| 1. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
- 2012
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 4, s. 37-63
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Tidskriftsartikel (refereegranskat)abstract
- Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
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| 2. |
- Lee, Wai Tung, et al.
(författare)
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Polarisation Development at the European Spallation Source
- 2023
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Ingår i: EPJ Web of Conferences. - 2100-014X. ; 286, s. 03004-03004
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Tidskriftsartikel (refereegranskat)abstract
- To meet the ever-increasing user demand, eleven of the fifteen European Spallation Source (ESS) instruments under construction aim to offer polarised neutrons for user experiments. They include an imaging instrument, a SANS instruments, two reflectometers, three diffractometers, and four spectrometers. In conjunction with in-kind contributions and instrumentation grants, the ESS Polarisation Project will support the incorporation of polarisation analysis on eight of the eleven instruments. The project aims to deliver polarised neutrons for first-science experiments as instruments enter operation. Different polariser and polarisation analyser techniques will be available to accommodate the specifics of experiments on a given instrument. Polarised 3He neutron spin filter using either Metastable Optical Pumping (MEOP) or Spin-Exchange Optical Pumping (SEOP) techniques will provide shared-use equipment among many instruments, with SEOP’s main application being in situ beam-polarisation. Several instruments will also use polarising-supermirror devices. To provide wide-bandwidth spin-flipping capability to the time-of-flight instruments, Adiabatic Fast Passage (AFP) neutron spin flippers, also known as gradient-field radiofrequency spin flippers will be the main method of choice. Devices based on the same AFP principle will also be used to flip 3He nuclear spins. We are constructing our first 3He polariser setup, including field coils to produce highly uniform magnetic field. Monte Carlo simulations are being done for the supermirror polarisers. To ensure science-focused development, we are working with university partners in doing scientific experiments with polarised neutrons. These are some of the activities developing polarisation analysis for ESS instruments in our project.
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| 5. |
- Brodtkorb, Thor-Henrik, 1976-, et al.
(författare)
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Screening for hypertrophic cardiomyopathy in young athletes : A cost-effectiveness analysis
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background: Screening to prevent sudden cardiac death among young athletes has been debated for some time and several countries have already introduced pre-participation cardiovascular screening to identify sports active individuals at risk. Although, hypertrophic cardiomyopathy (HCM) is the most common underlying disease that is documented to be detectable by screening the cost-effectiveness of such a screening strategy is still unclear. Methods: A screening program to detect HCM in young athletes was compared to a non screening strategy. Prevalence of HCM, mortality risks and test characteristics were estimated from published sources and formal expert elicitation. These estimates were incorporated in a decision analytic model to estimate costs and health outcomes, expressed in life years and quality adjusted life years (QALYs), over a lifetime perspective. Results: The screening strategy was associated with a mean incremental cost of €93 and a mean incremental gain of 0.0005 life years, yielding a cost per life year gained of €196 205. Taking quality of life into account, the screening strategy was associated with a loss of 0.034 QALY. Conclusions: The study shows that screening young athletes for hypertrophic cardiomyopathy is not likely to yield survival benefits at a cost normally considered to be cost-effective and if quality of life is considered in the analysis screening is associated with higher costs and a loss of QALYs. Thus, based on the present findings a strategy of screening young athletes for hypertrophic cardiomyopathy is unlikely to be cost effective.
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| 6. |
- Caselli, Lucrezia, et al.
(författare)
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Neutron reflectometry as a powerful tool to elucidate membrane interactions of drug delivery systems
- 2024
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Ingår i: Advances in Colloid and Interface Science. - 0001-8686. ; 325
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Tidskriftsartikel (refereegranskat)abstract
- The last couple of decades have seen an explosion of novel colloidal drug delivery systems, which have been demonstrated to increase drug efficacy, reduce side-effects, and provide various other advantages for both small-molecule and biomacromolecular drugs. The interactions of delivery systems with biomembranes are increasingly recognized to play a key role for efficient eradication of pathogens and cancer cells, as well as for intracellular delivery of protein and nucleic acid drugs. In parallel, there has been a broadening of methodologies for investigating such systems. For example, advanced microscopy, mass-spectroscopic “omic”-techniques, as well as small-angle X-ray and neutron scattering techniques, which only a few years ago were largely restricted to rather specialized areas within basic research, are currently seeing increased interest from researchers within wide application fields. In the present discussion, focus is placed on the use of neutron reflectometry to investigate membrane interactions of colloidal drug delivery systems. Although the technique is still less extensively employed for investigations of drug delivery systems than, e.g., X-ray scattering, such studies may provide key mechanistic information regarding membrane binding, re-modelling, translocation, and permeation, of key importance for efficacy and toxicity of antimicrobial, cancer, and other therapeutics. In the following, examples of this are discussed and gaps/opportunities in the research field identified.
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| 7. |
- Dalen, Love, et al.
(författare)
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Identifying Bird Remains Using Ancient DNA Barcoding
- 2017
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Ingår i: Genes. - : MDPI AG. - 2073-4425 .- 2073-4425. ; 8:6
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Tidskriftsartikel (refereegranskat)abstract
- Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.
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| 8. |
- Dupont, Chris L., et al.
(författare)
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Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:2, s. e89549-
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.
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| 9. |
- Ericson, Per G P, 1956-, et al.
(författare)
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Dating the diversification of the major lineages of Passeriformes (Aves)
- 2014
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 14:8, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Background: The avian Order Passeriformes is an enormously species-rich group, which comprises almost 60% ofall living bird species. This diverse order is believed to have originated before the break-up of Gondwana in the lateCretaceous. However, previous molecular dating studies have relied heavily on the geological split between NewZealand and Antarctica, assumed to have occurred 85–82 Mya, for calibrating the molecular clock and might thusbe circular in their argument.Results: This study provides a time-scale for the evolution of the major clades of passerines using seven nuclearmarkers, five taxonomically well-determined passerine fossils, and an updated interpretation of the New Zealandsplit from Antarctica 85–52 Mya in a Bayesian relaxed-clock approach. We also assess how different interpretationsof the New Zealand–Antarctica vicariance event influence our age estimates. Our results suggest that thediversification of Passeriformes began in the late Cretaceous or early Cenozoic. Removing the root calibration forthe New Zealand–Antarctica vicariance event (85–52 Mya) dramatically increases the 95% credibility intervals andleads to unrealistically old age estimates. We assess the individual characteristics of the seven nuclear genesanalyzed in our study. Our analyses provide estimates of divergence times for the major groups of passerines,which can be used as secondary calibration points in future molecular studies.Conclusions: Our analysis takes recent paleontological and geological findings into account and provides the bestestimate of the passerine evolutionary time-scale currently available. This time-scale provides a temporalframework for further biogeographical, ecological, and co-evolutionary studies of the largest bird radiation, andadds to the growing support for a Cretaceous origin of Passeriformes.
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| 10. |
- Ericson, Per G P, et al.
(författare)
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Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics
- 2020
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Ingår i: Systematic Biology. - 1063-5157 .- 1076-836X. ; 69:5, s. 820-829
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Tidskriftsartikel (refereegranskat)abstract
- The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits.
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