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- 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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- Abolhassani, H, et al.
(författare)
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Care of patients with inborn errors of immunity in thirty J Project countries between 2004 and 2021
- 2022
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Ingår i: Frontiers in immunology. - : Frontiers Media SA. - 1664-3224. ; 13, s. 1032358-
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Tidskriftsartikel (refereegranskat)abstract
- The J Project (JP) physician education and clinical research collaboration program was started in 2004 and includes by now 32 countries mostly in Eastern and Central Europe (ECE). Until the end of 2021, 344 inborn errors of immunity (IEI)-focused meetings were organized by the JP to raise awareness and facilitate the diagnosis and treatment of patients with IEI.ResultsIn this study, meeting profiles and major diagnostic and treatment parameters were studied. JP center leaders reported patients’ data from 30 countries representing a total population of 506 567 565. Two countries reported patients from JP centers (Konya, Turkey and Cairo University, Egypt). Diagnostic criteria were based on the 2020 update of classification by the IUIS Expert Committee on IEI. The number of JP meetings increased from 6 per year in 2004 and 2005 to 44 and 63 in 2020 and 2021, respectively. The cumulative number of meetings per country varied from 1 to 59 in various countries reflecting partly but not entirely the population of the respective countries. Altogether, 24,879 patients were reported giving an average prevalence of 4.9. Most of the patients had predominantly antibody deficiency (46,32%) followed by patients with combined immunodeficiencies (14.3%). The percentages of patients with bone marrow failure and phenocopies of IEI were less than 1 each. The number of patients was remarkably higher that those reported to the ESID Registry in 13 countries. Immunoglobulin (IgG) substitution was provided to 7,572 patients (5,693 intravenously) and 1,480 patients received hematopoietic stem cell therapy (HSCT). Searching for basic diagnostic parameters revealed the availability of immunochemistry and flow cytometry in 27 and 28 countries, respectively, and targeted gene sequencing and new generation sequencing was available in 21 and 18 countries. The number of IEI centers and experts in the field were 260 and 690, respectively. We found high correlation between the number of IEI centers and patients treated with intravenous IgG (IVIG) (correlation coefficient, cc, 0,916) and with those who were treated with HSCT (cc, 0,905). Similar correlation was found when the number of experts was compared with those treated with HSCT. However, the number of patients treated with subcutaneous Ig (SCIG) only slightly correlated with the number of experts (cc, 0,489) and no correlation was found between the number of centers and patients on SCIG (cc, 0,174).Conclusions1) this is the first study describing major diagnostic and treatment parameters of IEI care in countries of the JP; 2) the data suggest that the JP had tremendous impact on the development of IEI care in ECE; 3) our data help to define major future targets of JP activity in various countries; 4) we suggest that the number of IEI centers and IEI experts closely correlate to the most important treatment parameters; 5) we propose that specialist education among medical professionals plays pivotal role in increasing levels of diagnostics and adequate care of this vulnerable and still highly neglected patient population; 6) this study also provides the basis for further analysis of more specific aspects of IEI care including genetic diagnostics, disease specific prevalence, newborn screening and professional collaboration in JP countries.
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- Farkas, I., et al.
(författare)
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Rates and mechanisms of water exchange of UO22+(aq) and UO2(oxalate)F(H2O)(2)(-) : A variable-temperature O-17 and F-19 NMR study
- 2000
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 39:4, s. 799-805
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Tidskriftsartikel (refereegranskat)abstract
- This study consists of two parts: The first part comprised an experimental determination of the kinetic parameters for the exchange of water between UO2(H2O)(5)(2+) and bulk water, including an ab initio study at the SCF and MP2 levels of the geometry of UO2(H2O)(5)(2+), UO2(H2O)(4)(2+), and UO2(H2O)(6)(2+) and the thermodynamics of their reactions with water. In the second part we made an experimental study of the rate of water exchange in uranyl complexes and investigated how this might depend on inter- and intramolecular hydrogen bond interactions. The experimental studies, made by using O-17 NMR, with Tb3+ as a chemical shift reagent, gave the following kinetic parameters at 25 degrees C: k(ex) = (1.30 +/- 0.05) x 10(6) s(-1); Delta H double dagger = 26.(1) +/- 1.(4) kJ/mol; Delta S double dagger = -40 +/- 5 J/(K mol). Additional mechanistic indicators were obtained from the known coordination geometry of U(VI) complexes with unidentate ligands and from the theoretical calculations. A survey of the literature shows that there are no known isolated complexes of UO22+ with unidentate ligands which have a coordination number larger than 5. This was corroborated by quantum chemical calculations which showed that the energy gains by binding an additional water to UO2(H2O)(4)(2+) and UO2(H2O)(5)(2+) are 29.8 and -2.4 kcal/mol, respectively. A comparison of the change in Delta U for the reactions UO2(H2O)(5)(2+) --> UO2(H2O)(4)(2+) + H2O and UO2(H2O)(5)(2+) + H2O --> UO2(H2O)(6)(2+) indicates that the thermodynamics favors the second (associative) reaction in gas phase at 0 K, while the thermodynamics of water transfer between the first and second coordination spheres, UO2(H2O)(5)(2+) --> UO2(H2O)(4)(H2O)(2+) and UO2(H2O)(5)(H2O)(2+) --> UO2(H2O)(6)(2+), favors the first (dissociative) reaction. The energy difference between the associative and dissociative reactions is small, and solvation has to be included in ab initio models in order to allow quantitative comparisons between experimental data and theory. Theoretical calculations of the activation energy were not possible because of the excessive computing time required. On the basis of theoretical and experimental studies, we suggest that the water exchange in UO2(H2O)(5)(2+) follows a dissociative interchange mechanism. The rates of exchange of water in UO2(oxalate)F(H2O)(2-) (and UO2(oxalate)F-2(H2O)(2-) studied previously) are much slower than in the aquation, k(ex) = 1.6 x 10(4) s(-1), an effect which we assign to hydrogen bonding involving coordinated water and fluoride. The kinetic parameters for the exchange of water in UO2(H2O)(5)(2+) and quenching of photo excited *UO2(H2O)(5)(2+) are very near the same, indicating similar mechanisms.
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