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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. |
- Guo, Ying, et al.
(författare)
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Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum
- 2023
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 40:12
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Tidskriftsartikel (refereegranskat)abstract
- Rumpless chickens exhibit an abnormality in their tail development. The genetics and biology of this trait has been studied for decades to illustrate a broad variation in both the types of inheritance and the severity in the developmental defects of the tail. In this study, we created a backcross pedigree by intercrossing Piao (rumpless) with Xianju (normal) to investigate the genetic mechanisms and molecular basis of the rumpless trait in Piao chicken. Through genome-wide association and linkage analyses, the candidate region was fine-mapped to 798.5 kb (chromosome 2: 86.9 to 87.7 Mb). Whole-genome sequencing analyses identified a single variant, a 4.2 kb deletion, which was completely associated with the rumpless phenotype. Explorations of the expression data identified a novel causative gene, Rum, that produced a long, intronless transcript across the deletion. The expression of Rum is embryo-specific, and it regulates the expression of MSGN1, a key factor in regulating T-box transcription factors required for mesoderm formation and differentiation. These results provide genetic and molecular experimental evidence for a novel mechanism regulating tail development in chicken and report the likely causal mutation for the tail abnormity in the Piao chicken. The novel regulatory gene, Rum, will, due to its role in fundamental embryo development, be of interest for further explorations of a potential role in tail and skeletal development also in other vertebrates.
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| 4. |
- Guo, Ying, et al.
(författare)
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Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history
- 2021
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Ingår i: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571.
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Tidskriftsartikel (refereegranskat)abstract
- Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current com-mercial stocks bred for efficient meat and egg production. In-depth characteriza-tions of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.
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| 5. |
- 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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| 6. |
- 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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| 7. |
- Wang, Wei
(författare)
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Spatially Adaptive Analysis and Segmentation of Polarimetric SAR Data
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In recent years, Polarimetric Synthetic Aperture Radar (PolSAR) has been one of the most important instruments for earth observation, and is increasingly used in various remote sensing applications. Statistical modelling and scattering analysis are two main ways for PolSAR data interpretation, and have been intensively investigated in the past two decades. Moreover, spatial analysis was applied in the analysis of PolSAR data and found to be beneficial to achieve more accurate interpretation results. This thesis focuses on extracting typical spatial information, i.e., edges and regions by exploring the statistical characteristics of PolSAR data. The existing spatial analysing methods are mainly based on the complex Wishart distribution, which well characterizes the inherent statistical features in homogeneous areas. However, the non-Gaussian models can give better representation of the PolSAR statistics, and therefore have the potential to improve the performance of spatial analysis, especially in heterogeneous areas. In addition, the traditional fixed-shape windows cannot accurately estimate the distribution parameter in some complicated areas, leading to the loss of the refined spatial details. Furthermore, many of the existing methods are not spatially adaptive so that the obtained results are promising in some areas whereas unsatisfactory in other areas. Therefore, this thesis is dedicated to extracting spatial information by applying the non-Gaussian statistical models and spatially adaptive strategies. The specific objectives of the thesis include: (1) to develop reliable edge detection method, (2) to develop spatially adaptive superpixel generation method, and (3) to investigate a new framework of region-based segmentation. Automatic edge detection plays a fundamental role in spatial analysis, whereas the performance of classical PolSAR edge detection methods is limited by the fixed-shape windows. Paper 1 investigates an enhanced edge detection method using the proposed directional span-driven adaptive (DSDA) window. The DSDA window has variable sizes and flexible shapes, and can overcome the limitation of fixed-shape windows by adaptively selecting homogeneous samples. The spherically invariant random vector (SIRV) product model is adopted to characterize the PolSAR data, and a span ratio is combined with the SIRV distance to highlight the dissimilarity measure. The experimental results demonstrated that the proposed method can detect not only the obvious edges, but also the tiny and inconspicuous edges in heterogeneous areas. Edge detection and region segmentation are two important aspects of spatial analysis. As to the region segmentation, paper 2 presents an adaptive PolSAR superpixel generation method based on the simple linear iterative clustering (SLIC) framework. In the k-means clustering procedure, multiple cues including polarimetric, spatial, and texture information are considered to measure the distance. Since the constant weighting factor which balances the spectral similarity and spatial proximity may cause over- or under-superpixel segmentation in different areas, the proposed method sets the factor adaptively based on the homogeneity analysis. Then, in heterogeneous areas, the spectral similarity is more significant than the spatial constraint, generating superpixels which better preserved local details and refined structures. Paper 3 investigates another PolSAR superpixel generation method, which is achieved from the global optimization aspect, using the entropy rate method. The distance between neighbouring pixels is calculated based on their corresponding DSDA regions. In addition, the SIRV distance and the Wishart distance are combined together. Therefore, the proposed method makes good use of the entropy rate framework, and also incorporates the merits of the SIRV distance and the Wishart distance. The superpixels are generated in a homogeneity-adaptive manner, resulting in smooth representation of the land covers in homogeneous areas, and well preserved details in heterogeneous areas.
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