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| 2. |
- 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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| 3. |
- Hong, Danfeng, et al.
(författare)
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Interpretable Hyperspectral Artificial Intelligence : When nonconvex modeling meets hyperspectral remote sensing
- 2021
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Ingår i: IEEE GEOSCIENCE AND REMOTE SENSING MAGAZINE. - : Institute of Electrical and Electronics Engineers (IEEE). - 2473-2397. ; 9:2, s. 52-87
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Tidskriftsartikel (refereegranskat)abstract
- Hyperspectral (HS) imaging, also known as image spectrometry, is a landmark technique in geoscience and remote sensing (RS). In the past decade, enormous efforts have been made to process and analyze these HS products, mainly by seasoned experts. However, with an ever-growing volume of data, the bulk of costs in manpower and material resources poses new challenges for reducing the burden of manual labor and improving efficiency. For this reason, it is urgent that more intelligent and automatic approaches for various HS RS applications be developed. Machine learning (ML) tools with convex optimization have successfully undertaken the tasks of numerous artificial intelligence (AI)-related applications; however, their ability to handle complex practical problems remains limited, particularly for HS data, due to the effects of various spectral variabilities in the process of HS imaging and the complexity and redundancy of higher-dimensional HS signals. Compared to convex models, nonconvex modeling, which is capable of characterizing more complex real scenes and providing model interpretability technically and theoretically, has proven to be a feasible solution that reduces the gap between challenging HS vision tasks and currently advanced intelligent data processing models.
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| 4. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.
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| 5. |
- Li, Jinxiu, et al.
(författare)
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A Discovery of a Genetic Mutation Causing Reduction of Atrogin-1 Expression in Broiler Chicken Muscle
- 2019
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Ingår i: Frontiers in Genetics. - : FRONTIERS MEDIA SA. - 1664-8021. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Chickens are bred all over the world and have significant economic value as one of the major agricultural animals. The growth rate of commercial broiler chickens is several times higher than its Red Jungle fowl (RJF) ancestor. To further improve the meat production of commercial chickens, it is quite important to decipher the genetic mechanism of chicken growth traits. In this study, we found that broiler chickens exhibited lower levels of E3 ubiquitin ligase muscle atrophy F-box (MAFbx or Atrogin-1) relative to its RJF ancestor. As a ubiquitin ligase, Atrogin-1 plays a crucial role in muscle development in which its up-regulation often indicates the activation of muscle atrophic pathways. Here, we showed that the Atrogin-1 expression variance partly affects chicken muscle growth rates among different breeds. Furthermore, we demonstrated that the reduced expression of Atrogin-1 in broiler chickens was ascribed to a single nucleotide polymorphism (SNP), which inhibited the binding of transcription regulators and attenuated the enhancer activity. The decreased Atrogin-1 in broiler chickens suppresses the catabolism of muscle protein and preserves muscle mass. Our study facilitates the understanding of the molecular mechanism of chicken muscle development and has a high translational impact in chicken breeding.
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| 6. |
- Niu, Guoxiang, et al.
(författare)
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Subtropical forest macro-decomposers rapidly transfer litter carbon and nitrogen into soil mineral-associated organic matter
- 2024
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Ingår i: Forest Ecosystems. - 2095-6355. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Background: Forest soils in tropical and subtropical areas store a significant amount of carbon. Recent frameworks to assess soil organic matter (SOM) dynamics under evolving global conditions suggest that dividing bulk SOM into particulate and mineral-associated organic matter (POM vs. MAOM) is a promising method for identifying how SOM contributes to reducing global warming. Soil macrofauna, earthworms, and millipedes have been found to play an important role in facilitating SOM processes. However, how these two co-existing macrofaunae impact the litter decomposition process and directly impact the formation of POM and MAOM remains unclear. Methods: Here, we set up a microcosm experiment, which consisted of 20 microcosms with four treatments: earthworm and litter addition (E), millipedes and litter addition (M), earthworm, millipedes, and litter addition (E+M), and control (only litter addition) in five replicates. The soil and litter were sterilized prior to beginning the incubation experiment to remove any existing microbes. After incubating the samples for 42 days, the litter properties (mass, C, and N contents), soil physicochemical properties, as well as the C and N contents, and POM and MAOM 13C abundance in the 0–5 and 5–10 cm soil layers were measured. Finally, the relative influences of soil physicochemical and microbial properties on the distribution of C and N in the soil fractions were analyzed. Results: The litter mass, C, and N associated with all four treatments significantly decreased after incubation, especially under treatment E+M (litter mass: −58.8%, litter C: −57.0%, litter N: −75.1%, respectively), while earthworm biomass significantly decreased under treatment E. Earthworm or millipede addition alone showed no significant effects on the organic carbon (OC) and total nitrogen (TN) content in the POM fraction, but joint addition of both significantly increased OC and TN regardless of soil depth. Importantly, all three macrofauna treatments increased the OC and TN content and decreased the 13C abundance in the MAOM fraction. More than 65% of the total variations in the distribution of OC and TN throughout the two fractions can be explained by a combination of soil physicochemical and microbial properties. Changes in the OC distribution in the 0–5 cm soil layer are likely due to a decrease in soil pH and an increase in arbuscular mycorrhizal fungi (AMF), while those in the 5–10 cm layer are probably caused by increases in soil exchangeable Ca and Mg, in addition to fungi and gram-negative (GN) bacteria. The observed TN distribution changes in the 0–5 cm soil likely resulted from a decrease in soil pH and increases in AMF, GN, and gram-negative (GP) bacteria, while TN distribution changes in the 5–10 cm soil could be explained by increases in exchangeable Mg and GN bacteria. Conclusions: The results indicate that the coexistence of earthworms and millipedes can accelerate the litter decomposition process and store more C in the MAOM fractions. This novel finding helps to unlock the processes by which complex SOM systems serve as C sinks in tropical forests and addresses the importance of soil macrofauna in maintaining C-neutral atmospheric conditions under global climate change.
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| 7. |
- Xu, Xiaoxiang, et al.
(författare)
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Nanocarriers for Inner Ear Disease Therapy
- 2021
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Ingår i: Frontiers in Cellular Neuroscience. - : Frontiers Media SA. - 1662-5102. ; 15
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Forskningsöversikt (refereegranskat)abstract
- Hearing loss is a common disease due to sensory loss caused by the diseases in the inner ear. The development of delivery systems for inner ear disease therapy is important to achieve high efficiency and reduce side effects. Currently, traditional drug delivery systems exhibit the potential to be used for inner ear disease therapy, but there are still some drawbacks. As nanotechnology is developing these years, one of the solutions is to develop nanoparticle-based delivery systems for inner ear disease therapy. Various nanoparticles, such as soft material and inorganic-based nanoparticles, have been designed, tested, and showed controlled delivery of drugs, improved targeting property to specific cells, and reduced systemic side effects. In this review, we summarized recent progress in nanocarriers for inner ear disease therapy. This review provides useful information on developing promising nanocarriers for the efficient treatment of inner ear diseases and for further clinical applications for inner ear disease therapy.
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