| 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. |
- Liu, Hui, et al.
(författare)
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Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
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| 3. |
- Shi, Tian-Le, et al.
(författare)
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Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.
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| 4. |
- Willander, Magnus, 1948, et al.
(författare)
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Fundamentals and properties of zinc oxide nanostructures: optical and sensing applications
- 2008
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Ingår i: Superlattices and Microstructures. - : Elsevier BV. - 0749-6036 .- 1096-3677. ; 43:4, s. 352-61
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we will give an overview of the status of catalytic growth and of low-temperature chemical growth of ZnO nanostructures performed in our laboratory. Particularly results employing different substrates will be discussed. The second part deals with structural and optical properties of ZnO nanorods. The results from high resolution transmission electron microscope (HRTEM), scanning electron microscope (SEM), photoluminescence (PL), Cathodoluminescence (CL), and Electroluminescence (EL), on single nanowires will be shown. Our results on surface morphology, bulk and the position of the catalyst as well as the optical properties including UV emission, lasing and white emission will all be presented and discussed. In the third part experimental results from electroluminescence of ZnO nanorods on different substrates in the UV in addition to excellent white light emission obtained from samples grown at low temperature are to be given and discussed. Finally the sensing of molecules in water by ZnO nanorods will be discussed from a theoretical point of view. Also fundamental properties of polaritons and excitons in ZnO nanostructures are to be highlighted.
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| 5. |
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| 6. |
- Willander, Magnus, 1948, et al.
(författare)
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Solid and soft nanostructured materials: fundamentals and applications
- 2005
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Ingår i: Microelectronics Journal. - : Elsevier BV. - 0026-2692. ; 36:11, s. 940-949
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Tidskriftsartikel (refereegranskat)abstract
- The scientific work worldwide on nanostructured materials is extensive as well as the work on the applications of nanostructured materials. We will review quasi two-, one- and zero-dimensional solid and soft materials and their applications. We will restrict ourselves to a few examples from partly fundamental aspects and partly from application aspects. We will start with trapping of excitons in semiconductor nanostructures. The subjects are: physical realizations, phase diagrams, traps, local density approximations, and mesoscopic condensates. From these fundamental questions in solid nanomaterials we will move to trapping of molecules in water using nanostructured electrodes. We will also discuss how to manipulate water (create vortices) by nanostructure materials. The second part deals with nanorods (nano-wires). Particularly we will exemplify with ZnO nanorods. The reason for this is that ZnO has: a very strong excitons binding energy (60 meV) and strong photon–excitons coupling energy, a strong tendency to create nanostructures, and properties which make the material of interest for both optoelectronics and for medical applications. We start with the growth of crystalline ZnO nanorods on different substrates, both crystalline (silicon, silicon carbide, sapphire, etc) and amorphous substrates (silicon dioxide, plastic materials, etc) for temperatures from 50 °C up to 900 °C. The optical properties and crystalline properties of the nanorods will be analyzed. Applications from optoelectronics (lasers, LEDs, lamps, and detectors) are analyzed and also medical applications like photodynamic cancer therapy are taken up. The third part deals with nano-particles in ZnO for sun screening. Skin cancer due to the exposure from the sun can be prevented by ZnO particles in a paste put on the exposed skin.
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| 7. |
- Willander, Magnus, et al.
(författare)
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Some silicon-based heterostructures for optical applications
- 2005
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Ingår i: Journal of Electronic Materials. - : Springer Science Business Media. - 0361-5235 .- 1543-186X. ; 34:5, s. 515-521
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we will present our recent research on the growth and characterization of some Si-based heterostructures for optical and photonic devices. The heterostructures to be discussed are ZnO nanorods on Si, SiO2, and other substrates such as SiN and sapphire. We will also consider strained Si1-xGex/Si heterostructures for Si optoelectronics. The performance and functionality extension of Si technology for photonic applications due to the development of such heterostructures will be presented. We will focus on the results of structural and optical characterization in relation to device properties. The structural characterization includes x-ray diffraction for assessment of the crystallinity and stress in the films and secondary ion mass spectrometry for chemical analysis. The optical properties and electronic structure were investigated by using photoluminescence. The device application of these thin film structures includes detectors, lasers, and light emitting devices. Some of the Si-based heterostructures to be presented include devices emitting and detecting up to the blue-green and violet wave lengths.
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