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| 2. |
- 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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| 3. |
- 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. |
- Grøn, Ole, et al.
(författare)
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Acoustic mapping of submerged stone age sites—A HALD approach
- 2021
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Ingår i: Remote Sensing. - : MDPI AG. - 2072-4292. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- Acoustic response from lithics knapped by humans has been demonstrated to facilitate effective detection of submerged Stone Age sites exposed on the seafloor or embedded within its sediments. This phenomenon has recently enabled the non-invasive detection of several hitherto unknown submerged Stone Age sites, as well as the registration of acoustic responses from already known localities. Investigation of the acoustic-response characteristics of knapped lithics, which appear not to be replicated in naturally cracked lithic pieces (geofacts), is presently on-going through laboratory experiments and finite element (FE) modelling of high-resolution 3D-scanned pieces. Experimental work is also being undertaken, employing chirp sub-bottom systems (reflection seismic) on known sites in marine areas and inland water bodies. Fieldwork has already yielded positive results in this initial stage of development of an optimised Human-Altered Lithic Detection (HALD) method for mapping submerged Stone Age sites. This paper reviews the maritime archaeological perspectives of this promising approach, which potentially facilitates new and improved practice, summarizes existing data, and reports on the present state of development. Its focus is not reflection seismics as such, but a useful resonance phenomenon induced by the use of high-resolution reflection seismic systems.
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| 5. |
- Ji, Zhong-Hai, et al.
(författare)
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High-throughput screening and machine learning for the efficient growth of high-quality single-wall carbon nanotubes
- 2021
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Ingår i: Nano Reseach. - : Tsinghua University Press. - 1998-0124 .- 1998-0000. ; 14, s. 4610-4615
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Tidskriftsartikel (refereegranskat)abstract
- It has been a great challenge to optimize the growth conditions toward structure-controlled growth of single-wall carbon nanotubes (SWCNTs). Here, a high-throughput method combined with machine learning is reported that efficiently screens the growth conditions for the synthesis of high-quality SWCNTs. Patterned cobalt (Co) nanoparticles were deposited on a numerically marked silicon wafer as catalysts, and parameters of temperature, reduction time and carbon precursor were optimized. The crystallinity of the SWCNTs was characterized by Raman spectroscopy where the featured G/D peak intensity (IG/ID) was extracted automatically and mapped to the growth parameters to build a database. 1,280 data were collected to train machine learning models. Random forest regression (RFR) showed high precision in predicting the growth conditions for high-quality SWCNTs, as validated by further chemical vapor deposition (CVD) growth. This method shows great potential in structure-controlled growth of SWCNTs. [Figure not available: see fulltext.].
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| 6. |
- Liu, Zhigang, et al.
(författare)
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Gut microbiota mediates intermittent-fasting alleviation of diabetes-induced cognitive impairment
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1, s. 855-
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Tidskriftsartikel (refereegranskat)abstract
- Cognitive decline is one of the complications of type 2 diabetes (T2D). Intermittent fasting (IF) is a promising dietary intervention for alleviating T2D symptoms, but its protective effect on diabetes-driven cognitive dysfunction remains elusive. Here, we find that a 28-day IF regimen for diabetic mice improves behavioral impairment via a microbiota-metabolites-brain axis: IF enhances mitochondrial biogenesis and energy metabolism gene expression in hippocampus, re-structures the gut microbiota, and improves microbial metabolites that are related to cognitive function. Moreover, strong connections are observed between IF affected genes, microbiota and metabolites, as assessed by integrative modelling. Removing gut microbiota with antibiotics partly abolishes the neuroprotective effects of IF. Administration of 3-indolepropionic acid, serotonin, short chain fatty acids or tauroursodeoxycholic acid shows a similar effect to IF in terms of improving cognitive function. Together, our study purports the microbiota-metabolites-brain axis as a mechanism that can enable therapeutic strategies against metabolism-implicated cognitive pathophysiologies.
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| 7. |
- Petrache, C. M., et al.
(författare)
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Evidence of chiral bands in even-even nuclei
- 2018
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Ingår i: Physical Review C. - : American Physical Society. - 2469-9985 .- 2469-9993. ; 97:4
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Tidskriftsartikel (refereegranskat)abstract
- Evidence for chiral doublet bands has been observed for the first time in the even-even nucleus Nd136. One chiral band was firmly established. Four other candidates for chiral bands were also identified, which can contribute to the realization of the multiple pairs of chiral doublet bands (MχD) phenomenon. The observed bands are investigated by the constrained and tilted axis cranking covariant density functional theory (TAC-CDFT). Possible configurations have been explored. The experimental energy spectra, angular momenta, and B(M1)/B(E2) values for the assigned configurations are globally reproduced by TAC-CDFT. Calculated results support the chiral interpretation of the observed bands, which correspond to shapes with maximum triaxiality induced by different multiquasiparticle configurations in Nd136.
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| 8. |
- Ren, Bo, et al.
(författare)
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A Carbohydrate- Anion Recognition System in Aprotic Solvents
- 2014
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Ingår i: Chemistry - An Asian Journal. - : Wiley. - 1861-4728 .- 1861-471X. ; 9:5, s. 1298-1304
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Tidskriftsartikel (refereegranskat)abstract
- A carbohydrate-anion recognition system in nonpolar solvents is reported, in which complexes form at the B-faces of -D-pyranosides with H1-, H3-, and H5-cis patterns similar to carbohydrate- interactions. The complexation effect was evaluated for a range of carbohydrate structures; it resulted in either 1:1 carbohydrate-anion complexes, or 1:2 complex formation depending on the protection pattern of the carbohydrate. The interaction was also evaluated with different anions and solvents. In both cases it resulted in significant binding differences. The results indicate that complexation originates from van der Waals interactions or weak CHA(-) hydrogen bonds between the binding partners and is related to electron-withdrawing groups of the carbohydrates as well as increased hydrogen-bond-accepting capability of the anions.
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| 9. |
- Ren, Bo, et al.
(författare)
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An Iron(III) Catalyst with Unusually Broad Substrate Scope in Regioselective Alkylation of Diols and Polyols
- 2016
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Ingår i: Chemistry - A European Journal. - : Wiley-VCH Verlagsgesellschaft. - 0947-6539 .- 1521-3765. ; 22:7, s. 2481-2486
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Tidskriftsartikel (refereegranskat)abstract
- In this study, [Fe(dibm)(3)] (dibm=diisobutyrylmethane) is shown to have unusually broad scope as a catalyst for the selective monoalkylation of a diverse set of 1,2- and 1,3-diol-containing structures. The mechanism is proposed to proceed via a cyclic dioxolane-type intermediate, formed between the iron(III) species and two adjacent hydroxyl groups. This approach represents the first transition-metal catalysts that are able to replace stoichiometric amounts of organotin reagents in regioselective alkylation. The reactions generally lead to very high regioselectivities and high yields, on par with, or better than, previous methods used for regioselective alkylation.
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| 10. |
- Ren, Bo, et al.
(författare)
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Regioselective Acetylation of Diols and Polyols by Acetate Catalysis: Mechanism and Application.
- 2014
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Ingår i: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 79:17, s. 8134-8142
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Tidskriftsartikel (refereegranskat)abstract
- We propose a principle for H-bonding activation in acylation of hydroxyl groups, where the acylation is activated by the formation of hydrogen bonds between hydroxyl groups and anions. With the guidance of this principle, we demonstrate a method for the selective acylation of carbohydrates. By this method, diols and polyols are regioselectively acetylated in high yields under mild conditions using catalytic amts. of acetate. In comparison to other methods involving reagents such as organotin, organoboron, organosilicon, organobase, and metal salts, this method is more environmentally friendly, convenient, and efficient and is also assocd. with higher regioselectivity. We have performed a thorough quantum chem. study to decipher the mechanism, which suggests that acetate first forms a dual H-bond complex with a diol, which enables subsequent monoacylation by acetic anhydride under mild conditions. The regioselectivity appears to originate from the inherent structure of the diols and polyols and their specific interactions with the coordinating acetate catalyst. [on SciFinder(R)]
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