| 1. |
- Alm Rosenblad, Magnus, 1957, et al.
(författare)
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Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 13, s. 21-33
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Tidskriftsartikel (refereegranskat)abstract
- During a routine scan for Signal Recognition Particle (SRP) RNAs in eukaryotic sequences, we surprisingly found in silico evidence in GenBank for a 265-base long SRP RNA sequence in the ITS1 region of a total of 11 fully identified species in three ectomycorrhizal genera of the Basidiomycota (Fungi): Astraeus, Russula, and Lactarius. To rule out sequence artifacts, one specimen from a species indicated to have the SRP RNA-containing ITS region in each of these genera was ordered and re-sequenced. Sequences identical to the corresponding GenBank entries were recovered, or in the case of a non-original but conspecific specimen differed by three bases, showing that these species indeed have an SRP RNA sequence incorporated into their ITS1 region. Other than the ribosomal genes, this is the first known case of non-coding RNAs in the eukaryotic ITS region, and it may assist in the examination of other types of insertions in fungal genomes.
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| 2. |
- Bengtsson, Johan, 1985, et al.
(författare)
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Metaxa: Automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts
- 2011
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Ingår i: SocBiN Bioinformatics Conference, Helsinki, Finland, 2011.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. However, the gene is not only present in the nuclear genome of eukaryotes and the core genome of prokaryotes, but also in the mitochondria and chloroplasts of eukaryotes. The SSU genes in the core genome, mitochondria and chloroplast are conceptually paralogous and should in most situations not be aligned and analyzed jointly, e.g. when estimating species diversity. Identifying the origin of SSU sequences in complex sequence datasets is a time-consuming and largely manual undertaking. To ease this situation, we have created Metaxa, an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacte- rial, nuclear eukaryote, mitochondrial, or chloroplast origin. Metaxa very efficiently detects SSU sequences from fragments as short as 200 base pairs, and correctly classifies 97% of the identified genes at read lengths typically obtained from pyrosequencing. In addition, Metaxa shows a false positive rate of 0.00012% when run on random DNA fragments, showing the robustness of the method. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.
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| 3. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets
- 2011
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Ingår i: Antonie van Leeuwenhoek: international journal of general and molecular microbiology. - : Springer Science and Business Media LLC. - 0003-6072 .- 1572-9699. ; 100:3, s. 471-475
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Tidskriftsartikel (refereegranskat)abstract
- The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.
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| 4. |
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| 5. |
- Thorén, Anna, et al.
(författare)
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Rapid response team activation prior to in-hospital cardiac arrest: Areas for improvements based on a national cohort study
- 2023
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Ingår i: Resuscitation. - 0300-9572 .- 1873-1570. ; 193
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Rapid response teams (RRTs) are designed to improve the "chain of prevention" of in-hospital cardiac arrest (IHCA). We studied the 30-day survival of patients reviewed by RRTs within 24 hours prior to IHCA, as compared to patients not reviewed by RRTs.Methods: A nationwide cohort study based on the Swedish Registry of Cardiopulmonary Resuscitation, between January 1st, 2014, and December 31st, 2021. An explorative, hypothesis-generating additional in-depth data collection from medical records was performed in a small subgroup of general ward patients reviewed by RRTs.Results: In all, 12,915 IHCA patients were included. RRT-reviewed patients (n = 2,058) had a lower unadjusted 30-day survival (25% vs 33%, p < 0.001), a propensity score based Odds ratio for 30-day survival of 0.92 (95% Confidence interval 0.90-0.94, p < 0.001) and were more likely to have a respiratory cause of IHCA (22% vs 15%, p < 0.001). In the subgroup (n = 82), respiratory distress was the most common RRT trigger, and 24% of the RRT reviews were delayed. Patient transfer to a higher level of care was associated with a higher 30-day survival rate (20% vs 2%, p < 0.001).Conclusion: IHCA preceded by RRT review is associated with a lower 30-day survival rate and a greater likelihood of a respiratory cause of cardiac arrest. In the small explorative subgroup, respiratory distress was the most common RRT trigger and delayed RRT activation was frequent. Early detection of respiratory abnormalities and timely interventions may have a potential to improve outcomes in RRT-reviewed patients and prevent further progress into IHCA.
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| 6. |
- Thul, Peter J., et al.
(författare)
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A subcellular map of the human proteome
- 2017
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Ingår i: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 356:6340
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Tidskriftsartikel (refereegranskat)abstract
- Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.
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| 7. |
- Aczel, Balazs, et al.
(författare)
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Consensus-based guidance for conducting and reporting multi-analyst studies
- 2021
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Ingår i: eLIFE. - : eLife Sciences Publications. - 2050-084X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Any large dataset can be analyzed in a number of ways, and it is possible that the use of different analysis strategies will lead to different results and conclusions. One way to assess whether the results obtained depend on the analysis strategy chosen is to employ multiple analysts and leave each of them free to follow their own approach. Here, we present consensus-based guidance for conducting and reporting such multi-analyst studies, and we discuss how broader adoption of the multi-analyst approach has the potential to strengthen the robustness of results and conclusions obtained from analyses of datasets in basic and applied research.
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| 8. |
- Adrian-Kalchhauser, Irene, et al.
(författare)
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The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish
- 2017
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb). Results During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4 kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19 kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies. Conclusions Our results indicate that the round goby mitochondrial genome may contain novel features. Since mitochondrial genome organisation is tightly linked to energy metabolism, these features may be linked to its invasion success. Also, the unique tRNA arrangement among Ponto-Caspian gobies may be helpful in studying the evolution of this highly adaptive and invasive species group. Finally, we find that the phylogeny of gobiids can be further refined by the use of longer stretches of linked DNA sequence.
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| 9. |
- Alm, Carin, et al.
(författare)
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Better knowledger improves adherence to lifestyle changes and medication in patients with coronary heart disease.
- 2004
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Ingår i: European Journal of Cardiovascular Nursing. - : Oxford University Press (OUP). - 1474-5151 .- 1873-1953. ; 3:4, s. 321-330
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Tidskriftsartikel (refereegranskat)abstract
- Background: Many patients with coronary heart disease (CHD) are not managed adequately, and we often fail to reach treatment targets. Aim: To investigate if knowledge of risk factors for CHD, measured by a questionnaire, would show any relation to advice to compliance to lifestyle changes to attain treatment goals and adherence to drug therapy. Method: Men and women <71 years who had had a cardiac event were screened consecutively (509) from the medical records. Responders (392) were interviewed, examined and received a questionnaire. Three hundred and forty-seven patients answered the questionnaire regarding their general knowledge of risk factors for CHD, compliance to lifestyle changes to attain treatment goals and adherence to drug therapy. Results: There were statistically significant correlations between general knowledge about risk factors for CHD and compliance to certain lifestyle changes: weight, physical activity, stress management, diet, attainment of lipid level goals and the likelihood of taking prescribed blood pressure-lowering drugs. General knowledge of risk factors had no correlation to blood glucose or blood pressure levels nor on smoking habits or treatment patterns for prescribed lipid- and blood glucose-lowering drugs. Conclusion: Knowledge correlates to patient behaviour with respect to some risk factors, which should be recognised in preventive programs.
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| 10. |
- Alm, Carin, et al.
(författare)
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Knowing your risk factors for coronary heart disease improves adherence to advice on lifestyle changes and medication
- 2006
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Ingår i: The Journal of Cardiovascular Nursing. - 1550-5049. ; 21:5, s. 24-31
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Tidskriftsartikel (refereegranskat)abstract
- Implementation of guidelines for coronary heart disease prevention is less optimal in clinical practice. The aim of this study was to investigate if specific knowledge (patients' knowledge about their own coronary heart disease risk factors) would correlate to their adherence as measured by self-reported lifestyle changes, reaching defined treatment goals and adhering to treatment with prescribed drugs. The consecutive medical records of 509 men and women younger than 71 years, hospitalized for a cardiac event, were screened. Of these, 392 patients came for an interview and were subjected to a clinical examination. All patients received a questionnaire regarding their specific knowledge of risk factors and their adherence to lifestyle changes, which was completed by 347 patients. In addition, data were collected and analyzed on how their treatment goals were attained in 8 domains and their adherence to drug treatment. There were significant correlations between specific knowledge and self-reported lifestyle changes, the ability to reach treatment goals in all 8 domains, and adherence to prescribed drugs. Patients with coronary heart disease will benefit from increased specific knowledge of risk factors to adhere with lifestyle changes and prescribed medication after a cardiac event.
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