| 1. |
- 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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| 2. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 3. |
- Monteiro, Ana C. S., et al.
(författare)
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Identification, characterization and localization of chagasin, a tight-binding cysteine protease inhibitor in Trypanosoma cruzi
- 2001
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Ingår i: Journal of Cell Science. - 0021-9533. ; 114:21, s. 3933-3942
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Tidskriftsartikel (refereegranskat)abstract
- Lysosomal cysteine proteases from mammalian cells and plants are regulated by endogenous tight-binding inhibitors from the cystatin superfamily. The presence of cystatin-like inhibitors in lower eukaryotes such as protozoan parasites has not yet been demonstrated, although these cells express large quantities of cysteine proteases and may also count on endogenous inhibitors to regulate cellular proteolysis. Trypanosoma cruzi, the causative agent of Chagas heart disease, is a relevant model to explore this possibility because these intracellular parasites rely on their major lysosomal cysteine protease (cruzipain) to invade and multiply in mammalian host cells. Here we report the isolation, biochemical characterization, developmental stage distribution and subcellular localization of chagasin, an endogenous cysteine protease inhibitor in T. cruzi. We used high temperature induced denaturation to isolate a heat-stable cruzipain-binding protein (apparent molecular mass, 12 kDa) from epimastigote lysates. This protein was subsequently characterized as a tight-binding and reversible inhibitor of papain-like cysteine proteases. Immunoblotting indicated that the expression of chagasin is developmentally regulated and inversely correlated with that of cruzipain. Gold-labeled antibodies localized chagasin to the flagellar pocket and cytoplasmic vesicles of trypomastigotes and to the cell surface of amastigotes. Binding assays performed by probing living parasites with fluorescein (FITC)-cruzipain or FITC-chagasin revealed the presence of both inhibitor and protease at the cell surface of amastigotes. The intersection of chagasin and cruzipain trafficking pathways may represent a checkpoint for downstream regulation of proteolysis in trypanosomatid protozoa.
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| 4. |
- Salles-Filho, Sergio Luiz Monteiro, et al.
(författare)
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Monitoring and Evaluation as a Way to Complete and to Implement a Policy : The Case of Brazilian National Innovation Policy
- 2022
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The present National Innovation Policy (henceforth called PNI) was instituted in Brazil by Decree No. 10.537, of October 28, 2020, within the federal public administration. The policy's objective is to guide, coordinate and articulate strategies, programs, and actions across several public entities to foster innovation in the productive sector. Thus, it aims to increase the productivity and competitiveness of companies and other institutions throughout the innovation process. The policy is structured around six axes: funding innovation, innovation culture, technological background, market development, educational systems, and intellectual property. Objectives and guidelines are defined for each of these Axes. However, neither a previous Theory of Change, a Logical Framework, nor a monitoring and evaluation system was established to guide the implementation. Operationally speaking, the policy was implemented by gathering ongoing actions from eighteen different federal ministries and agencies and then assigning them to the axes above. It was an ad hoc measure to put the policy into practice. As can be inferred, the selected actions did not emerge as a breakdown from axes. In 2021 the design and implementation of a monitoring and evaluation model (M&E) were commissioned to an independent evaluation group. The objective was to develop an original methodology and indicators for monitoring and evaluating outputs, outcomes and impacts of the PNI. The challenge of the model is twofold: to adjust the matching amongst actions, axes, and the policy's objectives, and to implement a common framework for M&E able to coordinate the involved agencies. A Theory of Change and a Logical Framework were ex-post designed and validated, and based on these references, the model was conceived. It defined a classical template for monitoring the ongoing actions (using flags and lights according to execution), adding indicators of outcomes and impacts. It is an integrated M&E model that, once implemented, will require that new actions be justified not only in terms of their outputs but also on the expected outcomes and impacts. Standard indicators of science, technology and innovation outcomes and impacts from different sources as for OECD, UNESCO, Global Innovation Index and Sustainable Development Goals (SDG/UN) have been gathered and organized to be employed in the M&E process. Non-standard indicators are also foreseen so that the model can measure internationally comparable and specific indicators. The whole model is now under development and validation among stakeholders. We expect this process to go beyond the domain of M&E and influences the way priorities are defined, and governance is established and run. By involving different actors, incorporating the SDGs into the policy's core, the evaluation process facilitated the policy's implementation and coordination. Furthermore, the articulation between the different stakeholders, promoted by the M&E, minimized fragmentation and uncoordinated actions within the scope of the policy's formulation. It is in this sense that the evaluation process is a way to transform the policy itself
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| 5. |
- Ainsbury, Elizabeth, et al.
(författare)
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Integration of new biological and physical retrospective dosimetry methods into EU emergency response plans - joint RENEB and EURADOS inter-laboratory comparisons
- 2017
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Ingår i: International Journal of Radiation Biology. - : Informa UK Limited. - 0955-3002 .- 1362-3095. ; 93:1, s. 99-109
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: RENEB, 'Realising the European Network of Biodosimetry and Physical Retrospective Dosimetry,' is a network for research and emergency response mutual assistance in biodosimetry within the EU. Within this extremely active network, a number of new dosimetry methods have recently been proposed or developed. There is a requirement to test and/or validate these candidate techniques and inter-comparison exercises are a well-established method for such validation. Materials and methods: The authors present details of inter-comparisons of four such new methods: dicentric chromosome analysis including telomere and centromere staining; the gene expression assay carried out in whole blood; Raman spectroscopy on blood lymphocytes, and detection of radiation induced thermoluminescent signals in glass screens taken from mobile phones. Results: In general the results show good agreement between the laboratories and methods within the expected levels of uncertainty, and thus demonstrate that there is a lot of potential for each of the candidate techniques. Conclusions: Further work is required before the new methods can be included within the suite of reliable dosimetry methods for use by RENEB partners and others in routine and emergency response scenarios.
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| 6. |
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| 7. |
- Couch, Fergus J., et al.
(författare)
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Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
- 2016
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 7:11375, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- Common variants in 94 loci have been associated with breast cancer including 15 loci with genome-wide significant associations (P<5 x 10(-8)) with oestrogen receptor (ER)-negative breast cancer and BRCA1-associated breast cancer risk. In this study, to identify new ER-negative susceptibility loci, we performed a meta-analysis of 11 genome-wide association studies (GWAS) consisting of 4,939 ER-negative cases and 14,352 controls, combined with 7,333 ER-negative cases and 42,468 controls and 15,252 BRCA1 mutation carriers genotyped on the iCOGS array. We identify four previously unidentified loci including two loci at 13q22 near KLF5, a 2p23.2 locus near WDR43 and a 2q33 locus near PPIL3 that display genome-wide significant associations with ER-negative breast cancer. In addition, 19 known breast cancer risk loci have genome-wide significant associations and 40 had moderate associations (P<0.05) with ER-negative disease. Using functional and eQTL studies we implicate TRMT61B and WDR43 at 2p23.2 and PPIL3 at 2q33 in ER-negative breast cancer aetiology. All ER-negative loci combined account for similar to 11% of familial relative risk for ER-negative disease and may contribute to improved ER-negative and BRCA1 breast cancer risk prediction.
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| 8. |
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| 9. |
- Dominguez, Mev, et al.
(författare)
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Evaluation of MLH1 I219V Polymorphism in Unrelated South American Individuals Suspected of Having Lynch Syndrome.
- 2012
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Ingår i: Anticancer research. - 1791-7530. ; 32:10, s. 4347-4351
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Tidskriftsartikel (refereegranskat)abstract
- Some single-nucleotide polymorphisms are associated with higher risk of colorectal cancer development and are suggested to explain part of the genetic contribution to Lynch syndrome. Aim: To evaluate the mutL homolog 1 (MLH1) I219V polymorphism in 124 unrelated South American individuals suspected of having Lynch syndrome, based on frequency, association with pathogenic MLH1 and mutS homolog 2 (MSH2) mutation and clinical features.
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| 10. |
- Gomes, Ana, et al.
(författare)
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An hybrid evolutionary multiobjective algorithm for multiuser margin maximization in DSL
- 2016
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Ingår i: International Journal of Communication Systems. - : Wiley. - 1074-5351. ; 29:1, s. 194-209
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Tidskriftsartikel (refereegranskat)abstract
- This work describes and proposes the application of evolutionary algorithms on the multiuser spectrum and SNR margin optimization problem for multicarrier systems, such as digital subscriber line. The proposed method is designed such that it takes advantage of special characteristics of the well-known power adaptation techniques and uses them to solve the broader and more challenging problem of multiuser margin adaptation. Simulations show that the proposed method provides Pareto-optimal and diverse solutions when compared to a previous method to solve the same problem. Copyright (c) 2014 John Wiley & Sons, Ltd.
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