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| 2. |
- 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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| 4. |
- Ahmad, Nawaz, 1972-, et al.
(författare)
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Injection of CO2-saturated brine in geological reservoir : A way to enhanced storage safety
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Injection of free phase supercritical CO2 into deep geological reservoirs is associated with risk of considerable return flows towards the land surface due to the buoyancy of CO2, which is lighter than the resident brine in the reservoir. Such upward movements can be avoided if CO2 is injected in the dissolved phase (CO2aq). In this work, injection of CO2-saturated brine in a subsurface carbonate reservoir is modelled. Physical and geochemical interactions of injected low-pH CO2-saturated brine with the carbonate minerals (calcite, dolomite and siderite) are investigated in the reactive transport modelling. CO2-saturated brine, being low in pH, shows high reactivity with the reservoir minerals, resulting in a significant mineral dissolution and CO2 conversion in reactions. Over the injection period of 10 years, up to 16% of the injected CO2 is found consumed in geochemical reactions. Sorption included in the transport analysis resulted in additional quantities of CO2 mass stored. However, for the considered carbonate minerals, the consumption of injected CO2aq is found mainly in the form of ionic trapping.
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| 5. |
- Ahmad, Nawaz, 1972-, et al.
(författare)
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Non-isothermal reactive transport modelling of dissolved CO2 leaking through a fractured caprock
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Geological storage of CO2 is considered as one of the mitigation actions for climate change adverse effects. However, some fraction of CO2 dissolved in the brine following injection, may leak from the reservoir through permeable zones such as conducting fractures. In this study we perform the reactive transport modelling of single-phase brine saturated with dissolved CO2 (CO2aq) along a conducting fracture in a clay-rich caprock. This study investigates the role of temperature and various reaction systems on the fate of migrating CO2aq, its geochemical interactions with the carbonate minerals, its conversion in geochemical reactions and associated medium porosity and permeability evolutions along the transport pathway.About 0.64% of leaking CO2aq is found converted into other ions in its geochemical interactions with calcite (simplified geochemical system). Addition of mineral dolomite in the geochemical system (extended geochemical system) results in up to 11% higher mass conversion of CO2 in reactions as compared to the simplified geochemical system. Considering extended geochemical system and heat transport by moving brine resulted in about 27.34% higher mass conversion of CO2 in reactions as compared to the simplified geochemical system. A combination of extended geochemical system, heat transport and sorption resulted in about 82.59% higher mass conversion of CO2 compared to the simplified geochemical system. Leaking CO2aq travelled less than 250 m along the fractured pathway, for a velocity of nearly 19 m/year in the fracture, due to retardation caused by mass stored in aqueous and adsorbed states.
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| 6. |
- Ahmad, Nawaz, et al.
(författare)
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Reactive transport modeling of leaking CO2-saturated brine along a fractured pathway
- 2015
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Ingår i: International Journal of Greenhouse Gas Control. - : Elsevier. - 1750-5836 .- 1878-0148. ; 42, s. 672-689
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Tidskriftsartikel (refereegranskat)abstract
- One concern regarding the underground storage of carbon dioxide (CO2) is its potential leakage from reservoirs. Over short period of time, the leakage risk is related mainly to CO2 as a separate supercritical fluid phase. However, over longer periods upon complete dissolution of injected CO2 in the fluid, the leakage risk is associated with dissolved phase CO2. Over the geological time scales, large-scale groundwater motion may cause displacement of brine containing dissolved CO2 along the conducting pathways. In this paper, we present a comprehensive modeling framework that describes the reactive transport of CO2-saturated brine along a fracture in the clay caprock based on the future, hypothetical leakage of the dissolved phase CO2. This study shows that the transport of leaked dissolved CO2 is significantly retarded by a combination of various physical and geochemical processes, such as mass exchange between conducting fracture and the neighboring rock matrix through molecular diffusion, sorption and calcite dissolution in the rock matrix. Mass stored in aqueous and adsorbed states in the rock matrix caused retention of dissolved CO2 along the leakage pathway. Calcite dissolution reaction in the rock matrix resulted in consumption of leaking dissolved CO2 and reduced its mass along the leakage pathway. Consumption and retention of dissolved CO2 along the leakage pathway have important implications for analyzing the potential reduction of CO2 fluxes from storage reservoirs over large periods and long travel pathways.
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| 7. |
- Ahmad, Nawaz, 1972-, et al.
(författare)
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The role of advection and dispersion in the rock matrix on the transport of leaking CO2-saturated brine along a fractured zone
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- CO2 that is injected into a storage reservoir can leak in dissolved form because of brine displacement from the reservoir, which is caused by large-scale groundwater motion. Simulations of the reactive transport of leaking CO2aq along a conducting fracture in a clay-rich caprock are conducted to analyze the effect of various physical and geochemical processes. Whilst several modelling transport studies along rock fractures have considered diffusion as the only transport process in the surrounding rock matrix (diffusive transport), this study analyzes the combined role of advection and dispersion in the rock matrix in addition to diffusion (advection-dominated transport) on the migration of CO2aq along a leakage pathway and its conversion in geochemical reactions. A sensitivity analysis is performed to quantify the effect of fluid velocity and dispersivity. Variations in the porosity and permeability of the medium are observed in response to calcite dissolution and precipitation along the leakage pathway. We observe that advection and dispersion in the rock matrix play a significant role in the overall transport process. For the parameters that were used in this study, advection-dominated transport increased the leakage of CO2aq from the reservoir by nearly 305%, caused faster transport and increased the mass conversion of CO2aq in geochemical reactions along the transport pathway by approximately 12.20% compared to diffusive transport.
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| 8. |
- Ahmad, Nawaz, 1972-, et al.
(författare)
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The role of advection and dispersion in the rock matrix on the transport of leaking CO2-saturated brine along a fractured zone
- 2016
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Ingår i: Advances in Water Resources. - : Elsevier. - 0309-1708 .- 1872-9657. ; 98, s. 132-146
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Tidskriftsartikel (refereegranskat)abstract
- CO2 that is injected into a geological storage reservoir can leak in dissolved form because of brine displacement from the reservoir, which is caused by large-scale groundwater motion. Simulations of the reactive transport of leaking CO2aq along a conducting fracture in a clay-rich caprock are conducted to analyze the effect of various physical and geochemical processes. Whilst several modeling transport studies along rock fractures have considered diffusion as the only transport process in the surrounding rock matrix (diffusive transport), this study analyzes the combined role of advection and dispersion in the rock matrix in addition to diffusion (advection-dominated transport) on the migration of CO2aq along a leakage pathway and its conversion in geochemical reactions. A sensitivity analysis is performed to quantify the effect of fluid velocity and dispersivity. Variations in the porosity and permeability of the medium are found in response to calcite dissolution and precipitation along the leakage pathway. We observe that advection and dispersion in the rock matrix play a significant role in the overall transport process. For the parameters that were used in this study, advection-dominated transport increased the leakage of CO2aq from the reservoir by nearly 305%, caused faster transport and increased the mass conversion of CO2aq in geochemical reactions along the transport pathway by approximately 12.20% compared to diffusive transport.
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| 9. |
- Brangari, Albert C., et al.
(författare)
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Ecological and soil hydraulic implications of microbial responses to stress - A modeling analysis
- 2018
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Ingår i: Advances in Water Resources. - : Elsevier BV. - 0309-1708 .- 1872-9657. ; 116, s. 178-194
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Tidskriftsartikel (refereegranskat)abstract
- A better understanding of microbial dynamics in porous media may lead to improvements in the design and management of a number of technological applications, ranging from the degradation of contaminants to the optimization of agricultural systems. To this aim, there is a recognized need for predicting the proliferation of soil microbial biomass (often organized in biofilms) under different environments and stresses. We present a general multi-compartment model to account for physiological responses that have been extensively reported in the literature. The model is used as an explorative tool to elucidate the ecological and soil hydraulic consequences of microbial responses, including the production of extracellular polymeric substances (EPS), the induction of cells into dormancy, and the allocation and reuse of resources between biofilm compartments. The mechanistic model is equipped with indicators allowing the microorganisms to monitor environmental and biological factors and react according to the current stress pressures. The feedbacks of biofilm accumulation on the soil water retention are also described. Model runs simulating different degrees of substrate and water shortage show that adaptive responses to the intensity and type of stress provide a clear benefit to microbial colonies. Results also demonstrate that the model may effectively predict qualitative patterns in microbial dynamics supported by empirical evidence, thereby improving our understanding of the effects of pore-scale physiological mechanisms on the soil macroscale phenomena.
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| 10. |
- Caliz, Joan, et al.
(författare)
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The microbiota of an unpolluted calcareous soil faces up chlorophenols: Evidences of resistant strains with potential for bioremediation
- 2011
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Ingår i: Chemosphere. - : Elsevier Science B.V., Amsterdam.. - 0045-6535 .- 1879-1298. ; 83:2, s. 104-116
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Tidskriftsartikel (refereegranskat)abstract
- To highlight the effects of a variety of chlorophenols (CP) in relation to the response of an indigenous bacterial community, an agricultural Mediterranean calcareous soil has been studied in microcosms incubated under controlled laboratory conditions. Soil samples were artificially polluted with 2-monochlorophenol (MCP), 2,4,6-trichlorophenol (TCP) and pentachlorophenol (PCP), at concentrations ranging from 0.1 up to 5000 mg kg(-1). Both activity and composition of the microbial community were assessed during several weeks, respectively, by respirometric methods and PCR-DGGE analysis of extracted DNA and RNA. Significant decreases in soil respirometric values and changes in the bacterial community composition were observed at concentrations above 1000 mg kg(-1) MCP and TCP, and above 100 mg kg(-1) PCP. However, the persistence of several active bacterial populations in soil microcosms contaminated with high concentration of CP, as indicated by DGGE fingerprints, suggested the capacity of these native bacteria to survive in the presence of the pollutants, even without a previous adaptation or contact with them. The isolation of potential CP degraders was attempted by culture plating from microcosms incubated with high CP concentrations. Twenty-three different isolates were screened for their resistance to TCP and PCP. The most resistant isolates were identified as Kocuria palustris, Lysobacter gummosus, Bacillus sp. and Pseudomonas putida, according to 16S rRNA gene homology. In addition, these four isolates also showed the capacity to reduce the concentration of TCP and PCP from 15% to 30% after 5 d of incubation in laboratory assays (initial pollutant concentration of 50 mg L(-1)). Isolate ITP29, which could be a novel species of Bacillus, has been revealed as the first known member in this bacterial group with potential for CP bioremediation applications, usually wide-spread in the soil natural communities, which has not been reported to date as a CP degrader.
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