| 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. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Mohammed Taha, Hiba, et al.
(författare)
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The NORMAN Suspect List Exchange (NORMAN-SLE) : facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry
- 2022
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Ingår i: Environmental Sciences Europe. - : Springer. - 2190-4707 .- 2190-4715. ; 34:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101).Conclusions: The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the “one substance, one assessment” approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/).
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| 4. |
- Abel, Sebastian, et al.
(författare)
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Mixing and capping techniques for activated carbon based sediment remediation Efficiency and adverse effects for Lumbriculus variegatus
- 2017
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Ingår i: Water Research. - : Elsevier BV. - 0043-1354 .- 1879-2448. ; 114, s. 104-112
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Tidskriftsartikel (refereegranskat)abstract
- Activated carbon (AC) has been proven to be highly effective for the in-situ remediation of sediments contaminated with a wide range of hydrophobic organic contaminants (HOCs). However, adverse biological effects, especially to benthic organisms, can accompany this promising remediation potential. In this study, we compare both the remediation potential and the biological effects of several AC materials for two application methods: mixing with sediment (MIX) at doses of 0.1 and 1.0% based on sediment dw and thin layer capping (TLC) with 0.6 and 1.2 kg AC/m(2). Significant dose dependent reductions in PCB bioaccumulation in Lumbriculus variegatus of 35-93% in MIX treatments were observed. Contaminant uptake in TLC treatments was reduced by up to 78% and differences between the two applied doses were small. Correspondingly, significant adverse effects were observed for L. variegatus whenever AC was present in the sediment. The lowest application dose of 0.1% AC in the MIX system reduced L variegatus growth, and 1.0% AC led to a net loss of organism biomass. All TLC treatments let to a loss of biomass in the test organism. Furthermore, mortality was observed with 1.2 kg ACim(2) doses of pure AC for the TLC treatment. The addition of clay (Kaolinite) to the TLC treatments prevented mortality, but did not decrease the loss in biomass. While TLC treatments pose a less laborious alternative for AC amendments in the field, the results of this study show that it has lower remediation potential and could be more harmful to the benthic fauna.
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| 5. |
- 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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| 6. |
- Arp, Hans Peter H., et al.
(författare)
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Review of polyoxymethylene passive sampling methods for quantifying freely dissolved porewater concentrations of hydrophobic organic contaminants
- 2015
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Ingår i: Environmental Toxicology and Chemistry. - : Wiley. - 0730-7268 .- 1552-8618. ; 34:4, s. 710-720
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Forskningsöversikt (refereegranskat)abstract
- Methods involving polyoxymethylene (POM) as a passive sampler are increasing in popularity to assess contaminant freely dissolved porewater concentrations in soils and sediments. These methods require contaminant-specific POM-water partition coefficients, K-POM. Certain methods for determining K-POM perform reproducibly (within 0.2 log units). However, other methods can give highly varying K-POM values (up to 2 log units), especially for polycyclic aromatic hydrocarbons (PAHs). To account for this variation, the authors tested the influence of key methodological components in K-POM determinations, including POM thickness, extraction procedures, and environmental temperature and salinity, as well as uptake kinetics in mixed and static systems. All inconsistencies in the peer-reviewed literature can be accounted for by the likelihood that thick POM materials (500m or thicker) do not achieve equilibrium (causing negative biases up to 1 log unit), or that certain POM extraction procedures do not ensure quantitative extraction (causing negative biases up to 2 log units). Temperature can also influence K-POM, although all previous literature studies were carried out at room temperature. The present study found that K-POM values at room temperature are independent (within 0.2 log units) of POM manufacture method, of thickness between 17m and 80m, and of salinity between 0% and 10%. Regarding kinetics, monochloro- to hexachloro-polychlorinated biphenyls (PCBs) were within 0.2 log units of equilibrium after 28d in the mixed system, but only dichloro-PCBs achieved near equilibrium after 126d in the static system. Based on these insights, recommended methods and K-POM values to facilitate interlaboratory reproducibility are presented.
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| 7. |
- Arp, Hans Peter H., et al.
(författare)
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The presence, emission and partitioning behavior of polychlorinated biphenyls in waste, leachate and aerosols from Norwegian waste-handling facilities
- 2020
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Ingår i: Science of the Total Environment. - : ELSEVIER. - 0048-9697 .- 1879-1026. ; 715, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- Even though production and open use of polychlorinated biphenyls (PCBs) have been phased out in Western industrialised countries since the 1980s, PCBs were still present in waste collected from different waste handling facilities in Norway in 2013. Sums of seven indicator-PCBs (I-PCB7:PCB-28, -52, -101, -118, -138, -153 and -180) were highest in plastic waste (3700 +/- 1800 mu g/kg, n=15), waste electrical and electronic equipment (WEEE) (1300 +/- 400 mu g/kg, n=12) and fine vehicle fluff (1800 = 1400 mu g/kg, n=4) and lowest in glass waste, combustibles, bottom ash and fly ash (0.3 to 65 mu g/kg). Concentrations in leachate water varied from 1.7 to 2900 ng/L, with higher concentrations found at vehicle and WEEE handling facilities. Particles in leachate water exhibited similar PCB sorption properties as solid waste collected on site, with waste-water partitioning coefficients ranging from 10(5)to 10(7) .I-PCB7 in air samples collected at the sites were mostly in the gas phase (100-24000 pg/m(3)), compared to those associated with particles (9-1900 pg/m(3)). In contrast, brominated flame retardants (BFRs) in the same samples were predominantly found associated with particles (e.g. sum of 10 brominated diethyl ethers, Sigma BDE10, associated with particles 77-194,000 pg/m(3)) compared to the gas phase (Sigma DE10 6-473 pg/m(3)). Measured gas-phase I-PCB7 concentrations are less than predicted, assuming waste-air partitioning in equilibrium with predominant waste on site. However, the gas-particle partitioning behavior of PCBs and BFRs could be predicted using an established partitioning model for ambient aerosols. PCB emissions from Norwegian waste handling facilities occurred primarily in the form of atmospheric vapor or leachate particles.
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| 8. |
- Hale, Sarah E., et al.
(författare)
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A synthesis of parameters related to the binding of neutral organic compounds to charcoal
- 2016
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Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 144, s. 65-74
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Forskningsöversikt (refereegranskat)abstract
- The sorption strength of neutral organic compounds to charcoal, also called biochar was reviewed and related to charcoal and compound properties. From 29 studies, 507 individual Freundlich sorption.coefficients were compiled that covered the sorption strength of 107 organic contaminants. These sorption coefficients were converted into charcoal-water distribution coefficients (K-D) at aqueous concentrations of 1 ng/L, 1 mu g/L and 1 mg/L. Reported log K-D values at 1 mu g/L varied from 0.38 to 8.25 across all data. Variation was also observed within the compound classes; pesticides, herbicides and insecticides, PAHs, phthalates, halogenated organics, small organics, alcohols and PCBs. Five commonly reported variables; charcoal production temperature T, surface area SA, H/C and 0/C ratios and organic compound octanolwater partitioning coefficient, were correlated with K-D values using single and multiple-parameter linear regressions. The sorption strength of organic compounds to charcoals increased with increasing charcoal production temperature T, charcoal SA and organic pollutant octanol-water partitioning coefficient and decreased with increasing charcoal O/C ratio and charcoal H/C ratio. T was found to be correlated with SA (r(2) = 0.66) and O/C (r(2) = 0.50), particularly for charcoals produced from wood feedstocks (r2 = 0.73 and 0.80, respectively). The resulting regression: log K-D = (0.18 +/- 0.06) log K-ow + (5.74 +/- 1.40) log T + (0.85 +/- 0.15) log SA + (1.60 +/- 0.29) log OC + (-0.89 +/- 0.20) log HC + (-13.20 +/- 3.69), r(2) = 0.60, root mean squared error = 0.95, n = 151 was obtained for all variables. This information can be used as an initial screening to identify charcoals for contaminated soil and sediment remediation.
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| 9. |
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| 10. |
- 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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