| 1. |
- 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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| 2. |
- Carleo, Ilaria, et al.
(author)
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The Multiplanet System TOI-421*
- 2020
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In: Astronomical Journal. - : American Astronomical Society. - 1538-3881 .- 0004-6256. ; 160:3
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Journal article (peer-reviewed)abstract
- We report the discovery of a warm Neptune and a hot sub-Neptune transiting TOI-421 (BD-14 1137, TIC 94986319), a bright (V = 9.9) G9 dwarf star in a visual binary system observed by the Transiting Exoplanet Survey Satellite (TESS) space mission in Sectors 5 and 6. We performed ground-based follow-up observations-comprised of Las Cumbres Observatory Global Telescope transit photometry, NIRC2 adaptive optics imaging, and FIbre-fed Echelle Spectrograph, CORALIE, High Accuracy Radial velocity Planet Searcher, High Resolution echelle Spectrometer, and Planet Finder Spectrograph high-precision Doppler measurements-and confirmed the planetary nature of the 16 day transiting candidate announced by the TESS team. We discovered an additional radial velocity signal with a period of five days induced by the presence of a second planet in the system, which we also found to transit its host star. We found that the inner mini-Neptune, TOI-421 b, has an orbital period of P-b = 5.19672 +/- 0.00049 days, a mass of M-b = 7.17 +/- 0.66 M-circle plus, and a radius of R-b = R-circle plus, whereas the outer warm Neptune, TOI-421 c, has a period of P-c = 16.06819 +/- 0.00035 days, a mass of M-c = 16.42(-1.04)(+1.06)M(circle plus), a radius of R-c = 5.09(-0.15)(+0.16)R(circle plus), and a density of rho(c) = 0.685(-0.072)(+0.080) cm(-3). With its characteristics, the outer planet (rho(c) = 0.685(-0.0072)(+0.080) cm(-3)) is placed in the intriguing class of the super-puffy mini-Neptunes. TOI-421 b and TOI-421 c are found to be well-suited for atmospheric characterization. Our atmospheric simulations predict significant Ly alpha transit absorption, due to strong hydrogen escape in both planets, as well as the presence of detectable CH4 in the atmosphere of TOI-421 c if equilibrium chemistry is assumed.
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| 3. |
- Seidel, J. V., et al.
(author)
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Into the storm : Diving into the winds of the ultra-hot Jupiter WASP-76 b with HARPS and ESPRESSO
- 2021
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 653
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Journal article (peer-reviewed)abstract
- Context. Despite swift progress in the characterisation of exoplanet atmospheres in composition and structure, the study of atmospheric dynamics has not progressed at the same speed. While theoretical models have been developed to describe the lower layers of the atmosphere, and independently, the exosphere, little is known about the intermediate layers up to the thermosphere. Aims. We aim to provide a clearer picture of atmospheric dynamics for the class of ultra-hot Jupiters, which are highly irradiated gas giants, based on the example of WASP-76 b. Methods. We jointly analysed two datasets that were obtained with the HARPS and ESPRESSO spectrographs to interpret the resolved planetary sodium doublet. We then applied the MERC code, which retrieves wind patterns, speeds, and temperature profiles on the line shape of the sodium doublet. An updated version of MERC, with added planetary rotation, also provides the possibility of modelling the latitude dependence of the wind patterns. Results. We retrieve the highest Bayesian evidence for an isothermal atmosphere, interpreted as a mean temperature of 3389 ± 227 K, a uniform day- to nightside wind of 5.5-2.0+1.4 km s-1 in the lower atmosphere with a vertical wind in the upper atmosphere of 22.7-4.1+4.9 km s-1, switching atmospheric wind patterns at 10-3 bar above the reference surface pressure (10 bar). Conclusions. Our results for WASP-76 b are compatible with previous studies of the lower atmospheric dynamics of WASP-76 b and other ultra-hot Jupiters. They highlight the need for vertical winds in the intermediate atmosphere above the layers probed by global circulation model studies to explain the line broadening of the sodium doublet in this planet. This work demonstrates the capability of exploiting the resolved spectral line shapes to observationally constrain possible wind patterns in exoplanet atmospheres. This is an invaluable input to more sophisticated 3D atmospheric models in the future.
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| 4. |
- Hoeijmakers, H. J., et al.
(author)
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Hot Exoplanet Atmospheres Resolved with Transit Spectroscopy (HEARTS) : IV. A spectral inventory of atoms and molecules in the high-resolution transmission spectrum of WASP-121 b
- 2020
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 641
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Journal article (peer-reviewed)abstract
- Context. WASP-121 b is a hot Jupiter that was recently found to possess rich emission (day side) and transmission (limb) spectra, suggestive of the presence of a multitude of chemical species in the atmosphere. Aims. We survey the transmission spectrum of WASP-121 b for line-absorption by metals and molecules at high spectral resolution and elaborate on existing interpretations of the optical transmission spectrum observed with the Hubble Space Telescope (HST). Methods. We applied the cross-correlation technique and direct differential spectroscopy to search for sodium and other neutral and ionised atoms, TiO, VO, and SH in high-resolution transit spectra obtained with the HARPS spectrograph. We injected models assuming chemical and hydrostatic equilibrium with a varying temperature and composition to enable model comparison, and employed two bootstrap methods to test the robustness of our detections. Results. We detect neutral Mg, Na, Ca, Cr, Fe, Ni, and V, which we predict exists in equilibrium with a significant quantity of VO, supporting earlier observations by HST/WFC3. Non-detections of Ti and TiO support the hypothesis that Ti is depleted via a cold-trap mechanism, as has been proposed in the literature. Atomic line depths are under-predicted by hydrostatic models by a factor of 1.5 to 8, confirming recent findings that the atmosphere is extended. We predict the existence of significant concentrations of gas-phase TiO2, VO2, and TiS, which could be important absorbers at optical and near-IR wavelengths in hot Jupiter atmospheres. However, accurate line-list data are not currently available for them. We find no evidence for absorption by SH and find that inflated atomic lines can plausibly explain the slope of the transmission spectrum observed in the near-ultraviolet with HST. The Na I D lines are significantly broadened (FWHM ∼50 to 70 km s-1) and show a difference in their respective depths of ~15 scale heights, which is not expected from isothermal hydrostatic theory. If this asymmetry is of astrophysical origin, it may indicate that Na I forms an optically thin envelope, reminiscent of the Na I cloud surrounding Jupiter, or that it is hydrodynamically outflowing.
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| 5. |
- Seidel, J. V., et al.
(author)
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Hot Exoplanet Atmospheres Resolved with Transit Spectroscopy (HEARTS) : V. Detection of sodium on the bloated super-Neptune WASP-166b
- 2020
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 641
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Journal article (peer-reviewed)abstract
- Planet formation processes or evolution mechanisms are surmised to be at the origin of the hot Neptune desert. Studying exoplanets currently living within or at the edge of this desert could allow disentangling the respective roles of formation and evolution. We present the High Accuracy Radial velocity Planet Searcher (HARPS) transmission spectrum of the bloated super-Neptune WASP-166b, located at the outer rim of the Neptune desert. Neutral sodium is detected at the 3.4σ level (0.455†±â€ 0.135%), with a tentative indication of line broadening, which could be caused by winds blowing sodium farther into space, a possible manifestation of the bloated character of these highly irradiated worlds. We put this detection into context with previous work claiming a non-detection of sodium in the same observations and show that the high noise in the trace of the discarded stellar sodium lines was responsible for the non-detection. We highlight the impact of this low signal-to-noise ratio remnant on detections for exoplanets similar to WASP-166b.
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