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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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| 3. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 4. |
- Biurrun, Idoia, et al.
(författare)
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Benchmarking plant diversity of Palaearctic grasslands and other open habitats
- 2021
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Ingår i: Journal of Vegetation Science. - Oxford : John Wiley & Sons. - 1100-9233 .- 1654-1103. ; 32:4
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Tidskriftsartikel (refereegranskat)abstract
- Journal of Vegetation Science published by John Wiley & Sons Ltd on behalf of International Association for Vegetation Science.Aims: Understanding fine-grain diversity patterns across large spatial extents is fundamental for macroecological research and biodiversity conservation. Using the GrassPlot database, we provide benchmarks of fine-grain richness values of Palaearctic open habitats for vascular plants, bryophytes, lichens and complete vegetation (i.e., the sum of the former three groups). Location: Palaearctic biogeographic realm. Methods: We used 126,524 plots of eight standard grain sizes from the GrassPlot database: 0.0001, 0.001, 0.01, 0.1, 1, 10, 100 and 1,000 m2 and calculated the mean richness and standard deviations, as well as maximum, minimum, median, and first and third quartiles for each combination of grain size, taxonomic group, biome, region, vegetation type and phytosociological class. Results: Patterns of plant diversity in vegetation types and biomes differ across grain sizes and taxonomic groups. Overall, secondary (mostly semi-natural) grasslands and natural grasslands are the richest vegetation type. The open-access file ”GrassPlot Diversity Benchmarks” and the web tool “GrassPlot Diversity Explorer” are now available online (https://edgg.org/databases/GrasslandDiversityExplorer) and provide more insights into species richness patterns in the Palaearctic open habitats. Conclusions: The GrassPlot Diversity Benchmarks provide high-quality data on species richness in open habitat types across the Palaearctic. These benchmark data can be used in vegetation ecology, macroecology, biodiversity conservation and data quality checking. While the amount of data in the underlying GrassPlot database and their spatial coverage are smaller than in other extensive vegetation-plot databases, species recordings in GrassPlot are on average more complete, making it a valuable complementary data source in macroecology. © 2021 The Authors.
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| 5. |
- Dengjel, Joern, et al.
(författare)
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Identification of Autophagosome-associated Proteins and Regulators by Quantitative Proteomic Analysis and Genetic Screens
- 2012
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 11:3
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Tidskriftsartikel (refereegranskat)abstract
- Autophagy is one of the major intracellular catabolic pathways, but little is known about the composition of autophagosomes. To study the associated proteins, we isolated autophagosomes from human breast cancer cells using two different biochemical methods and three stimulus types: amino acid deprivation or rapamycin or concanamycin A treatment. The autophagosome- associated proteins were dependent on stimulus, but a core set of proteins was stimulus- independent. Remarkably, proteasomal proteins were abundant among the stimulus- independent common autophagosome- associated proteins, and the activation of autophagy significantly decreased the cellular proteasome level and activity supporting interplay between the two degradation pathways. A screen of yeast strains defective in the orthologs of the human genes encoding for a common set of autophagosome- associated proteins revealed several regulators of autophagy, including subunits of the retromer complex. The combined spatiotemporal proteomic and genetic data sets presented here provide a basis for further characterization of autophagosome biogenesis and cargo selection.
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| 6. |
- Baldermann, A., et al.
(författare)
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Impact of green clay authigenesis on element sequestration in marine settings
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Retrograde clay mineral reactions (reverse weathering), including glauconite formation, are first-order controls on element sequestration in marine sediments. Here, we report substantial element sequestration by glauconite formation in shallow marine settings from the Triassic to the Holocene, averaging 3 +/- 2 mmol.cm(-2).kyr(-1) for K, Mg and Al, 16 +/- 9 mmol.cm(-2).kyr(-1) for Si and 6 +/- 3 mmol.cm(-2).kyr(-1) for Fe, which is similar to 2 orders of magnitude higher than estimates for deep-sea settings. Upscaling of glauconite abundances in shallow-water (0-200 m) environments predicts a present-day global uptake of similar to <= 0.1 Tmol.yr(-1) of K, Mg and Al, and similar to 0.1-0.4 Tmol.yr(-1) of Fe and Si, which is similar to half of the estimated Mesozoic elemental flux. Clay mineral authigenesis had a large impact on the global marine element cycles throughout Earth's history, in particular during 'greenhouse' periods with sea level highstand, and is key for better understanding past and present geochemical cycling in marine sediments.
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| 7. |
- Estrada-Peña, A., et al.
(författare)
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Association of environmental traits with the geographic ranges of ticks (Acari Ixodidae) of medical and veterinary importance in the western Palearctic : a digital data set
- 2013
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Ingår i: Experimental & applied acarology. - : Springer Science and Business Media LLC. - 0168-8162 .- 1572-9702. ; 59:3, s. 351-366
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Tidskriftsartikel (refereegranskat)abstract
- We compiled information on the distribution of ticks in the western Palearctic (11°W, 45°E; 29°N, 71°N), published during 1970-2010. The literature search was filtered by the tick's species name and an unambiguous reference to the point of capture. Records from some curated collections were included. We focused on tick species of importance to human and animal health, in particular: Ixodes ricinus, Dermacentor marginatus, D. reticulatus, Haemaphysalis punctata, H. sulcata, Hyalomma marginatum, Hy. lusitanicum, Rhipicephalus annulatus, R. bursa, and the R. sanguineus group. A few records of other species (I. canisuga, I. hexagonus, Hy. impeltatum, Hy. anatolicum, Hy. excavatum, Hy. scupense) were also included. A total of 10,280 records was included in the data set. Almost 42 % of published references are not adequately referenced (and not included in the data set), host is reported for only 61 % of records and a reference to time of collection is missed for 84 % of published records. Ixodes ricinus accounted for 44.3 % of total records, with H. marginatum and D. marginatus accounting for 7.1 and 8.1 % of records, respectively. The lack of homogeneity of the references and potential pitfalls in the compilation were addressed to create a digital data set of the records of the ticks. We attached to every record a coherent set of quantitative descriptors for the site of reporting, namely gridded interpolated monthly climate and remotely sensed data on vegetation (NDVI). We also attached categorical descriptors of the habitat: a standard classification of land biomes and an ad hoc classification of the target territory from remotely sensed temperature and NDVI data. A descriptive analysis of the data revealed that a principal components reduction of the environmental (temperature and NDVI) variables described the distribution of the species in the target territory. However, categorical descriptors of the habitat were less effective. We stressed the importance of building reliable collections of ticks with specific references as to collection point, host and date of capture. The data set is freely downloadable.
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| 8. |
- Estrada-Peña, Agustín, et al.
(författare)
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Scientific opinion on geographic distribution of tick-borne infections and their vectors in Europe and the other regions of the Mediterranean Basin : EFSA Panel on Animal Health and Welfare (AHAW)
- 2010
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Ingår i: EFSA Journal. - Parma, Italy : European Food Safety Authority. - 1831-4732. ; 8:9, s. 1723 [280 pp.]-
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Forskningsöversikt (refereegranskat)abstract
- This report is the second of a series of two technical assessments of the role of ticks in transmission of animal diseases and zoonoses in Eurasia. A previous published scientific opinion (EFSA 2010a) focused on two diseases- Crimean-Congo haemorrhagic fever and African swine fever in Eurasia. The aim of this report is to provide a general overview of the geographic distribution of tick species which have proven involvement in the transmission of pathogens causing animal diseases and zoonoses in Eurasia.The report provides a review of the geographic distribution of the relevant tick species and TBDs in Eurasia by producing maps of the region that display the occurrences of ticks and tick borne pathogens. Systematic literature review of available publications for the last 10 years and other available literature from the experts were used in the retrieval of the geographical reported cases for the presence of ticks and tick borne pathogens. The report includes a description of the factors that influence the dynamics of the relevant tick species and identify possible high-risk areas in the EU for introduction considering the biological and ecological characteristics of the ticks and their ability to adapt to new areas. Surveillance tools and control measures for ticks were discussed.Findings from this review have provided evidence of the extent of ticks and TBDs in geographical ranges and the existing risk areas that should be considered as baseline information to assess potential risk of these diseases. The report indicates the validity of using available literature to support the presence of ticks and TBDs without further predication using weather and other environmental factors associated with the survival of the ticks. Surveillance tools for the detection of the ticks and their control measures are discussed in this report. The report concluded that animal and human movement play a significant impact on the spread of the ticks and TBDs. Climate changes and flight pattern of migratory birds can influence the presence and spread of the ticks and TBDs, These two factors acting by themselves have not been determined be responsible for the widespread distribution of ticks.
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| 9. |
- Estrada-Pena, Agustín, et al.
(författare)
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Scientific opinion on the Role of Tick Vectors in the Epidemiology of Crimean-Congo Hemorrhagic Fever and African Swine Fever in Eurasia : EFSA Panel on Animal Health and Welfare
- 2010
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Ingår i: EFSA Journal. - Parma, Italy : EFSA. - 1831-4732. ; 8:8, s. 1-156
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Tidskriftsartikel (refereegranskat)abstract
- The report provides an update on the role of the tick vectors in the epidemiology of African swine fever (ASF) and Crimean and Congo haemorrhagic fever (CCHF) in Eurasia, specifically to review of the geographical distribution of the relevant ticks with presentation of maps of their occurrence in Europe and Mediterranean basin; a description of the factors that define the relevant tick population dynamics and identify possible high risk areas in the EU; an update on the role of tick vectors associated with CCHF and ASF in Eurasia; and reviews available methods for the control of the relevant tick vectors. Data were collected through systematic literature review in a database from which maps of geographic distribution of ticks, CCHF virus and ASF virus were issued. The main vectors for CCHF are Hyalomma spp, Increase in the number of fragmented areas and the degradation of agricultural lands to bush lands are the two main factors in the creation of new foci of CCHF in endemic areas. Movement of livestock and wildlife species, which may carry infected ticks, contributes to the spread of the infection. The Middle East and Balkan countries are the most likely sources of introduction of CCHFV into other European countries. All the Ornithodoros species investigated so far can become infective with ASF virus and are perhaps biological vectors. These ticks are important in maintaining the local foci of the ASFV, but do not play an active role in the geographical spread of the virus. Wild boars have never been found infested by Ornithodoros spp. because wild boars normally do not rest inside protected burrows, but above the ground. There is no single ideal solution to the control of ticks relevant for CCHF or ASF. The integrated control approach is probably the most effective.
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| 10. |
- Farkas, Julia, et al.
(författare)
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Characterization of the effluent from a nanosilver producing washing machine
- 2011
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Ingår i: Environment International. - : Elsevier BV. - 0160-4120 .- 1873-6750. ; 37:6, s. 1057-1062
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Tidskriftsartikel (refereegranskat)abstract
- The increasing number of nanomaterial based consumer products raises concerns about their possible impact on the environment. This study provides an assessment of the effluent from a commercially available silver nanowashing machine. The washing machine released silver in its effluent at an average concentration of 11 mu g L(-1), as determined by inductive coupled mass spectrometry (ICP-MS). The presence of silver nanoparticles (AgNPs) was confirmed by single particle ICP-MS as well as ion selective electrode measurements and filtration techniques. Size measurements showed particles to be in the defined nanosize range, with an average size of 10 nm measured with transmission electron microscopy (TEM) and 60-100 nm determined with nanoparticle tracking analysis (NTA). The effluent was shown to have negative effects on a natural bacterial community as its abundance was clearly reduced when exposed to the nanowash water. If washing machines capable of producing AgNPs become a common feature of households in the future, wastewater will contain significant loadings of AgNPs which might be released into the environment.
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