were consistent in subgroup analyses. Conclusions The value of EVLW measured by TPTD is associated with mortality in critically ill patients and is significantly higher in non-survivors than in survivors. This finding may also be interpreted as an indirect confirmation of the reliability of TPTD for estimating EVLW at the bedside. Nevertheless, our results should be considered cautiously due to the high risk of bias of many studies included in the meta-analysis and the low rating of certainty of evidence. Trial registration the study protocol was prospectively registered on PROSPERO: CRD42019126985.
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| 6. |
- Liu, Zhixin, et al.
(författare)
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Microclimatic measurements in tropical cities: Systematic review and proposed guidelines
- 2022
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Ingår i: Building and Environment. - : Elsevier. - 0360-1323 .- 1873-684X. ; 222
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Forskningsöversikt (refereegranskat)abstract
- To tackle urban overheating induced by the combined effect of global warming and intensive urbanization, researchers have recommended assimilating microclimate-related strategies into urban design practices. Field measurements, playing a central role in urban climatology, have been widely applied worldwide. Reviewing the last five years' field measurement studies and existing guidelines and standards from WMO (World Meteorological Organization) and ISO (International Organization for Standardization), this study identified a gap between available guidelines and researchers' practical needs to ascertain the collection of high caliber data. Therefore, dedicated guidelines are required to explain the crucial conceptual and application issues and refine systematic field measurement methods. This demand is particularly acute for microscale and urban environments. This study proposed and explained integrated and comprehensive guidelines for systematic microclimate field measurements. The suggested workflow included four main steps: formulating field measurement plan, preparing for field measurements, sustaining measurement quality, and curating data. The complex and heterogeneous environment in urban areas was carefully evaluated to hone the data acquisition campaign and ascertain data quality. Relevant concepts and practices learned from existing guidelines and standards, experiences from actual field studies, and professional recommendations were distilled and incorporated into the guidelines. The significance of a complete report with full metadata was emphasized. Detailed hints, precautions, recommendations, examples, and a metadata checklist were provided as a helpful and actionable package of research procedures.
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| 7. |
- Yao, T., et al.
(författare)
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A review of climatic controls on δ18O in precipitation over the Tibetan Plateau : Observations and simulations
- 2013
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Ingår i: Reviews of geophysics. - : American Geophysical Union (AGU). - 8755-1209 .- 1944-9208. ; 51:4
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Forskningsöversikt (refereegranskat)abstract
- The stable oxygen isotope ratio (δ18O) in precipitation is an integrated tracer of atmospheric processes worldwide. Since the 1990s, an intensive effort has been dedicated to studying precipitation isotopic composition at more than 20 stations in the Tibetan Plateau (TP) located at the convergence of air masses between the westerlies and Indian monsoon. In this paper, we establish a database of precipitation δ18O and use different models to evaluate the climatic controls of precipitation δ18O over the TP. The spatial and temporal patterns of precipitation δ18O and their relationships with temperature and precipitation reveal three distinct domains, respectively associated with the influence of the westerlies (northern TP), Indian monsoon (southern TP), and transition in between. Precipitation δ18O in the monsoon domain experiences an abrupt decrease in May and most depletion in August, attributable to the shifting moisture origin between Bay of Bengal (BOB) and southern Indian Ocean. High-resolution atmospheric models capture the spatial and temporal patterns of precipitation δ18O and their relationships with moisture transport from the westerlies and Indian monsoon. Only in the westerlies domain are atmospheric models able to represent the relationships between climate and precipitation δ18O. More significant temperature effect exists when either the westerlies or Indian monsoon is the sole dominant atmospheric process. The observed and simulated altitude-δ18O relationships strongly depend on the season and the domain (Indian monsoon or westerlies). Our results have crucial implications for the interpretation of paleoclimate records and for the application of atmospheric simulations to quantifying paleoclimate and paleo-elevation changes.
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