| 1. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
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.
|
|
| 2. |
- Richards, Stephen, et al.
(författare)
-
Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
-
Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
-
Tidskriftsartikel (refereegranskat)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
|
|
| 3. |
- Allende Prieto, C., et al.
(författare)
-
Deep SDSS optical spectroscopy of distant halo stars I. Atmospheric parameters and stellar metallicity distribution
- 2014
-
Ingår i: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 568
-
Tidskriftsartikel (refereegranskat)abstract
- Aims. We analyze a sample of tens of thousands of spectra of halo turnoff stars, obtained with the optical spectrographs of the Sloan Digital Sky Survey (SDSS), to characterize the stellar halo population "in situ" out to a distance of a few tens of kpc from the Sun. In this paper we describe the derivation of atmospheric parameters. We also derive the overall stellar metallicity distribution based on F-type stars observed as flux calibrators for the Baryonic Oscillations Spectroscopic Survey (ROSS). Methods. Our analysis is based on an automated method that determines the set of parameters of a model atmosphere that reproduces each obserxrci spectrum best. We used an optimization algorithm and evaluate model fluxes by means of inter-polation in a precomputed grid, In our analysis, we account for the spectrograph's varying resolution as a function of fiber and wavelength. Our results for early SDSS (pre-BOSS upgrade) data compare well with those from the SEGUE Stellar Parameter Pipeline (SSPP). except for stars with log g (cgs units) lower than 2.5. Results. An analysis of stars in the globular cluster M 13 reveals a dependence of the inferred metallicity on surface gravity for stars with log g < 2.5, confirming the systematics identified in the comparison with the SSPP. We find that our rnetallicity estimates are, significantly more precise than the SSPP results. We also find excellent agreement with several independent analyses. We show that the SDSS color criteria for selecting F-type halo turnoff stars as flux calibrators efficiently excludes stars with high metallieities, but does not significantly distort the shape of the metallicity distribution at low rnetallicity. We obtain a halo metathcity distribution that is narrower and more asymmetric than in previous studies. The lowest gravity stars in our sample at tens of kpc from the Sun, indicate a shift of the metallicity distribution to lower abundances, consistent with what is expected from a dual halo system in the Milky Way.
|
|
