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- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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. |
- Santangelo, James S., et al.
(author)
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Global urban environmental change drives adaptation in white clover
- 2022
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 375
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Journal article (peer-reviewed)abstract
- Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural dines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
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| 4. |
- Bentham, James, et al.
(author)
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A century of trends in adult human height
- 2016
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In: eLIFE. - 2050-084X. ; 5
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Journal article (peer-reviewed)abstract
- Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.522.7) and 16.5 cm (13.319.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
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| 5. |
- Bentham, James, et al.
(author)
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A century of trends in adult human height
- 2016
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In: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 5
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Journal article (peer-reviewed)abstract
- Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3– 19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8– 144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
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| 8. |
- Auffray, Charles, et al.
(author)
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Making sense of big data in health research: Towards an EU action plan
- 2016
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In: Genome Medicine. - : BIOMED CENTRAL LTD. - 1756-994X. ; 8:71
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Journal article (peer-reviewed)abstract
- Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of "big data" for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health arid healthcare for all Europearis.
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| 9. |
- Fazey, Ioan, et al.
(author)
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Transforming knowledge systems for life on Earth : Visions of future systems and how to get there
- 2020
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In: Energy Research & Social Science. - : Elsevier. - 2214-6296 .- 2214-6326. ; 70
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Journal article (peer-reviewed)abstract
- Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
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| 10. |
- Geist, Juergen, et al.
(author)
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Captive breeding of European freshwater mussels as a conservation tool : A review
- 2023
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In: Aquatic conservation. - : John Wiley & Sons. - 1052-7613 .- 1099-0755. ; 33:11, s. 1321-1359
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Journal article (peer-reviewed)abstract
- Freshwater mussels are declining throughout their range. Their important ecological functions along with insufficient levels of natural recruitment have prompted captive breeding for population augmentation and questions about the usefulness and applicability of such measures. This article reviews the current state of captive breeding and rearing programmes for freshwater mussels in Europe. It considers the various species, strategies, and techniques of propagation, as well as the different levels of effort required according to rearing method, highlighting the key factors of success. Within the last 30 years, 46 breeding activities in 16 European countries have been reported, mainly of Margaritifera margaritifera and Unio crassus. Some facilities propagate species that are in a very critical situation, such as Pseudunio auricularius, Unio mancus, and Unio ravoisieri, or multiple species concurrently. In some streams, the number of released captive-bred mussels already exceeds the size of the remaining natural population. Rearing efforts range from highly intensive laboratory incubation to lower intensity methods using in-river mussel cages or silos. Most breeding efforts are funded by national and EU LIFE(+) grants, are well documented, and consider the genetic integrity of the propagated mussels. Limited long-term funding perspectives, the availability of experienced staff, water quality, and feeding/survival during early life stages are seen as the most important challenges. Successful captive breeding programmes need to be combined with restoration of the habitats into which the mussels are released. This work will benefit from an evidence-based approach, knowledge exchange among facilities, and an overall breeding strategy comprising multiple countries and conservation units.
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| 11. |
- Kovacs, Gabor G., et al.
(author)
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Aging-related tau astrogliopathy (ARTAG) : harmonized evaluation strategy
- 2016
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In: Acta Neuropathologica. - : Springer Science and Business Media LLC. - 0001-6322 .- 1432-0533. ; 131:1, s. 87-102
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Journal article (peer-reviewed)abstract
- Pathological accumulation of abnormally phosphorylated tau protein in astrocytes is a frequent, but poorly characterized feature of the aging brain. Its etiology is uncertain, but its presence is sufficiently ubiquitous to merit further characterization and classification, which may stimulate clinicopathological studies and research into its pathobiology. This paper aims to harmonize evaluation and nomenclature of aging-related tau astrogliopathy (ARTAG), a term that refers to a morphological spectrum of astroglial pathology detected by tau immunohistochemistry, especially with phosphorylation-dependent and 4R isoform-specific antibodies. ARTAG occurs mainly, but not exclusively, in individuals over 60 years of age. Tau-immunoreactive astrocytes in ARTAG include thorn-shaped astrocytes at the glia limitans and in white matter, as well as solitary or clustered astrocytes with perinuclear cytoplasmic tau immunoreactivity that extends into the astroglial processes as fine fibrillar or granular immunopositivity, typically in gray matter. Various forms of ARTAG may coexist in the same brain and might reflect different pathogenic processes. Based on morphology and anatomical distribution, ARTAG can be distinguished from primary tauopathies, but may be concurrent with primary tauopathies or other disorders. We recommend four steps for evaluation of ARTAG: (1) identification of five types based on the location of either morphologies of tau astrogliopathy: subpial, subependymal, perivascular, white matter, gray matter; (2) documentation of the regional involvement: medial temporal lobe, lobar (frontal, parietal, occipital, lateral temporal), subcortical, brainstem; (3) documentation of the severity of tau astrogliopathy; and (4) description of subregional involvement. Some types of ARTAG may underlie neurological symptoms; however, the clinical significance of ARTAG is currently uncertain and awaits further studies. The goal of this proposal is to raise awareness of astroglial tau pathology in the aged brain, facilitating communication among neuropathologists and researchers, and informing interpretation of clinical biomarkers and imaging studies that focus on tau-related indicators.
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| 12. |
- Strand, John A., et al.
(author)
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Anlagda våtmarker som flödesbuffrare : Hur skapar vi synergieffekter medbiologisk mångfald och pollinering?
- 2024
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Reports (other academic/artistic)abstract
- Anlagda våtmarker har använts som naturbaserade lösningar på miljöproblem sedan 1990-talet i Sverige, framför allt i jordbrukslandskapet. Inledningsvis var huvudsyftet kostnadseffektiva åtgärder för att minska övergödningseffekter i havet men även våtmarkers positiva effekt på den biologiska mångfalden betonades tidigt. Under det senaste decenniet har anlagda våtmarker också diskuterats som lösning på andra miljönyttor, som flödesbuffring, vattenmagasinering och för att hålla kvar kol i organogena marker. För de senare ekosystemtjänsterna är forskningsläget emellertid osäkert och för vissa, såsom flödesbuffring, har det saknats faktiska mätdata. Denna brist är speciellt tydligt på de större landskapsskalor som behöver studeras för att exempelvis förstå våtmarkers och våtmarkslandskapens förmåga att förhindra översvämning lokalt och av nedströms belägna områden. I frånvaro av mätdata har förväntade positiva effekter i stället modellerats fram genom att utgå från parametrar som nederbörd och avrinningsområdens egenskaper. För att studera betydelsen av anlagda våtmarker i jordbrukslandskapet på flödesbuffring, dvs vattenmagasineringsförmågan, samt hur denna förmåga påverkar biologisk mångfald, har projektet samlat ett konsortium av experter och forskare inom framför allt ekologi och hydrologi. Inom ramen för projektet har en omfattande och strategisk provtagning genomförts under 3 år, av hydrologiska och ekologiska parametrar samt biologisk mångfald. Förutom dessa fältmätningar har även markägarnas åsikter kring värdet av sina anlagda våtmarker undersökts. Resultaten visar att anlagda våtmarker i jordbrukslandskapet har en stor potential att fungera som flödesutjämnare och buffra vatten både i den enskilda våtmarken och på landskapsnivå. Samtidigt gynnas en stor mängd organismgrupper, inklusive specialiserade våtmarksarter på nationella hotlistor. Resultaten visar också att för både flödesbuffring och biologisk mångfald finns flera avgörande parametrar vad gäller placering och design som styr hur väl en våtmark faktiskt levererar dessa ekosystemtjänster. De anlagda våtmarkerna i studien är huvudsakligen grävda dammar optimerade för näringsavskiljning och var därigenom relativt små och tog huvudsakligen emot dräneringsvatten från åkermark. Trots storleken bidrog de undersökta våtmarkerna till att dämpa högflöden med 3–17 %, vilket är i paritet med mätningar från naturliga våtmarker i tidigare studier (cirka 10 %). Det visade sig också att våtmarkerna bibehöll sina buffrande funktioner både under kortare högflödesperioder samt under ett år med hög årsnederbörd, vilket indikerar att de kan fungera med liknande effektivitet i ett framtida klimat med högre avrinning. Vid extremnederbörd framstår dock de buffrade volymerna i dessa små våtmarker som otillräckliga för att kunna fungera som (enskild) åtgärd, både idag och i framtiden. Till skillnad från naturliga våtmarker fanns inga starka samband mellan flödesbuffringen i studiens anlagda våtmarker och deras position i avrinningsområdet. Varken våtmarkens höjd över havet eller nerströms/uppströms placering i avrinningsområdet påverkade buffringsförmågan. Det fanns dock andra faktorer som påverkade våtmarkernas buffring, som att buffringen ökade med storleken på våtmarkens tillrinningsområden. Den effekten var delvis oväntad eftersom våtmarker med stora tillrinningsområde borde fyllas snabbare, vara fulla under längre tid och därmed buffra mindre effektivt. Resultaten tyder dock på att den tekniska utformningen på våtmarkerna ger dem god buffringskapacitet trots hög hydrologisk belastning. Resultaten visar också att det finns marginal för att förbättra buffringen genom tekniska anläggningsmekanismer, särskilt i fråga om tömningsmöjligheterna och reglerbarheten i utloppskonstruktionerna. Våra data visar att endast 47 % av den teoretiska volymförändringspotentialen utnyttjades i våtmarkerna, vilket kan medge ökad buffringspotential genom aktiv tömning/sänkning inför stora nederbördssituationer. De kraftiga vattennivåvariationerna i många av våtmarkerna, i kombination med förekomst av både flacka partier och brantare släntlutning, var positivt för artrikedomen hos flera organismgrupper. Generellt gynnades mångfalden hos flera grupper av större strandvåtmarker och flacka stränder, men det fanns undantag. Till exempel gynnades nätbyggande spindlar av brantare stränder. Ett oväntat resultat var också den begränsade eller till och med negativa effekten av betande djur, vilket går stick i stäv med rekommendationer i manualer för våtmarksanläggning och skötsel. Sannolikt gynnas leddjuren av att vegetationen hålls kort men samtidigt kan de rent fysiska effekterna av trampet missgynna artgrupper som har sin larvutveckling i blöt jord. För att förstå dessa samband behövs mer forskning som går in på mekanismer samt hur effekten påverkas av djurslag, djurtäthet och jordart. För insekter som utvecklas i vatten, som trollsländor, sågs inga samband med hydrologiska parametrar, men det var uppenbart att små, anlagda våtmarker är veritabla artöar för trollsländor. Totalt noterades 68 % av alla Sveriges arter på en yta (800 km2) som motsvarar 0,0015 % av Sveriges yta. Artsammansättning skilde sig mellan våtmarker och för att nå höga artantal på landskapsnivå kan det därför vara en fördel med många olika våtmarker i en region. För pollinatörer, särskilt bin, fanns korrelation mellan förekomst och storleken på våtmarkernas minsta vattenareal (dvs, när de är som mest uttorkade). Markägarenkäten visade att markägarna överlag ser mest nyttor, snarare än problem, med anlagda våtmarker. Mest notabelt var den höga nöjdheten med våtmarker (91 %) samt att en mycket stor andel markägare (83 %) använder sin våtmark för personlig rekreation, där skridskoåkning var populärast. Slutsatsen från studierna är att anlagda våtmarker som konstruerats för näringsavskiljning och i viss mån biologisk mångfald kan fungera bra som flödesbuffrare. Dessutom finns stor potential för ökad buffringskapacitet genom att både utformning (inte minst in- och utloppslösningar och aktiv nivåstyrning i våtmarkerna), läge och skötsel har en stor påverkan på den totala effekten. Dessutom verkar det finnas möjliga synergieffekter mellan vattennivåvariationer och artrikedomen av leddjur, men för att nå en hög biologisk mångfald i anlagda våtmarker bör stränderna vara heterogena eller att olika våtmarker har olika struktur.
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