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- 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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- Alström, Per, Professor, et al.
(författare)
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Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
- 2024
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Ingår i: Zoological Journal of the Linnean Society. - : Oxford University Press. - 0024-4082 .- 1096-3642. ; 200:4, s. 1080-1108
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Tidskriftsartikel (refereegranskat)abstract
- The species complex comprising the rufous-naped lark Corypha africana, Sharpe's lark Corypha sharpii, the red-winged lark Corypha hypermetra, the Somali long-billed lark Corypha somalica and Ash's lark Corypha ashi encompasses 31 recognised taxa across sub-Saharan Africa, many of which are extremely poorly known and some not observed for decades. Only 17 taxa have been studied molecularly and none comprehensively for morphology, vocalisations or other behaviours. Here, we undertake comprehensive integrative taxonomic analyses based on plumage and morphometrics (for 97% of the taxa), mitochondrial and nuclear loci (77%), <= 1.3 million genome-wide single nucleotide polymorphisms (68%), song (many described for the first time; 52%) and additional behavioural data (45%). All polytypic species as presently circumscribed are paraphyletic, with eight primary clades separated by <= 6.3-6.8 Myr, broadly supported by plumage, morphometrics, song and other behaviours. The most recent divergences concern sympatric taxon pairs usually treated as separate species, whereas the divergence of all clades including C. africana subspecies is as old as sister species pairs in other lark genera. We propose the recognition of nine instead of five species, while C. ashi is synonymised with C. somalica rochei as C. s. ashi. The geographical distributions are incompletely known, and although the nine species are generally para-/allopatric, some might be sympatric.
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| 8. |
- Berge, L., et al.
(författare)
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Terahertz spectroscopy from air plasmas created by two-color femtosecond laser pulses: The ALTESSE project
- 2019
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Ingår i: Epl. - : IOP Publishing. - 0295-5075 .- 1286-4854. ; 126:2
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Tidskriftsartikel (refereegranskat)abstract
- Terahertz pulses are very popular because of their numerous applications, for example in security. Located between microwaves and optical waves in the electromagnetic spectrum, their spectral domain can now be exploited for molecular spectroscopy using terahertz emission from plasmas formed by femtosecond laser pulses ionizing gases such as air. Down-conversion of broadband optical spectra in a plasma produces intense radiation suitable for the detection of suspect materials remotely. The different physical mechanisms involved to create terahertz radiation by laser-matter interaction are reviewed. The new potentialities offered by intense ultrafast lasers allow the acquisition of unique spectral signatures characterizing various materials. Copyright (C) EPLA, 2019
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- Engelbrecht, J. A. A., et al.
(författare)
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Comparison of experimental results with theoretical models for the temperature dependence of the band gap of AlxGa1-xN epilayers
- 2022
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Ingår i: Journal of materials science. Materials in electronics. - : SPRINGER. - 0957-4522 .- 1573-482X. ; 33, s. 22492-22498
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Tidskriftsartikel (refereegranskat)abstract
- The band gap energies AlxGa1-xN epilayers prepared on two different substrates were assessed using Fourier Transform Infrared (FTIR) reflectance spectroscopy, photoluminescence (PL) and scanning electron microscopy electron dispersive spectroscopy (SEM-EDS). The results were compared to various theoretical formulae to calculate the band gap, and deviations elucidated.
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| 10. |
- Polme, S., et al.
(författare)
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FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
- 2020
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 105:1, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.
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| 12. |
- Alström, Per, Professor, et al.
(författare)
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Systematics of the avian family Alaudidae using multilocus and genomic data
- 2023
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Ingår i: Avian Research. - : Elsevier BV. - 2053-7166. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- The family Alaudidae, larks, comprises 93–100 species (depending on taxonomy) that are widely distributed across Africa and Eurasia, with single species extending their ranges to North and northernmost South America and Australia. A decade-old molecular phylogeny, comprising ∼80% of the species, revealed multiple cases of parallel evolution and large variation in rates of morphological evolution, which had misled taxonomists into creating many non-monophyletic genera. Here, we reconstruct the phylogeny of the larks, using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species (in total 133 taxa; not all loci available for all species). We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling (in total 51 samples of 44 taxa across 40 species). Our results confirm the previous findings of rampant morphological convergence and divergence, and reveal new cases of paraphyletic genera. We propose a new subfamily classification, and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the Alaudidae. Our study supports recently proposed species splits as well as some recent lumps, while also questioning some of the latter. This comprehensive phylogeny will form an important basis for future studies, such as comparative studies of lark natural history, ecology, evolution and conservation.
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| 13. |
- Engelbrecht, J. A. A., et al.
(författare)
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Assesment of a model to calculate the refractive index of AlXGa1-XN epilayers using the multi-oscillator model simulation of the infrared reflectance
- 2022
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Ingår i: Physica. B, Condensed matter. - : ELSEVIER. - 0921-4526 .- 1873-2135. ; 625
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Tidskriftsartikel (refereegranskat)abstract
- A formula for the calculation of the refractive index of AlXGa1-XN in the infrared region has previously been proposed. In this paper, the validity of the proposed model is assessed against the multi-oscillator model which simulates the infrared reflectance of AlXGa1-XN epilayers. Acceptable agreement was found between the two models for wavenumbers greater than 3500 cm(-1). Additional validation for the earlier proposed formula is obtained by the calculation of epilayer thicknesses of AlXGa1-XN samples in the infrared region.
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| 14. |
- Engelbrecht, J. A. A., et al.
(författare)
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Notes on the plasma resonance peak employed to determine doping in SiC
- 2015
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Ingår i: Infrared physics & technology. - : ELSEVIER SCIENCE BV. - 1350-4495 .- 1879-0275. ; 72, s. 95-100
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Tidskriftsartikel (refereegranskat)abstract
- The doping level of a semiconductor material can be determined using the plasma resonance frequency to obtain the carrier concentration associated with doping. This paper provides an overview of the procedure for the three most common polytypes of SiC. Results for 3C-SiC are presented and discussed. In phosphorus doped samples analysed, it is submitted that the 2nd plasma resonance cannot be detected due to high values of the free carrier damping constant gamma. (C) 2015 Elsevier B.V. All rights reserved.
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| 15. |
- Finch, B. W., et al.
(författare)
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Disjunct resident population of Melodious Lark Mirafra cheniana discovered in East Africa
- 2022
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Ingår i: Journal of Ornithology. - : Springer Science and Business Media LLC. - 2193-7192 .- 2193-7206. ; 164, s. 55-71
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Tidskriftsartikel (refereegranskat)abstract
- We describe the discovery of a previously unknown population of Melodious Lark Mirafra cheniana from northern Tanzania and southern Kenya, some 2000 km north of what was previously thought to be its northern limit in central Zimbabwe. The identification of this population as M. cheniana is based primarily on analyses of mitochondrial DNA and song. We also clarify relationships within this genus by sequencing material of White-tailed Lark Mirafra albicauda for the first time; although its relationships with other species in the group remain unclear, our analyses clearly show it to be different from M. cheniana in the newly discovered population. The discovery of a population of M. cheniana in East Africa conforms to a known pattern for closely related lark species to have disjunct distributions in southern and eastern Africa.
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| 16. |
- Martin-Sanchez, F., et al.
(författare)
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Synergy between medical informatics and bioinformatics : Facilitating genomic medicine for future health care
- 2004
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Ingår i: Journal of Biomedical Informatics. - : Elsevier BV. - 1532-0464 .- 1532-0480. ; 37:1, s. 30-42
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we review the results of BIOINFOMED, a study funded by the European Commission (EC) with the purpose to analyse the different issues and challenges in the area where Medical Informatics and Bioinformatics meet. Traditionally, Medical Informatics has been focused on the intersection between computer science and clinical medicine, whereas Bioinformatics have been predominantly centered on the intersection between computer science and biological research. Although researchers from both areas have occasionally collaborated, their training, objectives and interests have been quite different. The results of the Human Genome and related projects have attracted the interest of many professionals, and introduced new challenges that will transform biomedical research and health care. A characteristic of the 'post genomic' era will be to correlate essential genotypic information with expressed phenotypic information. In this context, Biomedical Informatics (BMI) has emerged to describe the technology that brings both disciplines (BI and MI) together to support genomic medicine. In recognition of the dynamic nature of BMI, institutions such as the EC have launched several initiatives in support of a research agenda, including the BIOINFOMED study.
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| 17. |
- Parker, Thomas C., et al.
(författare)
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Rhizosphere allocation by canopy-forming species dominates soil CO2 efflux in a subarctic landscape
- 2020
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Ingår i: New Phytologist. - : John Wiley & Sons. - 0028-646X .- 1469-8137. ; 227:6, s. 1818-1830
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Tidskriftsartikel (refereegranskat)abstract
- In arctic ecosystems, climate change has increased plant productivity. As arctic carbon (C) stocks predominantly are located belowground, the effects of greater plant productivity on soil C storage will significantly determine the net sink/source potential of these ecosystems, but vegetation controls on soil CO2 efflux remain poorly resolved.In order to identify the role of canopy‐forming species in belowground C dynamics, we conducted a girdling experiment with plots distributed across 1 km2 of treeline birch (Betula pubescens ) forest and willow (Salix lapponum ) patches in northern Sweden and quantified the contribution of canopy vegetation to soil CO2 fluxes and belowground productivity.Girdling birches reduced total soil CO2 efflux in the peak growing season by 53%, which is double the expected amount, given that trees contribute only half of the total leaf area in the forest. Root and mycorrhizal mycelial production also decreased substantially. At peak season, willow shrubs contributed 38% to soil CO2 efflux in their patches.Our findings indicate that C, recently fixed by trees and tall shrubs, makes a substantial contribution to soil respiration. It is critically important that these processes are taken into consideration in the context of a greening arctic because productivity and ecosystem C sequestration are not synonymous.
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| 18. |
- Ylänne, Henni, et al.
(författare)
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Reindeer control over subarctic treeline alters soil fungal communities with potential consequences for soil carbon storage
- 2021
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Ingår i: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 27:18, s. 4254-4268
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Tidskriftsartikel (refereegranskat)abstract
- The climate-driven encroachment of shrubs into the Arctic is accompanied by shifts in soil fungal communities that could contribute to a net release of carbon from tundra soils. At the same time, arctic grazers are known to prevent the establishment of deciduous shrubs and, under certain conditions, promote the dominance of evergreen shrubs. As these different vegetation types associate with contrasting fungal communities, the belowground consequences of climate change could vary among grazing regimes. Yet, at present, the impact of grazing on soil fungal communities and their links to soil carbon have remained speculative. Here we tested how soil fungal community composition, diversity and function depend on tree vicinity and long-term reindeer grazing regime and assessed how the fungal communities relate to organic soil carbon stocks in an alpine treeline ecotone in Northern Scandinavia. We determined soil carbon stocks and characterized soil fungal communities directly underneath and >3 m away from mountain birches (Betula pubescens ssp. czerepanovii) in two adjacent 55-year-old grazing regimes with or without summer grazing by reindeer (Rangifer tarandus). We show that the area exposed to year-round grazing dominated by evergreen dwarf shrubs had higher soil C:N ratio, higher fungal abundance and lower fungal diversity compared with the area with only winter grazing and higher abundance of mountain birch. Although soil carbon stocks did not differ between the grazing regimes, stocks were positively associated with root-associated ascomycetes, typical to the year-round grazing regime, and negatively associated with free-living saprotrophs, typical to the winter grazing regime. These findings suggest that when grazers promote dominance of evergreen dwarf shrubs, they induce shifts in soil fungal communities that increase soil carbon sequestration in the long term. Thus, to predict climate-driven changes in soil carbon, grazer-induced shifts in vegetation and soil fungal communities need to be accounted for.
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