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- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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- An, Junghwa, et al.
(author)
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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009
- 2010
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In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 404-408
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Journal article (peer-reviewed)abstract
- This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.
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| 5. |
- Fu, Le, et al.
(author)
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Biodegradable Si3N4 bioceramic sintered with Sr, Mg and Si for spinal fusion : Surface characterization and biological evaluation
- 2018
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In: Applied Materials Today. - : Elsevier BV. - 2352-9407. ; 12, s. 260-275
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Journal article (peer-reviewed)abstract
- Silicon nitride (Si3N4) is an industrial ceramic used in spinal fusion and maxillofacial reconstructionbecause of its excellent mechanical properties and good biocompatibility. This study compares the sur-face properties, apatite formation ability, bacterial infection, cell-biomaterial interactions, and in vivotoxicity (zebrafish) of newly developed Si3N4 bioceramics (sintered with bioactive sintering additivesSrO, MgO and SiO2) with two standard biomaterials; titanium (Ti) and traditional Si3N4 bioceramics (sin-tered with standard sintering additives Al2O3 and Y2O3). In general, Si3N4 bioceramics (both the newlydeveloped and the traditional) displayed less in vitro bacterial affinity than Ti, which may arise fromdifferences in the surface properties between these two types of material. The newly developed Si3N4bioceramics developed lower biofilm coverage and thinner biofilm, compared to traditional Si3N4 bioce-ramics. The effects of ionic dissolution products (leach) on proliferation and differentiation of MC3T3-E1cell were also investigated. Ionic dissolution products containing moderate amount of Sr, Mg and Siions (approximately 4.72 mg/L, 3.26 mg/L and 3.67 mg/L, respectively) stimulated osteoblast prolifera-tion during the first 2 days in culture. Interestingly, ionic dissolution products from the traditional Si3N4bioceramics that contained small amount of Si and Y ions achieved the greatest stimulatory effect foralkaline phosphatase activity after 7 days culture. The toxicity of ionic dissolution products was investi-gated in a putative developmental biology model: zebrafish (Danio rerio). No toxicity, or developmentalabnormalities, was observed in zebrafish embryos exposed to ionic dissolution products, for up to 144 hpost fertilization. These newly developed Si3N4 bioceramics with bioactive sintering additives show greatpotential as orthopedic implants, for applications such as spinal fusion cages. Future work will focus onevaluation of the newly developed Si3N4 bioceramics using a large animal model.
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| 6. |
- Hyde, K. D., et al.
(author)
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Global consortium for the classification of fungi and fungus-like taxa
- 2023
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In: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
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Journal article (peer-reviewed)abstract
- The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, 'to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation', or 'are there too many genera in the Boletales?' and even more importantly, 'what should be done with the tremendously diverse 'dark fungal taxa?' There are undeniable differences in mycologists' perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others' work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.
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| 7. |
- Liu, Sirui, et al.
(author)
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Design of Hygroscopic Bioplastic Products Stable in Varying Humidities
- 2023
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In: Macromolecular materials and engineering. - : Wiley. - 1438-7492 .- 1439-2054. ; 308:2
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Journal article (peer-reviewed)abstract
- Hygroscopic biopolymers like proteins and polysaccharides suffer from humidity-dependent mechanical properties. Because humidity can vary significantly over the year, or even within a day, these polymers will not generally have stable properties during their lifetimes. On wheat gluten, a model highly hygroscopic biopolymer material, it is observed that larger/thicker samples can be significantly more mechanically stable than thinner samples. It is shown here that this is due to slow water diffusion, which, in turn, is due to the rigid polymer structure caused by the double-bond character of the peptide bond, the many bulky peptide side groups, and the hydrogen bond network. More than a year is required to reach complete moisture saturation (≈10 wt.%) in a 1 cm thick plate of glycerol-plasticized wheat gluten, whereas this process takes only one day for a 0.5 mm thick plate. The overall moisture uptake is also retarded by swelling-induced mechanical effects. Hence, hygroscopic biopolymers are better suited for larger/thicker products, where the moisture-induced changes in mechanical properties are smeared out over time, to the extent that the product remains sufficiently tough over climate changes, for example, throughout the course of a year.
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| 8. |
- O´brien, Nathan, et al.
(author)
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In Situ Activation of an Indium(III) Triazenide Precursor for Epitaxial Growth of Indium Nitride by Atomic Layer Deposition
- 2020
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In: Chemistry of Materials. - : AMER CHEMICAL SOC. - 0897-4756 .- 1520-5002. ; 32:11, s. 4481-4489
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Journal article (peer-reviewed)abstract
- Indium nitride (InN) is characterized by its high electron mobility, making it a ground-breaking material for high frequency electronics. The difficulty of depositing high-quality crystalline InN currently impedes its broad implementation in electronic devices. Herein, we report a new highly volatile In(III) triazenide precursor and demonstrate its ability to deposit high-quality epitaxial hexagonal InN by atomic layer deposition (ALD). The new In(III) precursor, the first example of a homoleptic triazenide used in a vapor deposition process, was easily synthesized and purified by sublimation. Thermogravimetric analysis showed single step volatilization with an onset temperature of 145 degrees C and negligible residual mass. Strikingly, two temperature intervals with self-limiting growth were observed when depositing InN films. In the high-temperature interval, the precursor underwent a gas-phase thermal decomposition inside the ALD reaction chamber to produce a more reactive In(III) compound while retaining self-limiting growth behavior. Density functional theory calculations revealed a unique two-step decomposition process, which liberates three molecules of each propene and N-2 to give a smaller tricoordinated In(III) species. Stoichiometric InN films with very low levels of impurities were grown epitaxially on 4H-SiC. The InN films deposited at 325 degrees C had a sheet resistivity of 920 Omega/sq. This new triazenide precursor enables ALD of InN for semiconductor applications and provides a new family of M-N bonded precursors for future deposition processes.
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| 9. |
- Rouf, Polla, et al.
(author)
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Hexacoordinated Gallium(III) Triazenide Precursor for Epitaxial Gallium Nitride by Atomic Layer Deposition
- 2021
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In: Chemistry of Materials. - : AMER CHEMICAL SOC. - 0897-4756 .- 1520-5002. ; 33:9, s. 3266-3275
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Journal article (peer-reviewed)abstract
- Gallium nitride (GaN) is the main component of modern-day high electron mobility transistors due to its favorable electronic properties. As electronic devices become smaller with more complex surface architecture, the ability to deposit high-quality GaN films at low temperatures is required. Herein, we report a new highly volatile Ga(III) triazenide precursor and demonstrate its ability to deposit high-quality epitaxial GaN by atomic layer deposition (ALD). This new Ga(III) triazenide, the first hexacoordinated Ga-N bonded precursor used in a vapor deposition process, was easily synthesized and purified by either sublimation or recrystallisation. Thermogravimetric analysis showed single-step volatilization with an onset temperature of 155 degrees C and negligible residual mass. Three temperature intervals with self-limiting growth were observed when depositing GaN films. The GaN films grown in the second growth interval at 350 degrees C were epitaxial on 4H-SiC without an AlN seed layer and found to have a near stoichiometric Ga/N ratio with very low levels of impurities. In addition, electron microstructure analysis showed a smooth film surface and a sharp interface between the substrate and film. The band gap of these films was 3.41 eV with the Fermi level at 1.90 eV, showing that the GaN films were unintentionally n-type-doped. This new triazenide precursor enables ALD of GaN for semiconductor applications and provides a new Ga(III) precursor for future deposition processes.
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