| 1. |
- 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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| 2. |
- Alling, Vanja, et al.
(författare)
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The role of biochar in retaining nutrients in amended tropical soils
- 2014
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Ingår i: Journal of Plant Nutrition And Soil Science/Zeitschrift für Pflanzenernahrung und Bodenkunde. - : Wiley. - 1436-8730 .- 1522-2624. ; 177:5, s. 671-680
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Tidskriftsartikel (refereegranskat)abstract
- This study investigated the effect of biochar amendments on the retention and availability of plant nutrients and Al in seven acidic tropical soils from Zambia and Indonesia. The experiments carried out investigated whether the adsorption capacity of NH4+ in the soils increased upon the addition of biochar and which effect biochar had on available concentrations of NO3-, K+, Mn2+, Mg2+, PO43-, and Al3+. These nutrients were selected as they represent those important to plant growth and soil quality. No significant increases or decreases in aqueous NH4+-N concentration with additions of biochar were detected. The Gaines-Thomas model was used in order to calculate selectivity coefficients for NH4+ exchange (K-gt values). Following the addition of biochar to soil, K-gt values decreased showing a reduction in the selective binding of NH4+ in the biochar amended soil compared to the control. The concentration of NO3- increased following the addition of biochar to the soils. The addition of 5 and 10% biochar to the Indonesian soil did not significantly alter (t-test confidence level 0.05) the sorption of PO43- to the soil-biochar mixtures as compared to the soil alone. However, the addition of biochar to the soil from Zambia increased the sorption of PO43- compared to the soil alone. The concentrations of K+ and Mg2+ were significantly increased for almost all soils (t-test at the 0.05 confidence level) following the addition of biochar. Addition of biochar to all but two soils significantly decreased (t-test confidence level 0.05) Mn2+ concentrations. The concentration of Al3+ in the soils decreased exponentially significantly (t-test confidence level 0.05) following the amendment of biochar in accordance with the increase in pH observed when biochar was added to the soil. These results show that biochar has the ability to release essential plant growth nutrients as well as alleviate Al toxicity in these soils.
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| 3. |
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| 4. |
- Hale, Sarah E., et al.
(författare)
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Effects of Chemical, Biological, and Physical Aging As Well As Soil Addition on the Sorption of Pyrene to Activated Carbon and Biochar
- 2011
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 45:24, s. 10445-10453
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Tidskriftsartikel (refereegranskat)abstract
- In this study, the suitability of biochar and activated carbon (AC) for contaminated soil remediation is investigated by determining the sorption of pyrene to both materials in the presence and absence of soil and before as well as after aging. Biochar and AC were aged either alone or mixed with soil via exposure to (a) nutrients and microorganisms (biological), (b) 60 and 110 degrees C (chemical), and (c) freeze-thaw cycles (physical). Before and after aging, the pH, elemental composition, cation exchange capacity (CEC), microporous SA, and sorption isotherms of pyrene were quantified. Aging at 110 degrees C altered the physicochemical properties of all materials to the greatest extent (for example, pH increased by up to three units and CEC by up to 50% for biochar). Logarithmic K(Fr) values ranged from 7.80 to 8.21 (ng kg(-1)) (ng L(-1))(-nF) for AC and 5.22 to 6.21 (ng kg(-1))(ng L(-1))(-nF) for biochar after the various aging regimes. Grinding biochar to a smaller particle size did not significantly affect the sorption of d(10) pyrene, implying that sorption processes operate on the subparticle scale. Chemical aging decreased the sorption of pyrene to the greatest extent (up to 1.8 log unit for the biochar+soil). The sorption to AC was affected more by the presence of soil than the sorption to biochar was. Our results suggest that AC and biochar have a high sorption capacity for pyrene that is maintained both in the presence of soil and during harsh aging. Both materials could therefore be considered in contaminated land remediation.
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| 5. |
- Hale, Sarah E., et al.
(författare)
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Quantifying the Total and Bioavailable Polycyclic Aromatic Hydrocarbons and Dioxins in Biochars
- 2012
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Ingår i: Environmental Science and Technology. - Washington, DC : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 46:5, s. 2830-2838
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Tidskriftsartikel (refereegranskat)abstract
- Biochar soil amendment is advocated to mitigate climate change and improve soil fertility. A concern though, is that during biochar preparation PAHs and dioxins are likely formed. These contaminants can possibly be present in the biochar matrix and even bioavailable to exposed organisms. Here we quantify total and bioavailable PAHs and dioxins in a suite of over 50 biochars produced via slow pyrolysis between 250 and 900 degrees C, using various methods and biomass from tropical, boreal, and temperate areas. These slow pyrolysis biochars, which can be produced locally on farms with minimum resources, are also compared to biochar produced using the industrial methods of fast pyrolysis and gasification. Total concentrations were measured with a Soxhlet extraction and bioavailable concentrations were measured with polyoxymethylene passive samplers. Total PAH concentrations ranged from 0.07 mu g g(-1) to 3.27 mu g g(-1) for the slow pyrolysis biochars and were dependent on biomass source, pyrolysis temperature, and time. With increasing pyrolysis time and temperature, PAH concentrations generally decreased. These total concentrations were below existing environmental quality standards for concentrations of PAHs in soils. Total PAH concentrations in the fast pyrolysis and gasification biochar were 0.3 mu g g(-1) and 45 mu g g(-1), respectively, with maximum levels exceeding some quality standards. Concentrations of bioavailable PAHs in slow pyrolysis biochars ranged from 0.17 ng L-1 to 10.0 ng L-1 which is lower than concentrations reported for relatively clean urban sediments. The gasification produced biochar sample had the highest bioavailable concentration (162 +/- 71 ng L-1). Total dioxin concentrations were low (up to 92 mu g g(-1)) and bioavailable concentrations were below the analytical limit of detection. No clear pattern of how strongly PAHs were bound to different biochars was found based on the biochars' physicochemical properties.
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| 6. |
- Hale, Sarah E., et al.
(författare)
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Short-Term Effect of the Soil Amendments Activated Carbon, Biochar, and Ferric Oxyhydroxide on Bacteria and Invertebrates
- 2013
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 47:15, s. 8674-8683
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Tidskriftsartikel (refereegranskat)abstract
- The aim of the present study was to evaluate the secondary ecotoxicological effects of soil amendment materials that can be added to contaminated soils in order to sequester harmful pollutants. To this end, a nonpolluted agricultural soil was amended with 0.5, 2, and 5% of the following four amendments: powder activated carbon (PAC), granular activated carbon, corn stover biochar, and ferric oxyhydroxide powder, which have previously been proven to sequester pollutants in soil. The resulting immediate effects (i.e., without aging the mixtures before carrying out tests) on the springtail Folsomia candida, the earthworm species Aporectodea caliginosa and Eisenia fetida, the marine bacteria Vibrio fischeri, a suite of ten prokaryotic species, and a eukaryote (the yeast species Pichia anomalia) were investigated. Reproduction of F. candida was significantly increased compared to the unamended soil when 2% biochar was added to it. None of the treatments caused a negative effect on reproduction. All amendments had a deleterious effect on the growth of A. caliginosa when compared to the unamended soil, except the 0.5% amendment of biochar. In avoidance tests, E. fetida preferred biochar compared to all other amendments including the unamended soil. All amendments reduced the inhibition of luminescence to V. fischeri, i.e., were beneficial for the bacteria, with PAC showing the greatest improvement. The effects of the amendments on the suite of prokaryotic species and the eukaryote were variable, but overall the 2% biochar dose provided the most frequent positive effect on growth. It is concluded that the four soil amendments had variable but never strongly deleterious effects on the bacteria and invertebrates studied here during the respective recommended experimental test periods.
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| 7. |
- Jakob, Lena, et al.
(författare)
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PAH-sequestration capacity of granular and powder activated carbon amendments in soil, and their effects on earthworms and plants
- 2012
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Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 88:6, s. 699-705
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Tidskriftsartikel (refereegranskat)abstract
- A field lysimeter study was carried out to investigate whether the amendment of 2% powder and granular activated carbon (PAC and GAC) to a soil with moderate PAH contamination had an impact on the PAH bioaccumulation of earthworms and plants, since AC is known to be a strong sorbent for organic pollutants. Furthermore, secondary effects of AC on plants and earthworms were studied through growth and nutrient uptake, and survival and weight gain. Additionally, the effect of AC amendments on soil characteristics like pH, water holding capacity, and the water retention curve of the soil were investigated. Results show that the amendment of 2% PAC had a negative effect on plant growth while the GAC increased the growth rate of plants. PAC was toxic to earthworms, demonstrated by a significant weight loss, while the results for GAC were less clear due to ambiguous results of a field and a parallel laboratory study. Both kinds of AC significantly reduced biota to soil accumulation factors (BSAFs) of PAHs in earthworms and plants. The GAC reduced the BSAFs of earthworms by an average of 47 +/- 44% and the PAC amendment reduced them by 72 +/- 19%. For the investigated plants the BSAFs were reduced by 46 +/- 36% and 53 +/- 22% by the GAC and PAC, respectively.
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| 8. |
- Meynet, Paola, et al.
(författare)
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Effect of activated carbon amendment on bacterial community structure and functions in a pah impacted urban soil
- 2012
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 46:9, s. 5057-5066
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Tidskriftsartikel (refereegranskat)abstract
- We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAR degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAR degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of a available pollutants by biodegradation was most notable in unamended soil.
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| 9. |
- Oleszczuk, Patryk, et al.
(författare)
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Activated carbon and biochar amendments decrease pore water concentrations of polycyclic aromatic hydrocarbons (pahs) in sewage sludge
- 2012
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Ingår i: Bioresource Technology. - : Elsevier BV. - 0960-8524 .- 1873-2976. ; 111, s. 84-91
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Tidskriftsartikel (refereegranskat)abstract
- The aim of the research was to determine the influence of biochar and activated carbon (AC) on the freely dissolved concentration of polycyclic aromatic hydrocarbons (PAHs) in sewage sludge. Two different biochars (MSB and PMW) and two ACs (CP1 and BP2) were used in the present experiment. Addition of AC/biochar to sewage sludge caused significant decrease of freely dissolved PAHs concentration. Depending on the dose, the reduction of freely dissolved PAHs ranged from 56% to 95% (ACs) and from 0% to 57% (biochars). Only for the biochars was there a significant difference between short 7-d and long 30/60-d mixing time. It is concluded that both AC and biochar are effective at reducing PAH pore-water concentrations, the more expensive and non-carbon negative AC having the greatest effect.
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