| 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. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Wang, Fang, et al.
(författare)
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Emerging contaminants: A One Health perspective
- 2024
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Ingår i: Innovation. - 2666-6758. ; 5
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Forskningsöversikt (refereegranskat)abstract
- Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.
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| 4. |
- Xu, Jie, et al.
(författare)
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Totaling river discharge of the third pole from satellite imagery
- 2024
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Ingår i: REMOTE SENSING OF ENVIRONMENT. - 0034-4257 .- 1879-0704. ; 308
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Tidskriftsartikel (refereegranskat)abstract
- The high-mountain Third Pole (TP) in Asia is undergoing rapid warming, profoundly impacting river discharge. Changes in precipitation and the degradation of glaciers and permafrost exert a substantial impact on TP rivers, affecting millions downstream. Nevertheless, conventional estimation methods that rely on in -situ observations and models face considerable challenges due to inconsistent data quality and availability, complex terrain, and difficulty in representing hydrological processes. Here, we harnessed the power of high-resolution (3 m) Dove/ PlanetScope satellite images to meticulously measure river width and propose a novel formula for estimating discharge. This approach facilitates a coherent assessment of discharge at various river section shapes. Its efficacy is demonstrated through applying to thirteen high-mountain TP rivers, revealing an estimated total mountain discharge of 3786 billion m 3 during 2017 - 2021, equaling water from approximately 167 Great Lakes. These findings have immediate implications for integrated water resources management at the poorly-gauged transboundary basins of Asia.
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| 5. |
- Li, Qian, et al.
(författare)
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Genome-wide identification of resistance genes and cellular analysis of key gene knockout strain under 5-hydroxymethylfurfural stress in Saccharomyces cerevisiae
- 2023
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Ingår i: BMC Microbiology. - 1471-2180. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- In bioethanol production, the main by-product, 5-hydroxymethylfurfural (HMF), significantly hinders microbial fermentation. Therefore, it is crucial to explore genes related to HMF tolerance in Saccharomyces cerevisiae for enhancing the tolerance of ethanol fermentation strains. A comprehensive analysis was conducted using genome-wide deletion library scanning and SGAtools, resulting in the identification of 294 genes associated with HMF tolerance in S. cerevisiae. Further KEGG and GO enrichment analysis revealed the involvement of genes OCA1 and SIW14 in the protein phosphorylation pathway, underscoring their role in HMF tolerance. Spot test validation and subcellular structure observation demonstrated that, following a 3-h treatment with 60mM HMF, the SIW14 gene knockout strain exhibited a 12.68% increase in cells with abnormal endoplasmic reticulum (ER) and a 22.41% increase in the accumulation of reactive oxygen species compared to the BY4741 strain. These findings indicate that the SIW14 gene contributes to the protection of the ER structure within the cell and facilitates the clearance of reactive oxygen species, thereby confirming its significance as a key gene for HMF tolerance in S. cerevisiae.
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| 6. |
- Zhang, Dezhi, et al.
(författare)
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Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)
- 2024
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Ingår i: SYSTEMATIC BIOLOGY. - 1063-5157 .- 1076-836X. ; 73:2, s. 279-289
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Tidskriftsartikel (refereegranskat)abstract
- Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of 4 Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and similar to 39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which-in combination-support the following tree topology: ([{E. godlewskii, E. cia}, E. cioides], E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.
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| 7. |
- Hu, Zengyun, et al.
(författare)
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“Dry gets drier, wet gets wetter”: A case study over the arid regions of central Asia
- 2019
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Ingår i: International Journal of Climatology. - : Wiley. - 0899-8418 .- 1097-0088. ; 39:2, s. 1072-1091
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Tidskriftsartikel (refereegranskat)abstract
- © 2018 Royal Meteorological Society The “dry gets drier, wet gets wetter” (DGDWGW) paradigm well describes the pattern of precipitation changes over the oceans. However, it has also been usually considered as a simplified pattern of regional changes in wet/dry under global warming, although GCMs mostly do not agree this pattern over land. To examine the validity of this paradigm over land and evaluate how usage of drought indices estimated from different hydrological variables affects detection of regional wet/dry trends, we take the arid regions of central Asia as a case study area and estimate the drying and wetting trends during the period of 1950–2015 based on multiple drought indices. These indices include the standardized precipitation index (SPI), the standardized precipitation evapotranspiration index (SPEI), the Palmer drought severity index (PDSI) and self-calibrating PDSI (sc_PDSI) with both the Thornthwaite (th) and Penman–Monteith (pm) equations in PDSI calculation (namely, PDSI_th, PDSI_pm, sc_PDSI_th and sc_PDSI_pm). The results show that there is an overall agreement among the indices in terms of inter-annual variation, especially for the PDSIs. All drought indices except SPI show a drying trend over the five states of central Asia (CAS5: including Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan and Uzbekistan). The four PDSIs and SPEI reveal a wetting tendency over the northwestern China (NW; including Xinjiang Uygur Autonomous Region and Hexi Corridor). The contrasting trends between CAS5 and NW can also be revealed in soil moisture (SM) variations. The nonlinear wet and dry variations are dominated by the 3–7 years oscillations for the indices. Relationships between the six indices and climate variables show the major drought drivers have regional features: with mean temperature (TMP), precipitation total (PRE) and potential evapotranspiration (PET) for CAS5, and PRE and PET for NW. Finally, our analyses indicate that the dry and wet variations are strongly correlated with the El Niño/Southern Oscillation (ENSO).
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| 8. |
- Li, Gang, 1991, et al.
(författare)
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Bayesian genome scale modelling identifies thermal determinants of yeast metabolism
- 2021
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- The molecular basis of how temperature affects cell metabolism has been a long-standing question in biology, where the main obstacles are the lack of high-quality data and methods to associate temperature effects on the function of individual proteins as well as to combine them at a systems level. Here we develop and apply a Bayesian modeling approach to resolve the temperature effects in genome scale metabolic models (GEM). The approach minimizes uncertainties in enzymatic thermal parameters and greatly improves the predictive strength of the GEMs. The resulting temperature constrained yeast GEM uncovers enzymes that limit growth at superoptimal temperatures, and squalene epoxidase (ERG1) is predicted to be the most rate limiting. By replacing this single key enzyme with an ortholog from a thermotolerant yeast strain, we obtain a thermotolerant strain that outgrows the wild type, demonstrating the critical role of sterol metabolism in yeast thermosensitivity. Therefore, apart from identifying thermal determinants of cell metabolism and enabling the design of thermotolerant strains, our Bayesian GEM approach facilitates modelling of complex biological systems in the absence of high-quality data and therefore shows promise for becoming a standard tool for genome scale modeling.
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| 10. |
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