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- 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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| 4. |
- 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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| 5. |
- Cheng, Dantong, et al.
(författare)
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MicroRNA-20a-5p promotes colorectal cancer invasion and metastasis by downregulating Smad4
- 2016
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Ingår i: Oncotarget. - : IMPACT JOURNALS LLC. - 1949-2553. ; 7:29, s. 45199-45213
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Tidskriftsartikel (refereegranskat)abstract
- Background: Tumor metastasis is one of the leading causes of poor prognosis for colorectal cancer (CRC) patients. Loss of Smad4 contributes to aggression process in many human cancers. However, the underlying precise mechanism of aberrant Smad4 expression in CRC development is still little known. Results: miR-20a-5p negatively regulated Smad4 by directly targeting its 3UTR in human colorectal cancer cells. miR-20a-5p not only promoted CRC cells aggression capacity in vitro and liver metastasis in vivo, but also promoted the epithelial-to-mesenchymal transition process by downregulating Smad4 expression. In addition, tissue microarray analysis obtained from 544 CRC patients clinical characters showed that miR-20a-5p was upregulated in human CRC tissues, especially in the tissues with metastasis. High level of miR-20a-5p predicted poor prognosis in CRC patients. Methods: Five miRNA target prediction programs were applied to identify potential miRNA(s) that target(s) Smad4 in CRC. Luciferase reporter assay and transfection technique were used to validate the correlation between miR-20a-5p and Smad4 in CRC. Wound healing, transwell and tumorigenesis assays were used to explore the function of miR-20a-5p and Smad4 in CRC progression in vitro and in vivo. The association between miR-20a-5p expression and the prognosis of CRC patients was evaluated by Kaplan-Meier analysis and multivariate cox proportional hazard analyses based on tissue microarray data. Conclusions: miR-20a-5p, as an onco-miRNA, promoted the invasion and metastasis ability by suppressing Smad4 expression in CRC cells, and high miR-20a-5p predicted poor prognosis for CRC patients, providing a novel and promising therapeutic target in human colorectal cancer.
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| 6. |
- Gao, Xindi, et al.
(författare)
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Cryptococcal Hsf3 controls intramitochondrial ROS homeostasis by regulating the respiratory process
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Mitochondrial quality control prevents accumulation of intramitochondrial-derived reactive oxygen species (mtROS), thereby protecting cells against DNA damage, genome instability, and programmed cell death. However, underlying mechanisms are incompletely understood, particularly in fungal species. Here, we show that Cryptococcus neoformans heat shock factor 3 (CnHsf3) exhibits an atypical function in regulating mtROS independent of the unfolded protein response. CnHsf3 acts in nuclei and mitochondria, and nuclear- and mitochondrial-targeting signals are required for its organelle-specific functions. It represses the expression of genes involved in the tricarboxylic acid cycle while promoting expression of genes involved in electron transfer chain. In addition, CnHsf3 responds to multiple intramitochondrial stresses; this response is mediated by oxidation of the cysteine residue on its DNA binding domain, which enhances DNA binding. Our results reveal a function of HSF proteins in regulating mtROS homeostasis that is independent of the unfolded protein response.
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| 7. |
- Liu, X., et al.
(författare)
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Surface roughness prediction method of titanium alloy milling based on CDH platform
- 2022
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Ingår i: The International Journal of Advanced Manufacturing Technology. - : Springer Nature. - 0268-3768 .- 1433-3015. ; 119:11-12, s. 7145-7157
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Tidskriftsartikel (refereegranskat)abstract
- Generally, off-line methods are used for surface roughness prediction of titanium alloy milling. However, studies show that these methods have poor prediction accuracy. In order to resolve this shortcoming, a prediction method based on Cloudera’s Distribution including Apache Hadoop (CDH) platform is proposed in the present study. In this regard, data analysis and process platform are designed based on the CDH, which can upload, calculate, and store data in real time. Then this platform is combined with the Harris hawk optimization (HHO) algorithm and pattern search strategy, and an improved Harris hawk optimization optimization (IHHO) method is proposed accordingly. Then this method is applied to optimize the support vector machine (SVM) algorithm and predict the surface roughness in the CDH platform. The obtained results show that the prediction accuracy of IHHO method reaches 95%, which is higher than the conventional methods of SVM, BAT-SVM, gray wolf optimizer (GWO-SVM), and whale optimization algorithm (WOA-SVM).
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| 8. |
- Song, Kai, 1988-, et al.
(författare)
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Improve the roles of nature reserves in conservation of endangered pheasant in a highly urbanized region
- 2020
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Nature reserves play an extraordinarily important role in conserving animal populations and their habitats. However, landscape change and unreasonable zoning designations often render these protected areas inadequate. Therefore, regular evaluation of the efficacy of protected lands is critical for maintaining and improving management strategies. Using species distribution models and GAP analysis, we assessed the changes in suitable habitat for the Brown Eared-pheasant (Crossoptilon mantchuricum) in two Chinese nature reserves between 1995 and 2013. Our results showed that the habitat suitability of Brown Eared-pheasant has changed dramatically during this period, and fragmentation analyses showed an increase in concentration area and decrease in patch area. In particular, our findings show that the national nature reserves need to adjust their ranges to ensure the conservation of this flagship species. Our study further provides a new viewpoint for evaluating the efficacy of protected lands, particularly in highly urbanized regions where conservation goals must be balanced with changing landscapes.
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| 9. |
- Sun, Yue, et al.
(författare)
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Molten salt-mediated hierarchical porous carbon derived from biomass waste for high-performance capacitive storage
- 2024
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Ingår i: Journal of Power Sources. - 0378-7753. ; 618
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Tidskriftsartikel (refereegranskat)abstract
- Biomass-derived carbon (BDC) materials are the suitable precursors for the fabrication of carbon electrodes of supercapacitors because of the sustainability, environmental friendliness, power capability, and structural diversity. The fabrication of BDC with low cost and excellent electrochemical properties is important for the practical applications of BDC in energy storage fields. Herein, ambrosia melon peels are used as carbon precursors for the fabrication of sustainable BDC electrodes through the molten salt-mediated pyrolysis procedure. The ambrosia melon peels-derived porous carbon (AMPPC) possesses high specific surface area of 529.9 m2 g−1. The AMPPC electrode shows the charge storage behavior of electrical double-layer capacitance with high ionic conductivity, high specific capacitance (218.3 F g−1 at 0.5 A g−1) and outstanding rate performance. In addition, the symmetric supercapacitor based on the AMPPC electrodes presents high specific energy density and specific power density (8 kW kg−1). It can be used as energy source to power helicopter model, clock, and calculator. Thus, the work gives an inspiration of design of BDC from the low-cost biomass waste and provides a simple way for the fabrication of BDC for the carbon electrodes of supercapacitors, lithium-ion batteries and so on.
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| 10. |
- Sun, Yue, et al.
(författare)
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Surface chemistry and structure manipulation of graphene-related materials to address the challenges of electrochemical energy storage
- 2023
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Ingår i: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1364-548X .- 1359-7345. ; 59:18, s. 2571-2583
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Tidskriftsartikel (refereegranskat)abstract
- Energy storage devices are important components in portable electronics, electric vehicles, and the electrical distribution grid. Batteries and supercapacitors have achieved great success as the spearhead of electrochemical energy storage devices, but need to be further developed in order to meet the ever-increasing energy demands, especially attaining higher power and energy density, and longer cycling life. Rational design of electrode materials plays a critical role in developing energy storage systems with higher performance. Graphene, the well-known 2D allotrope of carbon, with a unique structure and excellent properties has been considered a “magic” material with its high energy storage capability, which can not only aid in addressing the issues of the state-of-the-art lithium-ion batteries and supercapacitors, but also be crucial in the so-called post Li-ion battery era covering different technologies, e.g., sodium ion batteries, lithium-sulfur batteries, structural batteries, and hybrid supercapacitors. In this feature article, we provide a comprehensive overview of the strategies developed in our research to create graphene-based composite electrodes with better ionic conductivity, electron mobility, specific surface area, mechanical properties, and device performance than state-of-the-art electrodes. We summarize the strategies of structure manipulation and surface modification with specific focus on tackling the existing challenges in electrodes for batteries and supercapacitors by exploiting the unique properties of graphene-related materials.
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