| 1. |
|
|
| 2. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
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.
|
|
| 3. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
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.
|
|
| 4. |
- Kristan, Matej, et al.
(författare)
-
The Visual Object Tracking VOT2015 challenge results
- 2015
-
Ingår i: Proceedings 2015 IEEE International Conference on Computer Vision Workshops ICCVW 2015. - : IEEE. - 9780769557205 ; , s. 564-586
-
Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge 2015, VOT2015, aims at comparing short-term single-object visual trackers that do not apply pre-learned models of object appearance. Results of 62 trackers are presented. The number of tested trackers makes VOT 2015 the largest benchmark on short-term tracking to date. For each participating tracker, a short description is provided in the appendix. Features of the VOT2015 challenge that go beyond its VOT2014 predecessor are: (i) a new VOT2015 dataset twice as large as in VOT2014 with full annotation of targets by rotated bounding boxes and per-frame attribute, (ii) extensions of the VOT2014 evaluation methodology by introduction of a new performance measure. The dataset, the evaluation kit as well as the results are publicly available at the challenge website(1).
|
|
| 5. |
- Cheng, Jie, et al.
(författare)
-
Interactions in Composite Film Formation of Mefp-1/graphene on Carbon Steel
- 2021
-
Ingår i: Coatings. - : MDPI AG. - 2079-6412. ; 11:10
-
Tidskriftsartikel (refereegranskat)abstract
- Mefp-1 adhesive protein derived from marine blue mussels, together with the 2D material graphene, was used to build the green composite film with enhanced anti-corrosion property and mechanical strength. The corrosion inhibition of the composite film, formed by different methods, was evaluated by using electrochemical impedance spectroscopy. The non-degraded adhesion of the composite film to the carbon steel substrate was proved by nano-scratch tests. Infrared spectroscopy was utilized to investigate the film formation process and "three-body interactions " between Mefp-1, graphene and carbon steel surface. The results show that the Mefp-1 adsorbs on the carbon steel surface mainly through the covalent bond between catechols and Fe(III). Meanwhile, Mefp-1 can bond to non-adhesive graphene by forming hydrogen bonds and pi-pi interaction non-covalent bonds, which facilitate the formation of a robust Mefp-1/graphene composite film on the carbon steel surface.
|
|
| 6. |
- Darwich, Adam S., et al.
(författare)
-
IMI - Oral biopharmaceutics tools project - Evaluation of bottom-up PBPK prediction success part 3 : Identifying gaps in system parameters by analysing In Silico performance across different compound classes
- 2017
-
Ingår i: European Journal of Pharmaceutical Sciences. - : Elsevier BV. - 0928-0987 .- 1879-0720. ; 96, s. 626-642
-
Tidskriftsartikel (refereegranskat)abstract
- Three Physiologically Based Pharmacokinetic software packages (GI-Sim, Simcyp (R) Simulator, and GastroPlus (TM)) were evaluated as part of the Innovative Medicine Initiative Oral Biopharmaceutics Tools project (OrBiTo) during a blinded "bottom-up" anticipation of human pharmacokinetics. After data analysis of the predicted vs. measured pharmacokinetics parameters, it was found that oral bioavailability (F-oral) was underpredicted for compounds with low permeability, suggesting improper estimates of intestinal surface area, colonic absorption and/or lack of intestinal transporter information. Foralwas also underpredicted for acidic compounds, suggesting overestimation of impact of ionisation on permeation, lack of information on intestinal transporters, or underestimation of solubilisation of weak acids due to less than optimal intestinal model pH settings or underestimation of bile micelle contribution. F-oral was overpredicted for weak bases, suggesting inadequate models for precipitation or lack of in vitro precipitation information to build informed models. Relative bioavailability was underpredicted for both high logP compounds as well as poorly water-soluble compounds, suggesting inadequate models for solubility/dissolution, underperforming bile enhancement models and/or lack of biorelevant solubility measurements. These results indicate areas for improvement in model software, modelling approaches, and generation of applicable input data. However, caution is required when interpreting the impact of drug-specific properties in this exercise, as the availability of input parameters was heterogeneous and highly variable, and the modellers generally used the data "as is" in this blinded bottom-up prediction approach.
|
|
| 7. |
- Fan, Mei-Cen, et al.
(författare)
-
Room-temperature extraction of individual elements from charged spent LiFePO4 batteries
- 2022
-
Ingår i: Rare Metals. - : Springer. - 1001-0521 .- 1867-7185.
-
Tidskriftsartikel (refereegranskat)abstract
- Recycling millions of metric tons of spent LiFePO4 batteries would benefit human health while reducing resource depletion and environmental pollution. However, recovering individual elements from the spent batteries without generating waste is challenging. Here, we present a distinctive approach for recycling spent LiFePO4 batteries at room temperature, where water is the only leaching agent consumed. FePO4 and lithium intercalated graphite act as a precursor material for selectively extracting lithium, iron, and phosphorus through charging the LiFePO4 batteries to the delithiated state. NaOH solution extracted Fe from FePO4 within 30 min and regenerated without consumption, similar to a catalyst. Under the optimal leaching conditions (1 mol·L−1 NaOH, 0.5 h, NaOH/Fe molar ratio of 4.5), Fe and P leaching efficiencies achieved 89.1% and 99.2%, respectively. The methodology reflected in this research reduced the material cost per kg cathode material to a fraction of previously published reports, only occupies 6.13% of previous reports. In addition, the method improved the battery recycling revenue calculated by the EverBatt model by 2.31 times and 1.94 times over pyrometallurgical and hydrometallurgical methods. The proposed method allows for the convenient recovery of the elemental components of spent LiFePO4 batteries.
|
|
| 8. |
- Fang, Zhiyong, et al.
(författare)
-
Selective Electro-oxidation of Alcohols to the Corresponding Aldehydes in Aqueous Solution via Cu(III) Intermediates from CuO Nanorods
- 2021
-
Ingår i: ACS Sustainable Chemistry and Engineering. - : American Chemical Society (ACS). - 2168-0485. ; 9:35, s. 11855-11861
-
Tidskriftsartikel (refereegranskat)abstract
- Electrochemical oxidation using renewable energy is an attractive strategy that provides a sustainable and mild approach for biomass transformation. Herein, the electrocatalytic oxidation of furfuryl alcohol in an aqueous solution was investigated using CuO nanorods. Two kinds of Cu-III intermediates, namely, (CuO2)(-) and (Cu2O6)(6-), were detected on the surface of the working electrode. (Cu2O6)(6-), generated in the potential range of 1.35-1.39 V versus the reversible hydrogen electrode (RHE), induced the oxidation of furfuryl alcohol to furaldehyde with a yield of >= 98%. (CuO2)(-), generated at a potential greater than 1.39 V versus RHE, which led to the oxidation of furfuryl alcohol to 2-furoic acid with a yield of >= 99%. Furthermore, the Cu-III-catalyzed system exhibited a measure of universal applicability, wherein (Cu2O6)(6-) and (CuO2)(-) induced the highly selective electro-oxidation of benzyl alcohol, vanillyl alcohol, and 4-pyridinemethanol to yield the corresponding aldehydes and acids, respectively.
|
|
| 9. |
- Li, Hanbing, et al.
(författare)
-
Dual Function of PI(4,5)P2 in Insulin-Regulated Exocytic Trafficking of GLUT4 in Adipocytes
- 2020
-
Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 432:16, s. 4341-4357
-
Tidskriftsartikel (refereegranskat)abstract
- Phosphoinositides are important signaling molecules involved in the regulation of vesicular trafficking. It has been implicated that phosphatidylinositol 4,5-bisphosphate [PI(4,5)P-2] is involved in insulin-regulated GLUT4 translocation in adipocytes. However, it remains unclear where and how PI(4,5)P-2 regulates discrete steps of GLUT4 vesicle translocation in adipocytes, especially on the exocytic arm of regulation. Here, we employed optogenetic tools to acutely control the PI(4,5)P-2 metabolism in living cells. By combination of TIRFM imaging, we were able to monitor the temporal-spatial-dependent PI(4,5)P-2 regulation on discrete steps of GLUT4 translocation in adipocytes. We found that the plasma membrane localized PI(4,5)P-2 is crucial for proper insulin signaling propagation and for insulin-stimulated GLUT4 vesicle translocation in 3T3-L1 adipocytes. Global depletion of PI(4,5)P-2 on the cell surface blunted insulin-stimulated Akt phosphorylation and abolished insulin effects in promotion of the docking and fusion of GLUT4 vesicle with the plasma membrane. Furthermore, by development of a novel optogenetic module to selectively modulate PI(4,5)P-2 levels on the GLUT4 vesicle docking site, we identified an important regulatory role of PI(4,5)P-2 in controlling of vesicle docking process. Local depletion of PI(4,5)P-2 at the vesicle docking site promoted GLUT4 vesicle undocking, diminished insulin-stimulated GLUT4 vesicle docking and fusion, but without perturbation of insulin signaling propagation in adipocytes. Our results provide strong evidence that cell surface PI(4,5)P-2 plays two distinct functions on regulation of the exocytic trafficking of GLUT4 in adipocytes. PI(4,5)P-2 not only regulates the proper activation of insulin signaling in general but also controls GLUT4 vesicle docking process at the vesicle-membrane contact sites.
|
|
| 10. |
|
|
