| 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. |
- Hacker, B. R., et al.
(författare)
-
Thermochronology of the Talkeetna intraoceanic arc of Alaska: Ar/Ar, U-Th/He, Sm-Nd, and Lu-Hf dating
- 2011
-
Ingår i: Tectonics. - 0278-7407. ; 30
-
Tidskriftsartikel (refereegranskat)abstract
- As one of two well-exposed intraoceanic arcs, the Talkeetna arc of Alaska affords an opportunity to understand processes deep within arcs. This study reports new Lu-Hf and Sm-Nd garnet ages, Ar-40/Ar-39 hornblende, mica and whole-rock ages, and U-Th/He zircon and apatite ages from the Chugach Mountains, Talkeetna Mountains, and Alaska Peninsula, which, in conjunction with existing geochronology, constrain the thermal history of the arc. Zircon U-Pb ages establish the main period of arc magmatism as 202-181 Ma in the Chugach Mountains and 183-153 Ma in the eastern Talkeetna Mountains and Alaska Peninsula. Approximately 184 Ma Lu-Hf and similar to 182 Ma Sm-Nd garnet ages indicate that 25-35 km deep sections of the arc remained above similar to 700 degrees C for as much as 15 Myr. The Ar-40/Ar-39 hornblende ages are chiefly 194-170 Ma in the Chugach Mountains and 175-150 Ma in the Talkeetna Mountains and Alaska Peninsula but differ from zircon U-Pb ages in the same samples by as little as 0 Myr and as much as 33 Myr, documenting a spatially variable thermal history. Mica ages have a broader distribution, from similar to 180 Ma to 130 Ma, suggesting local cooling and/or reheating. The oldest U-Th/He zircon ages are similar to 137 to 129 Ma, indicating no Cenozoic regional heating above similar to 180 degrees C. Although the signal is likely complicated by Cretaceous and Oligocene postarc magmatism, the aggregate thermochronology record indicates that the thermal history of the Talkeetna arc was spatially variable. One-dimensional finite difference thermal models show that this kind of spatial variability is inherent to intraoceanic arcs with simple construction histories. Citation: Hacker, B. R., P. B. Kelemen, M. Rioux, M. O. McWilliams, P. B. Gans, P. W. Reiners, P. W. Layer, U. Soderlund, and J. D. Vervoort (2011), Thermochronology of the Talkeetna intraoceanic arc of Alaska: Ar/Ar, U-Th/He, Sm-Nd, and Lu-Hf dating, Tectonics, 30, TC1011, doi:10.1029/2010TC002798.
|
|
| 3. |
- Bailey, Lydia R., et al.
(författare)
-
Characteristics and Consequences of Red Bed Bleaching by Hydrocarbon Migration : A Natural Example From the Entrada Sandstone, Southern Utah
- 2022
-
Ingår i: Geochemistry Geophysics Geosystems. - : John Wiley & Sons. - 1525-2027. ; 23:8
-
Tidskriftsartikel (refereegranskat)abstract
- Extensive regions of yellow and white ("bleached") sandstones within the terrestrial Jurassic red bed deposits of the Colorado Plateau reflect widespread interaction with subsurface reduced fluids which resulted in the dissolution of iron-oxide grain coatings. Reduced fluids such as hydrocarbons, CO2, and organic acids have been proposed as bleaching agents. In this study, we characterize an altered section of the Slick Rock member of the Jurassic Entrada Sandstone that exposes bleached sandstone with bitumen-saturated pore spaces. We observe differences in texture, porosity, mineralogy, and geochemistry between red, pink, yellow, and gray facies. In the bleached yellow facies we observe quartz overgrowths, partially dissolved K-feldspar, calcite cement, fine-grained illite, TiO2-minerals, and pyrite concretions. Clay mineral content is highest at the margins of the bleached section. Fe2O3 concentrations are reduced up to 3x from the red to gray facies but enriched up to 50x in iron-oxide concretions. Metals such as Zn, Pb, and rare-earth elements are significantly enriched in the concretions. Supported by a batch geochemical model, we conclude the interaction of red sandstones with reduced hydrocarbon-bearing fluids caused iron-oxide and K-feldspar dissolution, and precipitation of quartz, calcite, clay, and pyrite. Localized redistribution of iron into concretions can account for most of the iron removed during bleaching. Pyrite and carbonate stable isotopic data suggest the hydrocarbons were sourced from the Pennsylvanian Paradox Formation. Bitumen in pore spaces and pyrite precipitation formed a reductant trap required to produce Cu, U, and V enrichment in all altered facies by younger, oxidized saline brines.
|
|
| 4. |
|
|
| 5. |
- Drake, Henrik, Docent, 1979-, et al.
(författare)
-
Thermochronologic perspectives on the deep-time evolution of the deep biosphere
- 2021
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:45
-
Tidskriftsartikel (refereegranskat)abstract
- The Earth’s deep biosphere hosts some of its most ancient chemolithotrophic lineages. The history of habitation in this environment is thus of interest for understanding the origin and evolution of life. The oldest rocks on Earth, formed about 4 billion years ago, are in continental cratons that have experienced complex histories due to burial and exhumation. Isolated fracture-hosted fluids in these cratons may have residence times older than a billion years, but understanding the history of their microbial communities requires assessing the evolution of habitable conditions. Here, we present a thermochronological perspective on the habitability of Precambrian cratons through time. We show that rocks now in the upper few kilometers of cratons have been uninhabitable (>∼122 °C) for most of their lifetime or have experienced high-temperature episodes, such that the longest record of habitability does not stretch much beyond a billion years. In several cratons, habitable conditions date back only 50 to 300 million years, in agreement with dated biosignatures. The thermochronologic approach outlined here provides context for prospecting and interpreting the little-explored geologic record of the deep biosphere of Earth’s cratons, when and where microbial communities may have thrived, and candidate areas for the oldest records of chemolithotrophic microbes.
|
|
| 6. |
- Ferguson, Grant, et al.
(författare)
-
Acceleration of Deep Subsurface Fluid Fluxes in the Anthropocene
- 2024
-
Ingår i: Earth's Future. - : John Wiley & Sons. - 2328-4277. ; 12:4
-
Tidskriftsartikel (refereegranskat)abstract
- The Anthropocene has been framed around humanity's impact on atmospheric, biologic, and near-surface processes, such as land use and vegetation change, greenhouse gas emissions, and the above-ground hydrologic cycle. Groundwater extraction has lowered water tables in many key aquifers but comparatively little attention has been given to the impacts in the deeper subsurface. Here, we show that fluid fluxes from the extraction and injection of fluids associated with oil and gas production and inflow of water into mines likely exceed background flow rates in deep (>500 m) groundwater systems at a global scale. Projected carbon capture and sequestration (CCS), geothermal energy production, and lithium extraction to facilitate the energy transition will require fluid production rates exceeding current oil and co-produced water extraction. Natural analogs and geochemical modeling indicate that subsurface fluid manipulation in the Anthropocene will likely appear in the rock record. The magnitude and importance of these changes are unclear, due to a lack of understanding of how deep subsurface hydrologic and geochemical cycles and associated microbial life interact with the rest of the Earth system.
|
|
| 7. |
- Guenthner, William R., et al.
(författare)
-
Zircon, titanite, and apatite (U-Th)/He ages and age-eU correlations from the Fennoscandian Shield, southern Sweden
- 2017
-
Ingår i: Tectonics. - : John Wiley & Sons. - 0278-7407 .- 1944-9194. ; 36:7, s. 1254-1274
-
Tidskriftsartikel (refereegranskat)abstract
- Craton cores far from plate boundaries have traditionally been viewed as stable features that experience minimal vertical motion over 100-1000Ma time scales. Here we show that the Fennoscandian Shield in southeastern Sweden experienced several episodes of burial and exhumation from similar to 1800Ma to the present. Apatite, titanite, and zircon (U-Th)/He ages from surface samples and drill cores constrain the long-term, low-temperature history of the Laxemar region. Single grain titanite and zircon (U-Th)/He ages are negatively correlated (104-838Ma for zircon and 160-945Ma for titanite) with effective uranium (eU=U+0.235xTh), a measurement proportional to radiation damage. Apatite ages are 102-258Ma and are positively correlated with eU. These correlations are interpreted with damage-diffusivity models, and the modeled zircon He age-eU correlations constrain multiple episodes of heating and cooling from 1800Ma to the present, which we interpret in the context of foreland basin systems related to the Neoproterozoic Sveconorwegian and Paleozoic Caledonian orogens. Inverse time-temperature models constrain an average burial temperature of similar to 217 degrees C during the Sveconorwegian, achieved between 944Ma and 851Ma, and similar to 154 degrees C during the Caledonian, achieved between 366Ma and 224Ma. Subsequent cooling to near-surface temperatures in both cases could be related to long-term exhumation caused by either postorogenic collapse or mantle dynamics related to the final assembly of Rodinia and Pangaea. Our titanite He age-eU correlations cannot currently be interpreted in the same fashion; however, this study represents one of the first examples of a damage-diffusivity relationship in this system, which deserves further research attention.
|
|
