| 1. |
- Brodin, Johanna, et al.
(author)
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PCR-Induced Transitions Are the Major Source of Error in Cleaned Ultra-Deep Pyrosequencing Data
- 2013
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:7
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Journal article (peer-reviewed)abstract
- Background: Ultra-deep pyrosequencing (UDPS) is used to identify rare sequence variants. The sequence depth is influenced by several factors including the error frequency of PCR and UDPS. This study investigated the characteristics and source of errors in raw and cleaned UDPS data. Results: UDPS of a 167-nucleotide fragment of the HIV-1 SG3Denv plasmid was performed on the Roche/454 platform. The plasmid was diluted to one copy, PCR amplified and subjected to bidirectional UDPS on three occasions. The dataset consisted of 47,693 UDPS reads. Raw UDPS data had an average error frequency of 0.30% per nucleotide site. Most errors were insertions and deletions in homopolymeric regions. We used a cleaning strategy that removed almost all indel errors, but had little effect on substitution errors, which reduced the error frequency to 0.056% per nucleotide. In cleaned data the error frequency was similar in homopolymeric and non-homopolymeric regions, but varied considerably across sites. These site-specific error frequencies were moderately, but still significantly, correlated between runs (r = 0.15-0.65) and between forward and reverse sequencing directions within runs (r = 0.33-0.65). Furthermore, transition errors were 48-times more common than transversion errors (0.052% vs. 0.001%; p<0.0001). Collectively the results indicate that a considerable proportion of the sequencing errors that remained after data cleaning were generated during the PCR that preceded UDPS. Conclusions: A majority of the sequencing errors that remained after data cleaning were introduced by PCR prior to sequencing, which means that they will be independent of platform used for next-generation sequencing. The transition vs. transversion error bias in cleaned UDPS data will influence the detection limits of rare mutations and sequence variants.
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| 2. |
- Engert, Andreas, et al.
(author)
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The European Hematology Association Roadmap for European Hematology Research : a consensus document
- 2016
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In: Haematologica. - Pavia, Italy : Ferrata Storti Foundation (Haematologica). - 0390-6078 .- 1592-8721. ; 101:2, s. 115-208
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Journal article (peer-reviewed)abstract
- The European Hematology Association (EHA) Roadmap for European Hematology Research highlights major achievements in diagnosis and treatment of blood disorders and identifies the greatest unmet clinical and scientific needs in those areas to enable better funded, more focused European hematology research. Initiated by the EHA, around 300 experts contributed to the consensus document, which will help European policy makers, research funders, research organizations, researchers, and patient groups make better informed decisions on hematology research. It also aims to raise public awareness of the burden of blood disorders on European society, which purely in economic terms is estimated at (sic)23 billion per year, a level of cost that is not matched in current European hematology research funding. In recent decades, hematology research has improved our fundamental understanding of the biology of blood disorders, and has improved diagnostics and treatments, sometimes in revolutionary ways. This progress highlights the potential of focused basic research programs such as this EHA Roadmap. The EHA Roadmap identifies nine 'sections' in hematology: normal hematopoiesis, malignant lymphoid and myeloid diseases, anemias and related diseases, platelet disorders, blood coagulation and hemostatic disorders, transfusion medicine, infections in hematology, and hematopoietic stem cell transplantation. These sections span 60 smaller groups of diseases or disorders. The EHA Roadmap identifies priorities and needs across the field of hematology, including those to develop targeted therapies based on genomic profiling and chemical biology, to eradicate minimal residual malignant disease, and to develop cellular immunotherapies, combination treatments, gene therapies, hematopoietic stem cell treatments, and treatments that are better tolerated by elderly patients.
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| 3. |
- Jonsson, Micael, 1972-, et al.
(author)
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Effects of an antihistamine on carbon and nutrient recycling in streams
- 2015
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In: Science of the Total Environment. - : Elsevier. - 0048-9697 .- 1879-1026. ; 538, s. 240-245
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Journal article (peer-reviewed)abstract
- In stream ecosystems, microbes and macroinvertebrates consume leaf litter deposited from the riparian vegetation, and thereby recycle resources tied up in the litter. Several environmental variables influence rates of this recycling, but it is not well known if common pharmaceuticals, such as antihistamines, originating from waste-water effluent, have additional impacts. Exposure to dilute concentrations of antihistamines may adversely influence aquatic detritivorous invertebrates, because invertebrates use histamines for neurotransmission, resulting in hampered recycling of resource tied up in leaf detritus. In this study, we therefore investigated if the antihistamine fexofenadine, at a concentration of 2000 ng l(-1), alters rates of leaf litter decomposition in stream microcosms. Stonefly larvae (n = 10, per microcosm), together with natural microbial communities, served as main decomposer organisms on alder leaf litter. First, we used 30 microcosms containing fexofenadine, while the other 30 served as non-contaminated controls, and of each 30 microcosms, 14 contained stonefly larvae and microbes, while the remaining 16 contained only microbes. We found, in contrast to our hypothesis, that fexofenadine had no effect on leaf litter decomposition via impacts on the stonefly larvae. However, independent on if stoneflies were present or not, concentrations of organic carbon (TOC) and nitrogen (N) were strongly affected, with 20-26 and 24-31% lower concentrations of TOC and N, respectively, in the presence of fexofenadine. Second, in a scaled down follow-up experiment we found that microbial activity increased by 85%, resulting in a 10% decrease in pH, in the presence of fexofenadine. While the antihistamine concentration we used is higher than those thus far found in the field (1-10 ng l(-1)), it is still 100 times lower than the predicted no-effect concentration for fexofenadine. As such, our results indicate that low mu g l(-1) levels of antihistamines can have an effect on carbon and nutrient recycling in aquatic system. (C) 2015 Elsevier B.V. All rights reserved.
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| 4. |
- Merid, Simon Kebede, et al.
(author)
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Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
- 2020
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In: Genome Medicine. - Stockholm : Karolinska Institutet, Dept of Clinical Science and Education, Södersjukhuset. - 1756-994X.
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Journal article (peer-reviewed)abstract
- Background: Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods: We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung. Results: We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10- 7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. Conclusions: We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.
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| 5. |
- Ran, Caroline, et al.
(author)
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Glucocerebrosidase variant T369M is not a risk factor for Parkinson's disease in Sweden.
- 2022
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In: Neuroscience Letters. - : Elsevier. - 0304-3940 .- 1872-7972. ; 784
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Journal article (peer-reviewed)abstract
- INTRODUCTION: Genetic variants in the Beta-glucocerebrosidase gene (GBA1) is a known risk factor for Parkinson's disease. The GBA1 mutations L444P, N370S and many other have been shown to associate with the disease in populations with diverse background. Some GBA1 polymorphisms have a less pronounced effect, and their pathogenicity has been debated. We have previously found associations with L444P, N370S and E326K and Parkinson's disease in Sweden.METHOD: In this study we used pyrosequencing to genotype the T369M variant in a large Swedish cohort consisting of 1,131 patients with idiopathic Parkinson's disease, and 1,594 control subjects to evaluate the possibility of this variant conferring an increased risk for Parkinson's disease.RESULTS: The minor allele frequency was 2.15% in patients and 1.76% in controls. Statistical analysis showed that there was no significant difference in allele frequency between patients and control subjects, p-value 0.37, Odds Ratio 1.23 with a 95% confidence interval of 0.82-1.83.CONCLUSION: Our results suggest that T369M is not a risk factor for Parkinson's disease in the Swedish population.
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| 6. |
- Urhan, Utku, et al.
(author)
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Evidence against observational spatial memory for cache locations of conspecifics in marsh tits Poecile palustris
- 2017
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In: Behavioral Ecology and Sociobiology. - : Springer Science and Business Media LLC. - 0340-5443 .- 1432-0762. ; 71:2
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Journal article (peer-reviewed)abstract
- Abstract: Many species in the family Paridae, such as marsh tits Poecile palustris, are large-scale scatter hoarders of food that make cryptic caches and disperse these in large year-round territories. The perhaps most well-known species in the family, the great tit Parus major, does not store food itself but is skilled in stealing caches from the other species. We have previously demonstrated that great tits are able to memorise positions of caches they have observed marsh tits make and later return and steal the food. As great tits are explorative in nature and unusually good learners, it is possible that such “memorisation of caches from a distance” is a unique ability of theirs. The other possibility is that this ability is general in the parid family. Here, we tested marsh tits in the same experimental set-up as where we previously have tested great tits. We allowed caged marsh tits to observe a caching conspecific in a specially designed indoor arena. After a retention interval of 1 or 24 h, we allowed the observer to enter the arena and search for the caches. The marsh tits showed no evidence of such observational memorization ability, and we believe that such ability is more useful for a non-hoarding species. Why should a marsh tit that memorises hundreds of their own caches in the field bother with the difficult task of memorising other individuals’ caches? We argue that the close-up memorisation procedure that marsh tits use at their own caches may be a different type of observational learning than memorisation of caches made by others. For example, the latter must be done from a distance and hence may require the ability to adopt an allocentric perspective, i.e. the ability to visualise the cache from the hoarder’s perspective. Significance statement: Members of the Paridae family are known to possess foraging techniques that are cognitively advanced. Previously, we have demonstrated that a non-hoarding parid species, the great tit P. major, is able to memorise positions of caches that they have observed marsh tits P. palustris make. However, it is unknown whether this cognitively advanced foraging strategy is unique to great tits or if it occurs also in other parids. Here, we demonstrated that “pilfering by observational memorization strategy” is not a general strategy in parids. We believe that such ability is important for a non-hoarding species such as the great tit and, most likely, birds owning many caches do not need this foraging strategy.
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