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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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| 5. |
- Russel, D., et al.
(författare)
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Climate change appraisal in the EU
- 2010
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Ingår i: Making climate change work for us. - : Cambridge University Press. - 9780521119412 ; , s. 31-53
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 6. |
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| 7. |
- Hertin, J., et al.
(författare)
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Rationalising the policy mess? : Ex ante policy assessment and the utilisation of knowledge in the policy process
- 2009
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Ingår i: Environment and planning A. - : SAGE Publications. - 0308-518X .- 1472-3409. ; 41:5, s. 1185-1200
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Tidskriftsartikel (refereegranskat)abstract
- Procedures for the ex ante assessment of public policies are currently in vogue across the OECD. Their design is typically informed by a rational-instrumental model of problem solving, which assumes that knowledge is collected, evaluated, and then translated straightforwardly into ‘better policies’. But this model has been little affected by more than three decades of academic research which has demonstrated that the reality of everyday policy making is far messier. In this paper we analyse whether the uptake of ex ante assessment of policies is nonetheless capable of creating opportunities for policy deliberation and learning informed by new assessment knowledge. Drawing on an analysis of policy assessment procedures in three countries and the European Union, we find that there are several ways in which assessment knowledge is used in the policy process. Moreover, we argue that policy learning occurs despite, rather than because of, the instrumental design of new assessment procedures, which tends to act as a barrier to open deliberation and knowledge utilisation.
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| 9. |
- Rich, Evan A., et al.
(författare)
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Multi-epoch Direct Imaging and Time-variable Scattered Light Morphology of the HD 163296 Protoplanetary Disk
- 2019
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 875:1
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Tidskriftsartikel (refereegranskat)abstract
- We present H-band polarized scattered light imagery and JHK high-contrast spectroscopy of the protoplanetary disk around HD 163296 observed with the High-Contrast Coronographic Imager for Adaptive Optics (HiCIAO) and Subaru Coronagraphic Extreme Adaptive Optics (SCExAO)/Coronagraphic High Angular Resolution Imaging Spectrograph (CHARTS) instruments at Subaru Observatory. The polarimetric imagery resolve a broken ring structure surrounding HD 163296 that peaks at a distance along the major axis of 0 ''.65 (66 au) and extends out to 0 ''.98 (100 au) along the major axis. Our 2011 H-band data exhibit clear axisymmetry, with the NW and SE side of the disk exhibiting similar intensities. Our data are clearly different from 2016 epoch H-band observations of the Very Large Telescope (VLT)/Spectro-Polarimetric High-contrast Exoplanet REsearch (SPHERE), which found a strong 2.7 x asymmetry between the NW and SE side of the disk. Collectively, these results indicate the presence of time-variable, non-azimuthally symmetric illumination of the outer disk. While our SCExAO/CHARIS data are sensitive enough to recover the planet candidate identified from NIRC2 in the thermal infrared (IR), we fail to detect an object with JHK brightness nominally consistent with this object. This suggests that the candidate is either fainter in JHK bands than model predictions, possibly due to extinction from the disk or atmospheric dust/clouds, or that it is an artifact of the data set/data processing, such as a residual speckle or partially subtracted disk feature. Assuming standard hot-start evolutionary models and a system age of 5 Myr, we set new, direct mass limits for the inner (outer) Atacama Large Millimeter/submillimeter Array (ALMA)-predicted protoplanet candidate along the major (minor) disk axis of of 1.5 (2) M-J.
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| 10. |
- Shoberg, Russel J., et al.
(författare)
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Identification of a highly cross-reactive outer surface protein B epitope among diverse geographic isolates of Borrelia spp. causing Lyme disease
- 1994
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Ingår i: Journal of Clinical Microbiology. - : American Society for Microbiology (ASM). - 0095-1137 .- 1098-660X. ; 32:2, s. 489-500
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Tidskriftsartikel (refereegranskat)abstract
- The outer surface lipoprotein B (OspB) of Borrelia burgdorferi is a major component of the borrelial protein profile and has been shown to be highly immunogenic in experimentally immunized and infected mammals. However, the ospB loci of different strains show considerable heterology at the nucleic acid sequence level, and the progeny of a clonal strain of B. burgdorferi exhibited OspB polymorphisms with respect to apparent molecular weights and reactivities with monoclonal antibodies. These data suggest that OspB is not a good candidate for vaccination or diagnostic purposes. The present study describes a monoclonal antibody, designated 84C, directed against a very highly conserved domain of the OspB lipoprotein. Western immunoblot analysis with 84C demonstrated reactivity in 84.2% of human, tick, and other vertebrate isolate strains examined from widely diverse geographic regions, including strains of B. burgdorferi sensu stricto and two closely related species, B. garinii and B. afzelii. The 84C-binding region was delimited to a highly conserved 11-amino-acid region in the carboxyl terminus of OspB as demonstrated by (i) DNA sequence analysis of wild-type and 84C-resistant mutant ospB alleles and (ii) deletion mutagenesis of a recombinant ospB gene in Escherichia coli. Finally, the 84C epitope was demonstrated to be exposed on the borrelial surface in situ as (i) the monoclonal antibody 84C was able to agglutinate borrelias in culture and (ii) 84C-resistant escape variants were isolated. These data suggest that the potential value of OspB as a vaccine candidate or diagnostic tool be examined more closely, in the context of the 84C-reactive domain.
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