| 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. |
- 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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| 3. |
- 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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| 4. |
- Nylander, Anja, et al.
(författare)
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An investigation of the interaction between red blood cells and Streptococcus pyogenes
- 2010
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Konferensbidrag (refereegranskat)abstract
- Blood group antigens may be used as receptors by pathogens when infecting their hosts. Different blood groups therefore can be disease susceptibility factors. Thus, pathogens may have exerted a selection pressure on the evolution of blood group diversity. One aim of our study was to identify red blood cell (RBC) membrane structures that are bound by the common human pathogen. Streptococcus pyogenes, responsible for conditions like pharyngitis, Scarlet fever, necrotizing fasciitis and rheumatic heart disease. We also wanted to explore any differences in the ability of S. pyogenes to agglutinate RBC of different ABO groups and of selected null blood group phenotypes.Solubilized RBC membranes were incubated with different strains of S. pyogenes. RBC proteins that bound to bacteria were eluted and separated by SDS-PAGE. In our initial studies, a strong band at ~58 kDa and a weaker band at ~28 kDa were visualized by Coomassie staining. Subsequent analysis by mass spectrometry and Western blotting revealed the bands to correspond to IgG heavy and light chains. The IgG-related bands were strongest for bacterial strains expressing both protein H and M protein, surface structures known to bind IgG, while weaker or no bands were detected in those strains lacking one or both proteins. Results from subsequent experiments indicated that the interaction between S. pyogenes and RBCs was not limited to IgG, but that a number of other RBC membrane structures appear to bind specifically to S. pyogenes. Those proteins are currently being analysed by mass spectrometry.In agglutination studies of S. pyogenes and RBCs, either sensitised with IgG or stripped of IgG we confirmed that IgG has a role in the binding of RBCs by S. pyogenes. We observed no difference in the ability of S. pyogenes to agglutinate RBCs of different ABO groups, indicating that the ABO-specific differences in RBC surface oligosaccharides are not recognized. When we tested a panel of RBCs with rare null phenotypes we found that cells of the Helgeson phenotype, expressing very low levels of the Knops antigens on complement receptor 1 (CR1), agglutinated more weakly than other common and rare RBCs tested.We are still puzzled by the fact that the hemagglutination is stronger for S. pyogenes strains lacking the M-protein, known to bind both complement and IgG on the surface of the bacteria. Our hypothesis is that there might be some repulsive force acting between the M-protein and surface of RBC, making the interaction stronger when the M-protein is missing. This is supported by agglutination studies with papain-treated RBCs, where the negative charge is reduced.IgG is known to bind senescent cell antigens on erythroid band 3 and thus the amount of IgG increases on the RBC surface as it ages. We speculated that binding to IgG on the RBC surface by S. pyogenes could be a way to selectively target aged RBCs, possibly to acquire heme as a source of iron. Attempts to separate RBCs according to age were made on density gradients, followed by agglutination studies of the different fractions. Our initial results did not demonstrate any conclusive differences. Our data indicate that interactions between S. pyogenes and RBC are mediated at least through IgG and CR1 on the RBC surface. The clinical importance awaits exploration but may be relevant in the identification of resistance factors to infections among humans, and could thus lead to the development of alternative ways to treat infections caused by S. pyogenes.
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| 5. |
- Palm, Sara, 1984-
(författare)
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Early Environment, Adolescent Alcohol Drinking and Neurobiological Responses to Drugs
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Genes and environment interact to determine an individual’s vulnerability or resilience to several psychiatric disorders, including alcohol use disorder (AUD). Alcohol use is often initiated during adolescence and early onset drinking is associated with increased risk for later AUD. Childhood and adolescence are periods of extensive brain maturation, which makes young individuals more susceptible to environmental influence. However, little is known about early environmental influence on reward pathways and behaviors involved in the development of AUD. Changes in the endogenous opioid and dopamine systems, as well as individual differences in risk behaviors are all believed to play important roles in the increased vulnerability seen after adverse early life events and early onset drinking. The overall aim of the thesis was therefore to investigate the influence of early environmental factors on adolescent alcohol intake, endogenous opioids, dopamine dynamics and alcohol-induced effects in rats to increase our knowledge of neurobiological factors underlying vulnerability to AUD. Furthermore, individual behavioral differences and their correlation to basal and drug-induced neurobiological responses in rats were also investigated. Animal models of different early environments, e.g. maternal separation and social vs. single housing, and adolescent alcohol consumption have been used to study effects on behavior, endogenous opioid peptides and dopamine dynamics. The results identified the amygdala and dorsal striatum as interesting brain regions in which endogenous opioids and dopamine, respectively, are impacted by early environmental factors. The amygdala and the dorsal striatum are both hypothesized to be involved in the shift from initial drug use to compulsive use and changes in these areas may be underlying environmentally increased vulnerability to AUD. Furthermore, behavioral phenotypes in relation to individual neurobiological responses were identified. High risk-taking behavior was associated with a more pronounced response to amphetamine, but the inherent dopamine response was instead associated with risk-assessment behavior. In conclusion, several brain regions of interest for future research were identified. Furthermore, the results contribute to increased understanding of factors involved in the development of vulnerability for AUD in adolescents and young adults.
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