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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. |
- Osoegawa, Kazutoyo, et al.
(författare)
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Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop
- 2019
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Ingår i: Human Immunology. - : ELSEVIER SCIENCE INC. - 0198-8859 .- 1879-1166. ; 80:4, s. 228-236
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Tidskriftsartikel (refereegranskat)abstract
- The 17th International HLA and Immunogenetics Workshop (IHIW) organizers conducted a Pilot Study (PS) in which 13 laboratories (15 groups) participated to assess the performance of the various sequencing library preparation protocols, NGS platforms and software in use prior to the workshop. The organizers sent 50 cell lines to each of the 15 groups, scored the 15 independently generated sets of NGS HLA genotyping data, and generated "consensus" HLA genotypes for each of the 50 cell lines. Proficiency Testing (PT) was subsequently organized using four sets of 24 cell lines, selected from 48 of 50 PS cell lines, to validate the quality of NGS HLA typing data from the 34 participating IHIW laboratories. Completion of the PT program with a minimum score of 95% concordance at the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 loci satisfied the requirements to submit NGS HLA typing data for the 17th IHIW projects. Together, these PS and PT efforts constituted the 17th IHIW Quality Control project. Overall PT concordance rates for HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB3, HLA-DRB4 and HLA-DRB5 were 98.1%, 97.0% and 98.1%, 99.0%, 98.6%, 98.8%, 97.6%, 96.0%, 99.1%, 90.0% and 91.7%, respectively. Across all loci, the majority of the discordance was due to allele dropout. The high cost of NGS HLA genotyping per experiment likely prevented the retyping of initially failed HLA loci. Despite the high HLA genotype concordance rates of the software, there remains room for improvement in the assembly of more accurate consensus DNA sequences by NGS HLA genotyping software.
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| 4. |
- Sharma, Janpriy, et al.
(författare)
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Avenues of decarbonisation in the dynamics of processed food supply chains : Towards responsible production consumption
- 2024
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Ingår i: Heliyon. - : Cell Press. - 2405-8440. ; 10:5
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Tidskriftsartikel (refereegranskat)abstract
- Nowadays, the demand for processed food items is surging. To fulfil the enhanced demand, a significant impact is laid on the environment, which enhances the carbon footprint being generated. Hence, to overcome this, the avenues of decarbonisation need to be explored. The presented work is aimed at promoting the decarbonisation of the existing practices within the processed food supply chains. It finds strong compliance with the sustainable development goal (SDG-12), focusing on responsible production-consumption mechanisms. For the same, key enactors of decarbonisation are identified and mapped with the practices at various stages of food supply chains, i.e. upstream, downstream, and other allied practices. Based upon these enactors, a relational, hierarchical framework is developed to provide a comprehensive perspective on complex intricacies. This framework is analysed with an innovative approach which comprises the fundamentals of Interval-Valued Intuitionistic Hesitant Fuzzy Set with the Entropy measures. It results in the outranking of the enactors relative to its importance in the decarbonisation of processed food supply chains. Furthermore, the empirical findings are validated by the sensitivity analysis to felicitate robust decision-making. The outcomes of the presented work provide a roadmap and stepped approach to achieve the decarbonisation goals and make productionconsumption mechanisms sustainable. It finds implications in the development of the framework, policy formulation, and decisional attributes for the decarbonisation of food supply chains. It focuses on the adoption of strategies that align with global efforts to mitigate climate change and promote a sustainable future.
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| 5. |
- Tyagi, Shweta, et al.
(författare)
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E2F activation of S phase promoters via association with HCF-1 and the MLL family of histone H3K4 methyltransferases.
- 2007
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Ingår i: Molecular Cell. - : Elsevier (Cell Press). - 1097-2765 .- 1097-4164. ; 27:1, s. 107-119
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Tidskriftsartikel (refereegranskat)abstract
- E2F transcriptional regulators control human-cell proliferation by repressing and activating the transcription of genes required for cell-cycle progression, particularly the S phase. E2F proteins repress transcription in association with retinoblastoma pocket proteins, but less is known about how they activate transcription. Here, we show that the human G1 phase regulator HCF-1 associates with both activator (E2F1 and E2F3a) and repressor (E2F4) E2F proteins, properties that are conserved in insect cells. Human HCF-1-E2F interactions are versatile: their associations and binding to E2F-responsive promoters are cell-cycle selective, and HCF-1 displays coactivator properties when bound to the E2F1 activator and corepressor properties when bound to the E2F4 repressor. During the G1-to-S phase transition, HCF-1 recruits the mixed-lineage leukemia (MLL) and Set-1 histone H3 lysine 4 methyltransferases to E2F-responsive promoters and induces histone methylation and transcriptional activation. These results suggest that HCF-1 induces cell-cycle-specific transcriptional activation by E2F proteins to promote cell proliferation.
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