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- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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- Estes, James A., et al.
(author)
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Trophic Downgrading of Planet Earth
- 2011
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 333:6040, s. 301-306
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Research review (peer-reviewed)abstract
- Until recently, large apex consumers were ubiquitous across the globe and had been for millions of years. The loss of these animals may be humankind's most pervasive influence on nature. Although such losses are widely viewed as an ethical and aesthetic problem, recent research reveals extensive cascading effects of their disappearance in marine, terrestrial, and freshwater ecosystems worldwide. This empirical work supports long-standing theory about the role of top-down forcing in ecosystems but also highlights the unanticipated impacts of trophic cascades on processes as diverse as the dynamics of disease, wildfire, carbon sequestration, invasive species, and biogeochemical cycles. These findings emphasize the urgent need for interdisciplinary research to forecast the effects of trophic downgrading on process, function, and resilience in global ecosystems.
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| 8. |
- Anton, KA, et al.
(author)
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PKA-regulated VASP phosphorylation promotes extrusion of transformed cells from the epithelium
- 2014
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In: Journal of cell science. - : The Company of Biologists. - 1477-9137 .- 0021-9533. ; 127:16Pt 16, s. 3425-3433
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Journal article (peer-reviewed)abstract
- At the early stages of carcinogenesis, transformation occurs in single cells within tissues. In an epithelial monolayer, such mutated cells are recognized by their normal neighbors and are often apically extruded. The apical extrusion requires cytoskeletal reorganization and cell shape changes, but it is poorly understood what molecular switches are involved in regulation of these processes. Here, using SILAC-based quantitative mass spectrometry we have identified proteins that are modulated in transformed cells upon their interaction with normal cells. Phosphorylation of VASP at serine 239 is specifically upregulated in RasV12-transformed cells when they are surrounded by normal cells. VASP phosphorylation is required for the cell shape changes and apical extrusion of Ras-transformed cells. Furthermore, PKA is activated in Ras-transformed cells surrounded by normal cells, leading to VASP phosphorylation. These results indicate that the PKA/VASP pathway is a crucial regulator for tumor cell extrusion from the epithelium and shed light on the events occurring at the early stage of carcinogenesis.
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| 10. |
- Davis, Tamara M., et al.
(author)
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The Effect of Peculiar Velocities on Supernova Cosmology
- 2011
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In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 741, s. 67-
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Journal article (peer-reviewed)abstract
- We analyze the effect that peculiar velocities have on the cosmological inferences we make using luminosity distance indicators, such as Type Ia supernovae. In particular we study the corrections required to account for (1) our own motion, (2) correlations in galaxy motions, and (3) a possible local under- or overdensity. For all of these effects we present a case study showing the impact on the cosmology derived by the Sloan Digital Sky Survey-II Supernova Survey (SDSS-II SN Survey). Correcting supernova (SN) redshifts for the cosmic microwave background (CMB) dipole slightly overcorrects nearby SNe that share some of our local motion. We show that while neglecting the CMB dipole would cause a shift in the derived equation of state of Δw ~ 0.04 (at fixed Ω m ), the additional local-motion correction is currently negligible (Δw <~ 0.01). We then demonstrate a covariance-matrix approach to statistically account for correlated peculiar velocities. This down-weights nearby SNe and effectively acts as a graduated version of the usual sharp low-redshift cut. Neglecting coherent velocities in the current sample causes a systematic shift of Δw ~ 0.02. This will therefore have to be considered carefully when future surveys aim for percent-level accuracy and we recommend our statistical approach to down-weighting peculiar velocities as a more robust option than a sharp low-redshift cut.
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