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| 2. |
- 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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| 4. |
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- 2019
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Journal article (peer-reviewed)
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| 5. |
- Ngo, Hai Hoang Tuan, et al.
(author)
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Effect of light-touch intervention and associated factors to microbial contamination at small-scale pig slaughterhouses and traditional pork shops in Vietnam
- 2023
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In: International Journal of Food Microbiology. - : Elsevier. - 0168-1605 .- 1879-3460. ; 406
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Journal article (peer-reviewed)abstract
- Traditional pork value chains dominate the production and distribution of pork in Vietnam; however, the high level of microbiological contamination in pork may increase the risk of food-borne disease for consumers. There is limited evidence about how to feasibly and scalably reduce microbial contamination in pork sold in traditional markets. This study aimed to assess the effectiveness of light-touch interventions for changing worker behaviour in small-scale slaughterhouses and vendors at traditional pork shops, as well as to identify risk factors for pork contamination. The intervention packages consisted of providing hygiene tools and delivering a food safety training which had been designed in a participatory way and covered 10 small-scale slaughterhouses and 29 pork shops. Pig carcasses, retailed pork, contact surfaces, and hands were sampled to measure the total bacterial count (TBC) and Salmonella contamination before, three and six weeks after the intervention, and trainee practices were observed at the same time. Linear and generalized linear mixed effects models were constructed to identify risk factors for TBC and Salmonella contamination at the slaughterhouses and pork shops. The interventions at slaughterhouses and pork shops both showed a slight reduction of TBC contamination in pig carcasses and Salmonella prevalence in retailed pork, while the TBC in retailed pork decreased only marginally. For slaughterhouses, the regression model indicated that smoking or eating during slaughtering (indicating poor hygienic practices) was associated with TBC increasing, while cleaning floors and wearing boots reduced TBC contamination. For pork shops, using rough materials (cardboard or wood) to display pork was the only factor increasing TBC contamination in pork, whereas cleaning knives was associated with lower TBC. Besides, the presence of supporters and wearing aprons reduced the probability of Salmonella contamination in pork. The findings highlight the effectiveness of light-touch interventions in reducing microbial contamination in pig carcasses at small-scale slaughterhouses and pork at traditional shops over the study period.
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| 6. |
- Ngo, Hoang Tuan Hai, et al.
(author)
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Assessment of a light-touch intervention to reduce microbial contamination at small-scale pig slaughterhouses and traditional pork shops in Vietnam
- 2023
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In: International Journal of Food Microbiology. - : Elsevier. - 0168-1605 .- 1879-3460. ; 406
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Journal article (peer-reviewed)abstract
- Traditional pork value chains dominate the production and distribution of pork in Vietnam; however, there high microbiological contamination of pork may lead to health risks. There is limited evidence about how to sustainably and scalably reduce microbial contamination in pork sold in traditional markets. This study aimed to assess the effectiveness of light-touch interventions for changing worker behaviour in small-scale slaughterhouses and retailers at traditional pork shops, as well as to identify risk factors for pork contamination. The intervention packages consisted of providing hygiene tools and delivering a food safety training which had been designed in a participatory way and covered 10 small-scale slaughterhouses and 29 pork shops. Pig carcasses, retailed pork, contact surfaces, and hands were sampled to measure the total bacterial count (TBC) and Salmonella contamination and trainee practices were observed before, three and six weeks after the intervention. Linear and generalized linear mixed effects models were constructed to identify risk factors for TBC and Salmonella contamination at the slaughterhouses and pork shops. Intervention results showed a slight reduction of TBC contamination in pig carcasses from 4.46 to 4.23 log10 CFU/cm2 (p = 0.09) and Salmonella prevalence in retailed pork (reduction from 52% to 24% detection, p = 0.08), while the TBC in retailed pork decreased only marginally (5.47 vs. 5.36 log10 CFU/g, p = 0.23). For slaughterhouses, the regression model indicated that smoking or eating during slaughtering was a risk factor, associated with TBC increasing by 0.60 log10 CFU/g (95% confidence interval (CI): 0.12 to 0.96, p =0.02), while cleaning floors and wearing boots reduced TBC contamination with 0.53 log10 CFU/g (CI: –0.83 to 0.01, p = 0.03) and 1.04 log10 CFU/g (CI: –1.50 to –0.26, p = 0.03), respectively. For pork shops, using rough materials (cardboard or wood) to display pork was the only factor increasing TBC contamination in pork with 0.57 log10 CFU/g (CI: 0.22 to 0.91, p < 0.001), whereas wearing aprons was associated with lower TBC, with 0.45 log10 CFU/g (CI: –0.79 to –0.12, p = 0.02), and Salmonella contamination in pork (odds ratio (OR) = 0.13, CI: 0.02 to 0.72, p = 0.03). The findings highlight the effectiveness of light-touch interventions in reducing microbial contamination in pig carcasses and pork over the study period.
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| 7. |
- Gao, Hong, et al.
(author)
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The landscape of tolerated genetic variation in humans and primates
- 2023
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6648
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Journal article (peer-reviewed)abstract
- Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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