| 1. |
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| 2. |
- 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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| 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. |
- Liu, Huan, et al.
(författare)
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The first human induced pluripotent stem cell line of Kashin–Beck disease reveals involvement of heparan sulfate proteoglycan biosynthesis and PPAR pathway
- 2022
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Ingår i: The FEBS Journal. - : John Wiley & Sons. - 1742-464X .- 1742-4658. ; 289:1, s. 279-293
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: Kashin-Beck disease (KBD) is an endemic osteochondropathy. Due to a lack of suitable animal or cellular disease models, the research progress on KBD has been limited. Our goal was to establish the first disease-specific human induced pluripotent stem cells (hiPSCs) cellular disease model of KBD, and to explore its etiology and pathogenesis exploiting transcriptome sequencing.METHODS: HiPSCs were reprogrammed from dermal fibroblasts of two KBD and one healthy control donors via integration-free vectors. Subsequently, hiPSCs were differentiated into chondrocytes through three-week culture. Gene expression profiles in KBD, normal primary chondrocytes and hiPSC-derived chondrocytes were defined by RNA sequencing. A Venn diagram was constructed to show the number of shared differentially expressed genes (DEGs) between KBD and normal. Gene oncology and Kyoto Encyclopedia of Genes and Genomes annotations were performed, and six DEGs were further validated in other individuals by real-time quantitative reverse transcription PCR (RT-qPCR).RESULTS: KBD cellular disease models were successfully established by generation of hiPSC lines. Seventeen consistent and significant DEGs present in all compared groups (KBD and normal) were identified. RT-qPCR validation gave consistent results with the sequencing data. Glycosaminoglycan biosynthesis-heparan sulfate/heparin, PPAR signaling pathway and cell adhesion molecules (CAMs) pathways were identified to be significantly altered in KBD.CONCLUSION: Differentiated chondrocytes deriving from KBD-origin hiPSCs provide the first cellular disease model for etiological studies of KBD. This study also provides new sights into the pathogenesis and etiology of KBD and is likely to inform the development of targeted therapeutics for its treatment.
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| 5. |
- Liu, Linan, et al.
(författare)
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Silicon Effects on Biomass Carbon and Phytolith-Occluded Carbon in Grasslands Under High-Salinity Conditions
- 2020
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 11, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- Changes in climate and land use are causing grasslands to suffer increasingly fromabiotic stresses, including soil salinization. Silicon (Si) amendment has been frequentlyproposed to improve plant resistance to multiple biotic and abiotic stresses and increaseecosystem productivity while controlling the biogeochemical carbon (C) cycle. However,the effects of Si on plant C distribution and accumulation in salt-suffering grasslandsare still unclear. In this study, we investigated how salt ions affected major elementalcomposition in plants and whether Si enhanced biomass C accumulation in grasslandspecies in situ. In samples from the margins of salt lakes, our results showed that thediffering distance away from the shore resulted in distinctive phytocoenosis, includinghalophytes and moderately salt-tolerant grasses, which are closely related to changingsoil properties. Different salinity (NaC/KC, ranging from 0.02 to 11.8) in plants causednegative effects on plant C content that decreased from 53.9 to 29.2% with theincrease in salinity. Plant Si storage [0.02–2.29 g Si m?2 dry weight (dw)] and plantSi content (0.53 to 2.58%) were positively correlated with bioavailable Si in soils(ranging from 94.4 to 192 mg kg?1). Although C contents in plants and phytoliths werenegatively correlated with plant Si content, biomass C accumulation (1.90–83.5 g Cm?2 dw) increased due to the increase of Si storage in plants. Plant phytolith-occludedcarbon (PhytOC) increased from 0.07 to 0.28h of dry mass with the increase of Sicontent in moderately salt-tolerant grasses. This study demonstrates the potential ofSi in mediating plant salinity and C assimilation, providing a reference for potentialmanipulation of long-term C sequestration via PhytOC production and biomass Caccumulation in Si-accumulator dominated grasslands.
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| 6. |
- Ye, Lei, et al.
(författare)
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Preparation of Metallized Pellets from Blast Furnace Dust and Electric Arc Furnace Dust Based on Microwave Impedance Matching
- 2020
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Ingår i: 11th International Symposium on High-Temperature Metallurgical Processing. - Cham : Springer Nature. - 9783030365400 - 9783030365394 ; , s. 569-579
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Konferensbidrag (refereegranskat)abstract
- Blast furnace dust and electric arc furnace dust are two typical solid wastes in iron and steel industry. In order to overcome the shortcomings of traditional processes, such as low metal recovery efficiency and high secondary pollution, microwave energy was applied in this study to intensify the self-reduction of core-shell BF dust-EAF dust composite pellets based on impedance matching for realizing highly efficient migration and separation of iron, zinc, and lead. By reducing the composite pellets in microwave field, it was found that under the optimal conditions of proportion of EAF dust in shell to all EAF dust in the pellet of 20%, reduction temperature of 1000 degrees C, and dwell time of 15 min, metallized pellets with the total iron content of 68.73 wt %, iron metallization degree of 95.87%, zinc removal percentage of 88.78%, lead removal percentage of 94.38%, and compressive strength of 190.4 N/p were obtained.
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| 7. |
- Ye, Lei, et al.
(författare)
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Toward environmentally friendly direct reduced iron production : A novel route of comprehensive utilization of blast furnace dust and electric arc furnace dust
- 2021
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Ingår i: Waste Management. - : Elsevier. - 0956-053X .- 1879-2456. ; 135, s. 389-396
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Tidskriftsartikel (refereegranskat)abstract
- In this study, a novel method for producing direct reduced iron (DRI) powders based on microwave-assisted self reduction of core-shell composite pellets composed of blast furnace (BF) dust and hazardous electric arc furnace (EAF) dust followed by magnetic separation was reported. The proper core-shell structure of the composite pellets was designed according to the rule of impedance matching and properties of BF dust and EAF dust by adjusting the thickness of shell (i.e., thickness of impedance matching layer) via controlling the C/O molar ratio of the raw materials from 0.55 to 0.70. The results showed that the EAF dust with high content of CaO was beneficial to the mechanical strength of green, dried, and metallized pellets (collected after reduction), while the BF dust with high content of carbon enabled sufficient microwave-assisted reduction of the pellets, facilitating subsequent magnetic separation and also the removal of zinc from EAF dust. By reduction of the core-shell BF dust-EAF dust composite pellets with the C/O molar ratio of 0.65 at 1050 degrees C for 15 min, the resulting metallized pellets showed superior reduction and magnetic separation indexes with higher removal percentages of zinc and lead, in comparison with conventional metallized pellets. The DRI powders obtained after magnetic separation had total iron content of 91.2 wt%, iron metallization degree of 95.8%, yield of 68.1%, and iron recovery of 88.0%. This study provided a good example for efficient and environmentally friendly comprehensive utilization of typical and hazardous wastes in the iron and steel industry.
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| 8. |
- Ye, Qing, et al.
(författare)
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Microwave-assisted self-reduction of EAF dust-biochar composite briquettes for production of direct reduced iron
- 2020
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Ingår i: Powder Technology. - : ELSEVIER. - 0032-5910 .- 1873-328X. ; 362, s. 781-789
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Tidskriftsartikel (refereegranskat)abstract
- This study applied microwave energy for rapid self-reduction of electric arc furnace (EAF) dust-biochar composite briquettes to produce powdered direct reduced iron (DRI). based on the good electromagnetic response of EAF dust-biochar composite briquettes. The reduction experimental results showed that the iron-bearing components in the dust were reduced to metallic iron, leading to a high iron metallization degree of the reduced briquettes (94.7%). Meanwhile, the zinc-containing phases of EAF dust in the composite briquettes were converted to metallic zinc which then volatilized together with lead in the form of PbCl2. The volatilization percentages of zinc and lead were 99.6% and 92.9%, respectively, after reduction with the mass ratio of biochar to EAF dust of 0.25 and heating rate of 25 degrees C/min at 1050 degrees C for 15 min. By magnetic separation of the reduced briquettes, a magnetic concentrate with iron content of 91.32 wt% and recovery of 87.36% was obtained, meeting the quality requirements of DRI. (C) 2019 Elsevier B.V. All rights reserved.
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| 9. |
- Ye, Qing, et al.
(författare)
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Thermodynamic Analysis of Carbothermic Reduction of Electric Arc Furnace Dust
- 2019
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Ingår i: 10th International Symposium On High-Temperature Metallurgical Processing. - Cham : Springer International Publishing. - 9783030059552 - 9783030059545 ; , s. 117-124
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Konferensbidrag (refereegranskat)abstract
- Electric arc furnace (EAF) dust is a kind of secondary resource which contains multiple metallic elements, including Fe, Mn and Cr. Pyrometallurgical processes for recovering metal elements from EAF dust have been investigated for many years although they are suffered from high energy consumption due to the spinel-structured components of EAF dust. In this study, the thermodynamic analysis of carbothermic reduction of EAF dust was performed. The main components of EAF dust were magnetite (Fe3O4), hausmannite (Mn3O4) and chromate spinel (FeCr2O4). The gangue minerals were mainly composed of magnesium silicates. The thermodynamic analysis indicated that magnetite and hausmannite can be reduced to metallic iron and MnO, respectively. Meanwhile, the chromate spinel will be reduced to chromium oxide and then to form CaCr2O4. The results also demonstrated that the gangue components can promote the separation of Fe and Cr, agreeing well with the experimental results.
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| 10. |
- Colineau, Lucie, et al.
(författare)
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Interaction of Streptococcus pyogenes with extracellular matrix components resulting in immunomodulation and bacterial eradication
- 2020
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Ingår i: Matrix Biology Plus. - : Elsevier BV. - 2590-0285. ; 6-7
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Tidskriftsartikel (refereegranskat)abstract
- Streptococcus pyogenes is a major human pathogen that causes a variety of diseases ranging from mild skin and throat infections to fatal septicemia. In severe invasive infections, S. pyogenes encounters and interacts with components of the extracellular matrix (ECM), including small leucine rich-proteoglycans (SLRPs). In this study, we report a novel antimicrobial role played by SLRPs biglycan, decorin, fibromodulin and osteoadherin, specifically in promoting the eradication of S. pyogenes in a human sepsis model of infection. SLRPs can be released from the ECM and de novo synthesized by a number of cell types. We reveal that infection of human monocytes by S. pyogenes induces the expression of decorin. Furthermore, we show that the majority of genetically distinct and clinically relevant S. pyogenes isolates interact with SLRPs resulting in decreased survival in blood killing assays. Biglycan and decorin induce TLR2 and TLR4 signaling cascades resulting in secretion of proinflammatory and chemotactic molecules and recruitment of professional phagocytes. Surprisingly, SLRP-mediated elimination of S. pyogenes occurs independently of TLR activation. Our results indicate that SLRPs act in concert with human serum, enhancing deposition of complement activation fragments and the classical activator C1q on the bacterial surface, facilitating efficient microbial eradication. Addition of the complement C3 inhibitor compstatin significantly reverses SLRP-induced blood killing, confirming active complement as a key mediator in SLRP-mediated bacterial destruction. Taken together our results add to the functional repertoire of SLRPs, expanding to encompass their role in controlling bacterial infection.
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