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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- 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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| 4. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 5. |
- An, Junghwa, et al.
(författare)
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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 404-408
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Tidskriftsartikel (refereegranskat)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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| 6. |
- Zhang, Wei, et al.
(författare)
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Knockdown of MMP-7 inhibits cell proliferation and enhances sensitivity to 5-fluorouracil and X-ray irradiation in colon cancer cells
- 2014
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Ingår i: Clinical and Experimental Medicine (Testo stampato). - : Springer Verlag (Germany). - 1591-8890 .- 1591-9528. ; 14:1, s. 99-106
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Tidskriftsartikel (refereegranskat)abstract
- The role of matrix metalloproteinase-7 (MMP-7) in the pathogenesis of colon cancer is not understood thoroughly. Previous studies from our group have shown that the expression levels of MMP-7 were highly elevated in colorectal cancer patient specimens and were correlated with Dukes Staging, histological differentiation grade and CEA level. The goal of this study was to investigate the cellular impact of MMP-7 in colon cancer. In this study, we used the SW480 colon cancer cell lines of MMP-7 knockdown by lentivirus-mediated RNA interference as a model system to investigate the impact of MMP-7 on cell proliferation and sensitivity to 5-Fluorouracil (5-FU) and X-ray irradiation (IR). Cell proliferation and sensitivity to 5-FU and IR were measured by MTT assay and colony formation assay. Cell cycle was evaluated by flow cytometry. We showed that the down regulation of MMP-7 inhibits colon cancer cell proliferation and sensitizes tumour cells to 5-FU and IR (P less than 0.05). Decreased MMP-7 expression in SW480 cells by RNA interference triggered cell cycle arrest at G1 phase (P less than 0.05). Down regulation of MMP-7 may inhibit the cell proliferation of colon cancer cells and increase tumour cells sensitivity to radiotherapy and chemotherapy. RNAi-mediated silencing of MMP-7 may represent a powerful therapeutic approach for controlling human colorectal cancer growth.
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| 7. |
- Zhao, Guang-Jiu, et al.
(författare)
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Photoinduced intramolecular charge transfer and S-2 fluorescence in thiophene-pi-conjugated donor-acceptor systems : Experimental and TDDFT studies
- 2008
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 14:23, s. 6935-6947
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Tidskriftsartikel (refereegranskat)abstract
- Experimental and theoretical methods were used to study newly synthesized thiophene-pi-cojugated donor-acceptor compounds, which were found to exhibit efficient intramolecular charge-transfer emission in polar solvents with relatively large Stokes shifts and strong solvatochromism. To gain insight into the solvatochromic behavior of these compounds, the dependence of the spectra on solvent polarity was studied on the basis of Lippert-Mataga models. We found that intramolecular charge transfer in these donor-acceptor systems is significantly dependent on the electron-with-drawing substituents at the thienyl 2-position. The dependence of the absorption and emission spectra of these compounds in methanol on the concentration of trifluoroacetic acid was used to confirm intramolecular charge-tranfer emission. Moreover, the calculated absorption and emission energies, which are in accordance with the experimental values, suggested that fluorescence can be emitted from different geometric confirmations. In addition, a novel S-2 fluorescence phenomenon for some of these compounds was also be observed. The fluorescence excitation spectra were used to confirm the S-2 fluorescence. We demonstrate that S-2 fluorescence can be explained by the calculated energy gap between the S-2 and S-1 states of these molecules. Furthermore, nonlinear optical behavior of the thiophene-pi-conjugated compound with diethylcyanomethylphosphonate substituents was predicted in theory.
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| 8. |
- Cao, Wei, et al.
(författare)
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Ionic organic cage-encapsulated metal clusters for switchable catalysis
- 2021
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Ingår i: Cell Reports Physical Science. - : Elsevier BV. - 2666-3864. ; 2:9
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Tidskriftsartikel (refereegranskat)abstract
- The capability to build up stable, switchable catalysts for complex artificial systems that can mimic the responsiveness of biological systems to multiple triggers is highly desirable and challenging. Herein, we engineer such a system by physically locking catalytically active metal clusters (MCs) inside individual cationic molecular organic cages (I-Cages), where the responsive and task-specific counteranions of I-Cages impart MCs with a programmable gating effect. This allows for precise spatial and temporal control over chemical reactions by regulating accessibility of reagents to the MC sites. Following this strategy, we have successfully tailored catalytic activity of a series of model catalysis (e.g., methanolysis of ammonia borane, and the reduction of 4-nitroaniline) by employing light and pH stimuli, as well as their combination, for programmable-activity control.
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| 9. |
- Fan, Zheyong, et al.
(författare)
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GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations
- 2022
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 1089-7690 .- 0021-9606. ; 157:11
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Tidskriftsartikel (refereegranskat)abstract
- We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in Fan et al. [Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package gpumd. We increase the accuracy of NEP models both by improving the radial functions in the atomic-environment descriptor using a linear combination of Chebyshev basis functions and by extending the angular descriptor with some four-body and five-body contributions as in the atomic cluster expansion approach. We also detail our efficient implementation of the NEP approach in graphics processing units as well as our workflow for the construction of NEP models and demonstrate their application in large-scale atomistic simulations. By comparing to state-of-the-art MLPs, we show that the NEP approach not only achieves above-average accuracy but also is far more computationally efficient. These results demonstrate that the gpumd package is a promising tool for solving challenging problems requiring highly accurate, large-scale atomistic simulations. To enable the construction of MLPs using a minimal training set, we propose an active-learning scheme based on the latent space of a pre-trained NEP model. Finally, we introduce three separate Python packages, viz., gpyumd, calorine, and pynep, that enable the integration of gpumd into Python workflows.
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| 10. |
- Huang, Ruihua, et al.
(författare)
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Star-shaped porous nitrogen-doped metal-organic framework carbon as an electrochemical platform for sensitive determination of Cd(II) in environmental and tobacco samples
- 2022
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Ingår i: Analytica Chimica Acta. - : Elsevier. - 0003-2670 .- 1873-4324. ; 1228
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Tidskriftsartikel (refereegranskat)abstract
- In this study, cetyltrimethylammonium bromide and zeolitic imidazolate framework-8 (ZIF-8) were first assembled via the chemical co-precipitation, and high-quality carbon-based metal-free nanomaterials were synthesized using a heat-treatment process. The internal and morphological characteristics of hexagonal Star ZIF-8 were investigated using scanning electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. The electrochemical sensor with a good response to Cd(II) was prepared via square-wave anodic stripping voltammetry (SWASV) with Star ZIF-8 nanomaterial-modified glassy carbon electrodes. The main parameters were adjusted to obtain the optimal stripping response and a wide linear range. Concurrently, under the calculation of SWASV, the sensitivity of Star ZIF-8-Nafion/GCE to Cd(II) was increased by five orders of magnitude (0.5–230 μg/L), and the determination level was even low to 0.48 μg/L. Based on the high anti-interference ability and stability of the sensor, the application potential of Star ZIF-8 carbon-based metal-free nanomaterials for the detection of trace Cd(II) in was confirmed.
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