| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 2. |
- Li, Doudou, et al.
(author)
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Gut microbiota-derived metabolite trimethylamine-N-oxide and multiple health outcomes : an umbrella review and updated meta-analysis
- 2022
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In: American Journal of Clinical Nutrition. - : Oxford University Press. - 0002-9165 .- 1938-3207. ; 116:1, s. 230-243
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Research review (peer-reviewed)abstract
- Background: Trimethylamine-N-oxide (TMAO) is a gut microbiota-derived metabolite produced from dietary nutrients. Many studies have discovered that circulating TMAO concentrations are linked to a wide range of health outcomes.Objectives: This study aimed to summarize health outcomes related to circulating TMAO concentrations.Methods: We searched the Embase. Medline, Web of Science, and Scopus databases from inception to 15 February, 2022 to identify and update meta-analyses examining the associations between 'TAO and multiple health outcomes. For each health outcome, we estimated the summary effect size. 95% prediction CI. between-study heterogeneity. evidence of small-study effects, and evidence of excess-significance bias. These metrics were used to evaluate the evidence credibility of the identified associations.Results: This umbrella review identified 24 meta-analyses that investigated the association between circulating 'TAO concentrations and health outcomes including all-cause mortality, cardiovascular diseases (CVDs), diabetes mellitus (DM), cancer. and renal function. We updated these meta-analyses by including a total of 82 individual studies on 18 unique health outcomes. Among them, 14 associations were nominally significant. After evidence credibility assessment, we found 6 (33%) associations (i.e., all-cause mortality, CVD mortality, major adverse cardiovascular events, hypertension. DM, and glomerular filtration rate) to present highly suggestive evidence.Conclusions: TMAO might be a novel biomarker related to human health conditions including all-cause mortality, hypertension. CVD, DM. cancer, and kidney function. Further studies are needed to investigate whether circulating 'MAO concentrations could be an intervention target for chronic disease.
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| 3. |
- Fernandes, Alwyn R., et al.
(author)
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Recommended terms and abbreviations for polychlorinated alkanes (PCAs) as the predominant component of chlorinated paraffins (CPs)
- 2023
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In: TrAC. Trends in analytical chemistry. - : Elsevier. - 0165-9936 .- 1879-3142. ; 169
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Research review (peer-reviewed)abstract
- Despite several decades of study, ambiguities persist in terms used to express environmental and biotic occurrences of polychlorinated alkanes (PCAs), the main ingredient of chlorinated paraffins (CPs). This can lead to misinterpretation of data between analytical chemists, toxicologists, risk assessors/managers and regulators. The terms recommended here to harmonise reporting and reduce ambiguity use the conventional definition of PCAs - linear chlorinated alkanes (typically, C≥10) with one chlorine per carbon, although some evidence of multiple chlorination exists. Other recommendations include.● reporting the “Sum of measured PCAs” because “Total PCAs” is currently unquantifiable.●reporting individual chain lengths, e.g., ΣPCAs-C11, ΣPCAs-C13, allows easier comparability and allows toxicology and risk assessment to consider different PCA combinations.● maintain studies on individual PCAs in order to better characterise chemical, environmental and health risk behaviour.The terms could be extended in future to assimilate new findings on individual PCAs, multiple chlorination and chirality.
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| 4. |
- Yuan, Bo, et al.
(author)
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Methods for trace analysis of short-, medium-, and long-chain chlorinated paraffins : Critical review and recommendations
- 2019
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In: Analytica Chimica Acta. - : Elsevier BV. - 0003-2670 .- 1873-4324. ; 1074, s. 16-32
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Research review (peer-reviewed)abstract
- Many methods for quantifying chlorinated paraffins (CPs) yield only a total concentration of the mixture as a single value. With appropriate analytical instrumentation and quantification methods, more reliable and detailed analysis can be performed by quantifying total concentrations of short-, medium-, and longchain CPs (SCCPs, MCCPs, and LCCPs), and in the current optimal situation by quantifying individual carbon-chlorine congener groups (CnClm). Sample extraction and clean-up methods for other persistent organochlorines that have been adapted for recovery of CPs must be applied prior to quantification with appropriate quality assurance and quality control to ensure applicability of the methods for SCCPs, MCCPs, and LCCPs. Part critical review, part tutorial, and part perspective, this paper provides practical guidance to analytical chemists who are interested in establishing a method for analysis of CPs in their lab facilities using commercial reference standards, or for expanding existing analysis of total CPs or SCCPs to analysis of SCCPs, MCCPs, and LCCPs, or to analysis of CnClm congener groups.
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