| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
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| 3. |
- Franzén, Erika, et al.
(författare)
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The EXPANd trial : effects of exercise and exploring neuroplastic changes in people with Parkinson's disease
- 2019
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Ingår i: BMC Neurology. - : Springer Science and Business Media LLC. - 1471-2377. ; 19:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Parkinson's disease (PD) affects many physiological systems essential for balance control. Recent studies suggest that intensive and cognitively demanding physical exercise programs are capable of inducing plastic brain changes in PD. We have developed a highly challenging balance training (the HiBalance) program that emphasizes critical aspects of balance control through progressively introducing more challenging exercises which incorporates dual-tasking. Earlier studies have shown it to be effective in improving balance, gait and dual-tasking. The study design has thereafter been adjusted to link intervention-induced behavioral changes to brain morphology and function. Specifically, in this randomized controlled trial, we will determine the effects of the HiBalance program on balance, gait and cognition and relate this to task-evoked functional MRI (fMRI), as well as brain-derived neurotrophic factor (BDNF) in participants with mild-moderate PD.Methods: One hundred participants with idiopathic PD, Hoehn & Yahr stage 2 or 3, >= 60 years of age, >= 21 on Montreal Cognitive Assessment will be recruited in successive waves and randomized into either the HiBalance program or to an active control group (the HiCommunication program, targeting speech and communication). Both interventions will be performed in small groups, twice a week with 1 h sessions for 10 weeks. In addition, a 1 h, once a week, home exercise program will also be performed. A double-blinded design will be used. At the pre- and post-assessments, participants will be assessed on balance (main outcome), gait, cognitive functions, physical activity, voice/speech function, BDNF in serum and fMRI (3 T Philips) during performance of motor-cognitive tasks.Discussion: Since there is currently no cure for PD, findings of neuroplastic brain changes in response to exercise would revolutionize the way we treat PD, and, in turn, provide new hope to patients for a life with better health, greater independence and improved quality of life.
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| 4. |
- Gustavsson, Anders, et al.
(författare)
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Corrigendum to “Cost of disorders of the brain in Europe 2010” [Eur. Neuropsychopharmacol. 21 (2011) 718–779]
- 2012
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Ingår i: European Neuropsychopharmacology. - : Elsevier BV. - 0924-977X .- 1873-7862. ; 22:3, s. 237-238
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Tidskriftsartikel (refereegranskat)abstract
- The spectrum of disorders of the brain is large, covering hundreds of disorders that are listed in either the mental or neurological disorder chapters of the established international diagnostic classification systems. These disorders have a high prevalence as well as short- and long-term impairments and disabilities. Therefore they are an emotional, financial and social burden to the patients, their families and their social network. In a 2005 landmark study, we estimated for the first time the annual cost of 12 major groups of disorders of the brain in Europe and gave a conservative estimate of €386 billion for the year 2004. This estimate was limited in scope and conservative due to the lack of sufficiently comprehensive epidemiological and/or economic data on several important diagnostic groups. We are now in a position to substantially improve and revise the 2004 estimates. In the present report we cover 19 major groups of disorders, 7 more than previously, of an increased range of age groups and more cost items. We therefore present much improved cost estimates. Our revised estimates also now include the new EU member states, and hence a population of 514 million people.
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| 5. |
- Gustavsson, Anders, et al.
(författare)
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Cost of disorders of the brain in Europe 2010.
- 2011
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Ingår i: European Neuropsychopharmacology. - Amsterdam : Elsevier BV. - 0924-977X .- 1873-7862. ; 21:10, s. 718-79
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The spectrum of disorders of the brain is large, covering hundreds of disorders that are listed in either the mental or neurological disorder chapters of the established international diagnostic classification systems. These disorders have a high prevalence as well as short- and long-term impairments and disabilities. Therefore they are an emotional, financial and social burden to the patients, their families and their social network. In a 2005 landmark study, we estimated for the first time the annual cost of 12 major groups of disorders of the brain in Europe and gave a conservative estimate of €386 billion for the year 2004. This estimate was limited in scope and conservative due to the lack of sufficiently comprehensive epidemiological and/or economic data on several important diagnostic groups. We are now in a position to substantially improve and revise the 2004 estimates. In the present report we cover 19 major groups of disorders, 7 more than previously, of an increased range of age groups and more cost items. We therefore present much improved cost estimates. Our revised estimates also now include the new EU member states, and hence a population of 514 million people.AIMS: To estimate the number of persons with defined disorders of the brain in Europe in 2010, the total cost per person related to each disease in terms of direct and indirect costs, and an estimate of the total cost per disorder and country.METHODS: The best available estimates of the prevalence and cost per person for 19 groups of disorders of the brain (covering well over 100 specific disorders) were identified via a systematic review of the published literature. Together with the twelve disorders included in 2004, the following range of mental and neurologic groups of disorders is covered: addictive disorders, affective disorders, anxiety disorders, brain tumor, childhood and adolescent disorders (developmental disorders), dementia, eating disorders, epilepsy, mental retardation, migraine, multiple sclerosis, neuromuscular disorders, Parkinson's disease, personality disorders, psychotic disorders, sleep disorders, somatoform disorders, stroke, and traumatic brain injury. Epidemiologic panels were charged to complete the literature review for each disorder in order to estimate the 12-month prevalence, and health economic panels were charged to estimate best cost-estimates. A cost model was developed to combine the epidemiologic and economic data and estimate the total cost of each disorder in each of 30 European countries (EU27+Iceland, Norway and Switzerland). The cost model was populated with national statistics from Eurostat to adjust all costs to 2010 values, converting all local currencies to Euro, imputing costs for countries where no data were available, and aggregating country estimates to purchasing power parity adjusted estimates for the total cost of disorders of the brain in Europe 2010.RESULTS: The total cost of disorders of the brain was estimated at €798 billion in 2010. Direct costs constitute the majority of costs (37% direct healthcare costs and 23% direct non-medical costs) whereas the remaining 40% were indirect costs associated with patients' production losses. On average, the estimated cost per person with a disorder of the brain in Europe ranged between €285 for headache and €30,000 for neuromuscular disorders. The European per capita cost of disorders of the brain was €1550 on average but varied by country. The cost (in billion €PPP 2010) of the disorders of the brain included in this study was as follows: addiction: €65.7; anxiety disorders: €74.4; brain tumor: €5.2; child/adolescent disorders: €21.3; dementia: €105.2; eating disorders: €0.8; epilepsy: €13.8; headache: €43.5; mental retardation: €43.3; mood disorders: €113.4; multiple sclerosis: €14.6; neuromuscular disorders: €7.7; Parkinson's disease: €13.9; personality disorders: €27.3; psychotic disorders: €93.9; sleep disorders: €35.4; somatoform disorder: €21.2; stroke: €64.1; traumatic brain injury: €33.0. It should be noted that the revised estimate of those disorders included in the previous 2004 report constituted €477 billion, by and large confirming our previous study results after considering the inflation and population increase since 2004. Further, our results were consistent with administrative data on the health care expenditure in Europe, and comparable to previous studies on the cost of specific disorders in Europe. Our estimates were lower than comparable estimates from the US.DISCUSSION: This study was based on the best currently available data in Europe and our model enabled extrapolation to countries where no data could be found. Still, the scarcity of data is an important source of uncertainty in our estimates and may imply over- or underestimations in some disorders and countries. Even though this review included many disorders, diagnoses, age groups and cost items that were omitted in 2004, there are still remaining disorders that could not be included due to limitations in the available data. We therefore consider our estimate of the total cost of the disorders of the brain in Europe to be conservative. In terms of the health economic burden outlined in this report, disorders of the brain likely constitute the number one economic challenge for European health care, now and in the future. Data presented in this report should be considered by all stakeholder groups, including policy makers, industry and patient advocacy groups, to reconsider the current science, research and public health agenda and define a coordinated plan of action of various levels to address the associated challenges.RECOMMENDATIONS: Political action is required in light of the present high cost of disorders of the brain. Funding of brain research must be increased; care for patients with brain disorders as well as teaching at medical schools and other health related educations must be quantitatively and qualitatively improved, including psychological treatments. The current move of the pharmaceutical industry away from brain related indications must be halted and reversed. Continued research into the cost of the many disorders not included in the present study is warranted. It is essential that not only the EU but also the national governments forcefully support these initiatives.
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| 6. |
- Holgersson, Georg, et al.
(författare)
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Swedish lung cancer radiation study group: the prognostic value of anaemia, thrombocytosis and leukocytosis at time of diagnosis in patients with non-small cell lung cancer
- 2012
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Ingår i: Medical Oncology. - : Humana Press (Springer Imprint). - 1357-0560 .- 1559-131X. ; 29:5, s. 3176-3182
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Tidskriftsartikel (refereegranskat)abstract
- There is a need to improve the prognostic and predictive indicators in non-small cell lung cancer (NSCLC). At present, the main focus is on genetic predictive markers while the prognostic value of the standard blood variables related to haematopoiesis has been subjected to relatively limited attention. To study the prognostic potential of haemoglobin (Hgb), platelet (Plt) and white blood cell (WBC) levels at time of diagnosis in NSCLC patients, 835 NSCLC patients, stage I-IV, who received radiotherapy with curative intention (andgt; 50 Gy), were included in the study. WBC, Plt, Hgb, gender, age at diagnosis, stage, surgery and first-line chemotherapy were studied in relation to overall survival. For patients with Hgb andlt; 110 g/L and Hgb a parts per thousand yen 110 g/L), the median survival was 11.2 and 14.5 months, respectively (p = 0.0032). For WBC andgt; 9.0 x 10(9)/L and andlt; 9.0 x 10(9)/L, the median survival was 11.6 and 15.4 months, respectively (p andlt; 0.0001). For Plt andgt; 350 x 10(9)/L and andlt; 350 x 10(9)/L, the median survival was 11.2 and 14.9 months, respectively (p andlt; 0.0001). The median survival in patients with pathological results in all three markers was half of that in patients with normal levels of all three markers (8.0 and 16.0 months, respectively (p andlt; 0.0001). The level of the three studied haematological biomarkers corresponds significantly to outcome in NSCLC. These results indicate that standard haematological variables may be used as guidance for the clinician in the decision-making regarding treatment intensity and patient information.
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| 7. |
- Holgersson, Georg, et al.
(författare)
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The value of induction chemotherapy for survival in patients with non-small cell lung cancer treated with radiotherapy.
- 2012
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Ingår i: Anticancer research. - : The International Institute of Anticancer Research. - 1791-7530 .- 0250-7005. ; 32:4, s. 1339-46
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Tidskriftsartikel (refereegranskat)abstract
- AIM: The aim of the present study was to retrospectively investigate the impact of induction chemotherapy on treatment outcome in patients treated with curatively intended radiotherapy for non-small cell lung cancer (NSCLC). PATIENTS AND METHODS: Patients with a diagnosed NSCLC that have been subjected to curatively intended irradiation (≥50 Gy) and treated in an oncology department in Sweden during the years 1990-2000 were included in the study. Operated patients and patients having received concomitant chemotherapy were excluded. The included patients were localised by a manual search of all the oncology departments' medical records and radiation charts. RESULTS: Patients treated with induction chemotherapy (n=79) had a significantly better overall survival compared with patients treated with radiotherapy alone (p=0.0097) in a univariate Cox regression analysis. A platinum/taxane combination produced the greatest survival benefit; hazard ratio=0.49 (95% confidence interval=0.31 to 0.75). CONCLUSION: We found that patients treated with induction chemotherapy in addition to radiotherapy for NSCLC have a better overall survival than patients treated with radiotherapy alone and that the best results are achieved using a platinum/taxane combination.
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| 8. |
- Thompson, Paul M., et al.
(författare)
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The ENIGMA Consortium : large-scale collaborative analyses of neuroimaging and genetic data
- 2014
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Ingår i: BRAIN IMAGING BEHAV. - : Springer Science and Business Media LLC. - 1931-7557 .- 1931-7565. ; 8:2, s. 153-182
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Tidskriftsartikel (refereegranskat)abstract
- The Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in neuroscience, genetics, and medicine, ENIGMA studies have analyzed neuroimaging data from over 12,826 subjects. In addition, data from 12,171 individuals were provided by the CHARGE consortium for replication of findings, in a total of 24,997 subjects. By meta-analyzing results from many sites, ENIGMA has detected factors that affect the brain that no individual site could detect on its own, and that require larger numbers of subjects than any individual neuroimaging study has currently collected. ENIGMA's first project was a genome-wide association study identifying common variants in the genome associated with hippocampal volume or intracranial volume. Continuing work is exploring genetic associations with subcortical volumes (ENIGMA2) and white matter microstructure (ENIGMA-DTI). Working groups also focus on understanding how schizophrenia, bipolar illness, major depression and attention deficit/hyperactivity disorder (ADHD) affect the brain. We review the current progress of the ENIGMA Consortium, along with challenges and unexpected discoveries made on the way.
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| 9. |
- Timpka, Toomas, 1957-, et al.
(författare)
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Community-level football injury epidemiology : traumatic injuries treated at Swedish emergency medical facilities
- 2018
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Ingår i: European Journal of Public Health. - : Oxford University Press. - 1101-1262 .- 1464-360X. ; 28:1, s. 94-99
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Tidskriftsartikel (refereegranskat)abstract
- Background: Despite the popularity of the sport, few studies have investigated community-level football injury patterns. This study examines football injuries treated at emergency medical facilities using data from three Swedish counties.Methods: An open-cohort design was used based on residents aged 0-59 years in three Swedish counties (pop. 645 520). Data were collected from emergency medical facilities in the study counties between 1 January 2007 and 31 December 2010. Injury frequencies and proportions for age groups stratified by sex were calculated with 95% confidence intervals (95% CIs) and displayed per diagnostic group and body location.Results: Each year, more than 1/200 person aged 0-59 years sustained at least one injury during football play that required emergency medical care. The highest injury incidence was observed among adolescent boys [2009 injuries per 100 000 population years (95% CI 1914-2108)] and adolescent girls [1413 injuries per 100 000 population years (95% CI 1333-1498)]. For female adolescents and adults, knee joint/ligament injury was the outstanding injury type (20% in ages 13-17 years and 34% in ages 18-29 years). For children aged 7-12 years, more than half of the treated injuries involved the upper extremity; fractures constituted about one-third of these injuries.Conclusions: One of every 200 residents aged 0-59 years in typical Swedish counties each year sustained a traumatic football injury that required treatment in emergency healthcare. Further research on community-level patterns of overuse syndromes sustained by participation in football play is warranted.
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| 10. |
- Abé, Christoph, et al.
(författare)
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Cortical thickness, volume and surface area in patients with bipolar disorder types I and II.
- 2016
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Ingår i: Journal of psychiatry & neuroscience : JPN. - : CMA Joule Inc.. - 1488-2434 .- 1180-4882. ; 41:4, s. 240-50
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Tidskriftsartikel (refereegranskat)abstract
- Bipolar disorder (BD) is a common chronic psychiatric disorder mainly characterized by episodes of mania, hypomania and depression. The disorder is associated with cognitive impairments and structural brain abnormalities, such as lower cortical volumes in primarily frontal brain regions than healthy controls. Although bipolar disorder types I (BDI) and II (BDII) exhibit different symptoms and severity, previous studies have focused on BDI. Furthermore, the most frequently investigated measure in this population is cortical volume. The aim of our study was to investigate abnormalities in patients with BDI and BDII by simultaneously analyzing cortical volume, thickness and surface area, which yields more information about disease- and symptom-related neurobiology.
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| 11. |
- Abé, Christoph, et al.
(författare)
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Longitudinal Cortical Thickness Changes in Bipolar Disorder and the Relationship to Genetic Risk, Mania, and Lithium Use.
- 2020
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Ingår i: Biological psychiatry. - : Elsevier BV. - 1873-2402 .- 0006-3223. ; 87:3, s. 271-281
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Tidskriftsartikel (refereegranskat)abstract
- Bipolar disorder (BD) is a highly heritable psychiatric disorder characterized by episodes of manic and depressed mood states and associated with cortical brain abnormalities. Although the course of BD is often progressive, longitudinal brain imaging studies are scarce. It remains unknown whether brain abnormalities are static traits of BD or result from pathological changes over time. Moreover, the genetic effect on implicated brain regions remains unknown.Patients with BD and healthy control (HC) subjects underwent structural magnetic resonance imaging at baseline (123 patients, 83 HC subjects) and after 6 years (90 patients, 61 HC subjects). Cortical thickness maps were generated using FreeSurfer. Using linear mixed effects models, we compared longitudinal changes in cortical thickness between patients with BD and HC subjects across the whole brain. We related our findings to genetic risk for BD and tested for effects of demographic and clinical variables.Patients showed abnormal cortical thinning of temporal cortices and thickness increases in visual/somatosensory brain areas. Thickness increases were related to genetic risk and lithium use. Patients who experienced hypomanic or manic episodes between time points showed abnormal thinning in inferior frontal cortices. Cortical changes did not differ between diagnostic BD subtypes I and II.In the largest longitudinal BD study to date, we detected abnormal cortical changes with high anatomical resolution. We delineated regional effects of clinical symptoms, genetic factors, and medication that may explain progressive brain changes in BD. Our study yields important insights into disease mechanisms and suggests that neuroprogression plays a role in BD.
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| 12. |
- Abé, Christoph, et al.
(författare)
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Manic episodes are related to changes in frontal cortex: a longitudinal neuroimaging study of bipolar disorder 1.
- 2015
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Ingår i: Brain : a journal of neurology. - : Oxford University Press (OUP). - 1460-2156. ; 138:Pt 11, s. 3440-8
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Tidskriftsartikel (refereegranskat)abstract
- Higher numbers of manic episodes in bipolar patients has, in cross-sectional studies, been associated with less grey matter volume in prefrontal brain areas. Longitudinal studies are needed to determine if manic episodes set off progressive cortical changes, or if the association is better explained by premorbid brain conditions that increase risk for mania. We followed patients with bipolar disorder type 1 for 6 years. Structural brain magnetic resonance imaging scans were performed at baseline and follow-up. We compared patients who had at least one manic episode between baseline and follow-up (Mania group, n = 13) with those who had no manic episodes (No-Mania group, n = 18). We used measures of cortical volume, thickness, and area to assess grey matter changes between baseline and follow-up. We found significantly decreased frontal cortical volume (dorsolateral prefrontal and inferior frontal cortex) in the Mania group, but no volume changes in the No-Mania group. Our results indicate that volume decrease in frontal brain regions can be attributed to the incidence of manic episodes.
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| 13. |
- Allen, Lisa Zeigler, et al.
(författare)
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The Baltic Sea Virome : Diversity and Transcriptional Activity of DNA and RNA Viruses
- 2017
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Ingår i: mSystems. - 2379-5077. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Tornetrask in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Tornetrask. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage.
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| 14. |
- Alneberg, Johannes, et al.
(författare)
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Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes
- 2020
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Ingår i: Communications Biology. - : Nature Publishing Group. - 2399-3642. ; 3:1, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes. The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.
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| 15. |
- Alneberg, Johannes, et al.
(författare)
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Recovering 2,032 Baltic Sea microbial genomes by optimized metagenomic binning
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Aquatic microorganism are key drivers of global biogeochemical cycles and form the basis of aquatic food webs. However, there is still much left to be learned about these organisms and their interaction within specific environments, such as the Baltic Sea. Crucial information for such an understanding can be found within the genome sequences of organisms within the microbial community.In this study, the previous set of Baltic Sea clusters, constructed by Hugert et al., is greatly expanded using a large set of metagenomic samples, spanning the environmental gradients of the Baltic Sea. In total, 124 samples were individually assembled and binned to obtain 2,032 Metagenome Assembled Genomes (MAGs), clustered into 353 prokaryotic and 14 eukaryotic species- level clusters. The prokaryotic genomes were widely distributed over the prokaryotic tree of life, representing 20 different phyla, while the eukaryotic genomes were mostly limited to the division of Chlorophyta. The large number of reconstructed genomes allowed us to identify key factors determining the quality of the genome reconstructions.The Baltic Sea is heavily influenced of human activities of which we might not see the full implications. The genomes reported within this study will greatly aid further studies in our strive for an understanding of the Baltic Sea microbial ecosystem.
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| 16. |
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| 17. |
- Amini, Rose-Marie, et al.
(författare)
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Treatment outcome in patients younger than 60 years with advanced stages (IIB-IV) of Hodgkin's disease: the Swedish National Health Care Programme experience
- 2000
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Ingår i: European Journal of Haematology. - : Wiley. - 0902-4441 .- 1600-0609. ; 65:6, s. 379-389
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Despite improved treatment results achieved in Hodgkin's disease (HD), only about 70% of patients with advanced stages are cured. The primary aim of this study was to evaluate the outcome of advanced stages (IIB-IVB) of HD in younger patients in an unselected population-based group of patients. The patients were recommended individualized treatment with respect to number of chemotherapy (CT) courses and post-CT radiotherapy (RT) based on pretreatment characteristics and tumour response. Secondly, we investigated if variables of prognostic importance could be detected.PATIENTS AND METHODS: Between 1985-92, 307 patients between 17-59 yr of age (median 36) were diagnosed with HD in stages IIB-IVB in 5/6 health care regions in Sweden. Median follow-up time was 7.8 yr (1.3-13). Retrospectively, laboratory parameters were collected.RESULTS: In total, 267 (87%) patients had a complete response (CR). The overall and disease-free 10-yr survivals in the whole cohort were 76% and 67%, respectively. There was no difference in survival between the groups of patients who received 6 or 8 cycles of CT. Survival was not higher for patients in CR after CT when RT was added. For those in PR after CT, additional RT raised the frequencies of CR. A selected group of pathologically staged patients was successfully treated with a short course (2 cycles) of CT + RT. In univariate analyses survival was affected by age, stage IVB, bone-marrow involvement, B-symptoms, S-LDH, S-Alb and reaching CR or not after 2, 4 and 6 cycles of CT. In a multivariate analysis, age and reaching CR after 6 cycles of CT remained statistically significant.CONCLUSIONS: The lack of difference in survival between the groups of patients who received 6 versus 8 cycles of CT indicates a successful selection of patients for the shorter treatment. Reaching a rapid CR significantly affected outcome. Whether some patients need less CT than the generally recommended 8 courses can properly only be evaluated in a randomised study. Additional RT may play a role in successful outcome, particularly if residual tumours are present, but its precise role can also only be defined in prospectively randomised studies. Reaching CR after CT was the most important variable affecting survival besides age.
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| 18. |
- Angelis, Stavros, et al.
(författare)
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User Requirements Analysis and Case Studies Report. Content Strategy Report. : Europeana Cloud Deliverable 1.3 and 1.6: User Requirements Analysis and Case Studies Report (1.3) and Content Strategy Report (1.6)
- 2015
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The present Deliverable (1.3) comprises of two joint reports: former Deliverable 1.3 (User Requirements and Case Studies report) and Deliverable 1.6 (Content Strategy Report). As a product of a multi-scale, interdisciplinary effort, Deliverable 1.3 (User Requirements and Case Studies report / Content Strategy Report) employs a multi-faceted approach to make sense of the information needs and behaviour of Humanities and Social Sciences researchers both within and outside the Europeana ecosystem, while achieving profound understanding of the ways these communities interact with existing Europeana content and metadata. Through extensive and widely-levelled empirical research (Case Studies, Web Survey, Interviews, Focus Groups) complimented by thorough desk research (Literature review, study of particular thematic areas), and building on work previously conducted in the context of other Digital Humanities Research Infrastructures (DARIAH, EHRI, ARIADNE, NeDiMAH) Work Package 1 managed to reach a long list of non-prioritized User Requirements as well as a set of flexible Content Recommendations for the upcoming development of Europeana Research.
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| 19. |
- Aronsson, Martin, et al.
(författare)
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Coordination of planning processes for traffic operators on rail networks; Annual Report 1, Swedish national railway administration (Banverket) R&D-project - SPOK
- 2003. - 1
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This project is concerned with how to improve the capacity allocation process. In particular the project aims at proposing an enhanced format for train path applications, study the technical limitations for timetabling support tools and in the longer term to implement support systems for the train path allocation process. This report describes the various factors that affect the application process, and report the opinions from several actors in the field. Since the deregulation of the Swedish railway, and with new EU directives, the foundations for the capacity allocation process is changing rapidly. There is a strong need for clear and predictable principles that are fair and operator neutral and implements the prioritisation given to different types of traffic and for improved methodologies and decision support tools in the capacity allocation process. This is crucial to support both the possibility for the traffic operators to state demands and the timetable designers in judging conflicting train paths. A conclusion is that almost all the requirements on the timetable presented in this report can in fact be stated as properties and relations of events in the timetable.
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| 20. |
- Aronsson, Martin, et al.
(författare)
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TUFF-PO, Kravsättning av tidplaner utifrån personalplaneringsbehov
- 2002. - 1
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- TUFF-PO rör personalplaneringsarbetet, specifikt planering för bemanning av tåg med lokförare, i tidiga faser då tidtabellen ännu inte är fastställd men då ett antal villkor och begränsningar på tågen och deras rörelser är kända. TUFF-PO genererar förslag och data som möjliggör effektiv personalplanering i senare skeden, genom att skapa begränsningar på tidtabelläggningen, begränsningar som tar bort dåliga och ineffektiva lösningar ur personalplaneringsperspektivet och bevarar de goda och effektiva lösningarna. Fokus för detta arbete är på tid och krav på tid, inte direkt på kostnader. Ansatsen i TUFF-PO är inte att försöka konstruera personalomlopp och inte heller personalslingor utan att titta på arbetsperioder för att utifrån dessa försöka finna gemensamma egenskaper som tycks gynna bra personalomlopp i senare planeringsskeden. Dessa egenskaper lägger grunden för de begränsningar som bildar krav på tidtabelläggningen. Preliminära resultat pekar på att det är möjligt att skapa kvalitativt bättre personalplaner. Vi tar upp och belyser både generella frågeställningar och den prototypimplementering som är gjord för att validera resultaten.
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| 21. |
- Aronsson, Martin, et al.
(författare)
-
Översikt av metoder och förutsättningar för tåglägestilldelning
- 2003. - 1
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Denna rapport beskriver status hos den forskning som är relevant för tåglägestilldelning samt analyserar och kommenterar några av de reglerande dokument såsom lagar och förordningar samt instruktioner och information som Banverket och Tågtrafikledningen tagit fram. för att styra tåglägestilldelningsprocessen. Rapporten ger också en översikt av forskningsfronten vad gäller systemstöd för tåglägestilldelningen och ger en kortfattad en beskrivning av några av de tekniker som kan vara användbara i ett stödsystem för tåglägestilldelning samt lyfter fram deras respektive för och nackdelar.
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| 22. |
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| 23. |
- Arup, Ulf, et al.
(författare)
-
Professor Ingvar Kärnfelt - a birthday tribute
- 2009
-
Ingår i: The Lichenologist. - Cambridge : Cambridge University Press. - 0024-2829 .- 1096-1135. ; 41:5, s. 453-456
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- On 19 July 2009 Ingvar Kärnefelt celebrated his 65th birthday. This could have meant that we, his former students, would be celebrating him in his retirement from his position as head of the Biological Museums at Lund University. We are grateful that this is not the case, as Ingvar will carry on, probably for at least one or two more years. Instead, we celebrate Ingvar because he is the main reason for all of us having studied lichenology in Lund. This special issue of The Lichenologist is dedicated to him as a birthday tribute in honour of his long and fruitful lichenological career. The main authors of all the papers in this issue are former students of Ingvar. For several of us he has not only acted as supervisor but later also as the director of the Botanical Museum where we meet him in our daily work.
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| 24. |
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| 25. |
- Arup, Ulf, et al.
(författare)
-
The sister group relation of Parmeliaceae (Lecanorales, Ascomycota)
- 2007
-
Ingår i: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 99:1, s. 42-49
-
Tidskriftsartikel (refereegranskat)abstract
- The family Parmeliaceae (Lecanorales, Ascomycota) is possibly the largest, best known and most thoroughly studied lichen family within its order. Despite this fact the relationship between Parmeliaceae and other groups in Lecanorales is still poorly known. The aim of the present study is to contribute to finding the sister group of Parmeliaceae as an aid in future studies on the phylogeny and character evolution of the group. We do this by sampling all potential relatives to the Parmeliaceae that we have identified, i.e. Cypsoplaca, Japewia, Mycoblastus, Protoparmelia, and Tephromela, a good representation of the major groups within the Parmeliaceae s. lat. and a good representation of other taxa in the core Lecanorales. We use molecular data from two genes, the large subunit of the nuclear ribosomal RNA gene (nrLSU) and the small subunit of the mitochondrial ribosomal RNA gene (mrSSU), and a Bayesian analysis of the combined data. The results show that the closest relatives to Parmeliaceae are the two genera Protoparmelia and Gypsoplaca, which are crustose lichens. Parmeliaceae in our sense is a well supported group, including also the family segregates Alectoriaceae, Hypogymniaceae, Usneaceae and Anziaceae.
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| 26. |
- Asplund Samuelsson, Johannes, et al.
(författare)
-
Diversity and expression of bacterial metacaspases in an aquatic ecosystem
- 2016
-
Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 7, s. 1-18
-
Tidskriftsartikel (refereegranskat)abstract
- Metacaspases are distant homologs of metazoan caspase proteases, implicated in stress response, and programmed cell death (PCD) in bacteria and phytoplankton. While the few previous studies on metacaspases have relied on cultured organisms and sequenced genomes, no studies have focused on metacaspases in a natural setting. We here present data from the first microbial community-wide metacaspase survey; performed by querying metagenomic and metatranscriptomic datasets from the brackish Baltic Sea, a water body characterized by pronounced environmental gradients and periods of massive cyanobacterial blooms. Metacaspase genes were restricted to ~4% of the bacteria, taxonomically affiliated mainly to Bacteroidetes, Alpha- and Betaproteobacteria and Cyanobacteria. The gene abundance was significantly higher in larger or particle-associated bacteria (<0.8 μm), and filamentous Cyanobacteria dominated metacaspase gene expression throughout the bloom season. Distinct seasonal expression patterns were detected for the three metacaspase genes in Nodularia spumigena, one of the main bloom-formers. Clustering of normalized gene expression in combination with analyses of genomic and assembly data suggest functional diversification of these genes, and possible roles of the metacaspase genes related to stress responses, i.e., sulfur metabolism in connection to oxidative stress, and nutrient stress induced cellular differentiation. Co-expression of genes encoding metacaspases and nodularin toxin synthesis enzymes was also observed in Nodularia spumigena. The study shows that metacaspases represent an adaptation of potentially high importance for several key organisms in the Baltic Sea, most prominently Cyanobacteria, and open up for further exploration of their physiological roles in microbes and assessment of their ecological impact in aquatic habitats.
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| 27. |
- Berg, Carlo, et al.
(författare)
-
Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics
- 2018
-
Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745.
-
Tidskriftsartikel (refereegranskat)abstract
- Marine and brackish surface waters are highly dynamic habitats that undergo repeated seasonal variations in microbial community composition and function throughout time. While succession of the various microbial groups has been well investigated, little is known about the underlying gene-expression of the microbial community. We investigated microbial interactions via metatranscriptomics over a spring to fall seasonal cycle in the brackish Baltic Sea surface waters, a temperate brackish water ecosystem periodically promoting massive cyanobacterial blooms, which have implications for primary production, nutrient cycling, and expansion of hypoxic zones. Network analysis of the gene expression of all microbes from 0.22 to 200 mu m in size and of the major taxonomic groups dissected the seasonal cycle into four components that comprised genes peaking during different periods of the bloom. Photoautotrophic nitrogen-fixing Cyanobacteria displayed the highest connectivity among the microbes, in contrast to chemoautotrophic ammonia-oxidizing Thaumarchaeota, while heterotrophs dominated connectivity among pre- and post-bloom peaking genes. The network was also composed of distinct functional connectivities, with an early season balance between carbon metabolism and ATP synthesis shifting to a dominance of ATP synthesis during the bloom, while carbon degradation, specifically through the glyoxylate shunt, characterized the post-bloom period, driven by Alphaproteobacteria as well as by Gammaproteobacteria of the SAR86 and SAR92 clusters. Our study stresses the exceptionally strong biotic driving force executed by cyanobacterial blooms on associated microbial communities in the Baltic Sea and highlights the impact cyanobacterial blooms have on functional microbial community composition.
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| 28. |
- Bergman, Birgitta, et al.
(författare)
-
The cyanobacterium–Azolla symbiosis: Interactions and cell differentiation
- 2007
-
Ingår i: Abstracts of the Annual Main Meeting of the Society for Experimental Biology, Glasgow, Scotland, 31st March - 4th April, 2007. - : Elsevier BV.
-
Konferensbidrag (populärvet., debatt m.m.)abstract
- Selected cyanobacteria form stable nitrogen-fixing symbioses with diverse eukaryotes. The water-fern Azolla carries a nitrogen-fixing cyanobacterium (cyanobiont) in its leaves and shows a pronounced intimacy between its partners. It is the only perpetual N2-fixing symbiosis, i.e. the cyanobiont is vertically transmitted in sporocarps between plant generations. The cyanobiont also seems incapable of independent growth which may suggest gene loss and that the symbiosis is on its way to evolve into a N2-fixing plant. Proteomic analyses of the cyanobiont (2-D coupled to MS) resulted in an identification of about 79% of proteins analysed. Processes upregulated were related to energy production, nitrogen and carbon metabolism and stress, while photosynthesis and metabolic turnover rates were downregulated, stressing a slow heterotrophic mode of growth, high heterocyst frequencies and nitrogen-fixing capacities. Peptide mass spectra of NifH demonstrated the presence of a 300–400 Da protein modification localized to a 13 amino acid sequence. Additionally, a short phylogenetic distance between the cyanobiont and some sequenced cyanobacteria (Section IV) and the database hits of the proteins identified by proteomics, together suggest that the Azolla cyanobiont may represent a novel cyanobacterial genus. The genome of the cyanobiont will be sequenced in 2007 (DOE/JGI, USA).
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| 29. |
- Brindefalk, Björn, et al.
(författare)
-
Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters
- 2016
-
Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 18:12, s. 4442-4455
-
Tidskriftsartikel (refereegranskat)abstract
- Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from similar to 0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 mu m), relative to the medium (0.8-3.0 mu m) and large (> 3.0 mu m) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.
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| 30. |
- Bäckström, Martin, et al.
(författare)
-
Attitudes among nurses in Sweden and factors for their reporting of adverse drug reactions
- 2011
-
Ingår i: Abstracts 27th International Conference on Pharmacoepidemiology & Therapeutic Risk Management Hyatt Regency Chicago. - : Wiley. ; , s. S202-S203
-
Konferensbidrag (refereegranskat)abstract
- Background: Adverse drug reactions (ADRs) is a common cause for hospitalization and death. Spontaneous reporting of ADRs remains as one of the cornerstones in post marketing drug safety surveillance. In March 2007 the Medical Product Agency (MPA) in Sweden decided to also accept reports of suspected ADRs from all nurses. Objectives: This study was designed to investigate attitudes and factors for reporting adverse drug reactions (ADRs) from nurses within the health care system in Sweden. Methods: A questionnaire was distributed to 753 randomly selected nurses in Sweden. Results: The most important factors in their decision to report as suspected ADRs were the severity, if the drug was newly approved and if the reaction were unusual. The nurses with a shorter professional experience responded to a higher degree than their colleagues that they made other priorities, did not have the time or where unaware/uncertain what and how to report. Almost two - thirds of the responders assessed that they had insufficient pharmacological knowledge. A vast majority (84%) of the responders would prefer a possibility to report a suspected ADR using a web - based formula. Conclusions: Nurses in Sweden have a fairly good knowledge about the existing rules for reporting. However, there is room for improvement in some areas. Further education and information is needed.
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| 31. |
- Celepli, Narin, et al.
(författare)
-
Meta-omic analyses of Baltic Sea cyanobacteria : diversity, community structure and salt acclimation
- 2017
-
Ingår i: Environmental Microbiology. - : Wiley-Blackwell. - 1462-2912 .- 1462-2920. ; 19:2, s. 673-686
-
Tidskriftsartikel (refereegranskat)abstract
- Cyanobacteria are important phytoplankton in the Baltic Sea, an estuarine-like environment with pronounced north to south gradients in salinity and nutrient concentrations. Here, we present a metagenomic and -transcriptomic survey, with subsequent analyses targeting the genetic identity, phylogenetic diversity, and spatial distribution of Baltic Sea cyanobacteria. The cyanobacterial community constituted close to 12% of the microbial population sampled during a pre-bloom period (June-July 2009). The community was dominated by unicellular picocyanobacteria, specifically a few highly abundant taxa (Synechococcus and Cyanobium) with a long tail of low abundance representatives, and local peaks of bloom-forming heterocystous taxa. Cyanobacteria in the Baltic Sea differed genetically from those in adjacent limnic and marine waters as well as from cultivated and sequenced picocyanobacterial strains. Diversity peaked at brackish salinities 3.5-16psu, with low N:P ratios. A shift in community composition from brackish to marine strains was accompanied by a change in the repertoire and expression of genes involved in salt acclimation. Overall, the pre-bloom cyanobacterial population was more genetically diverse, widespread and abundant than previously documented, with unicellular picocyanobacteria being the most abundant clade along the entire Baltic Sea salinity gradient.
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| 32. |
- Davidson, Lee Ti, et al.
(författare)
-
Admission of patients with chest pain and/or breathlessness from the emergency department in relation to risk assessment and copeptin levels - an observational study
- 2022
-
Ingår i: Upsala Journal of Medical Sciences. - : UPSALA MED SOC. - 0300-9734 .- 2000-1967. ; 127:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: One of the most critical decisions that emergency department (ED) physicians make is the discharge versus admission of patients. We aimed to study the association of the decision in the ED to admit patients with chest pain and/or breathlessness to a ward with risk assessment using the Rapid Emergency Triage and Treatment System (RETTS), the National Early Warning Score (NEWS), and plasma levels of the biomarkers copeptin, midregional proadrenomedulin (MR-proADM), and midregional proatrial natriuretic peptide (MR-proANP). Methods: Patients presenting at the ED with chest pain and/or breathlessness with less than one week onset were enrolled. Patients were triaged according to RETTS. NEWS was calculated from the vital signs retrospectively. Results: Three hundred and thirty-four patients (167 males), mean age 63.8 +/- 16.8 years, were included. Of which, 210 (62.8%) patients complained of chest pain, 65 (19.5%) of breathlessness, and 59 (17.7%) of both. Of these, 176 (52.7%) patients were admitted to a ward, and 158 (47.3%) patients were discharged from the ED. In binary logistic models, age, gender, vital signs (O-2 saturation and heart rate), NEWS class, and copeptin were associated with admission to a ward from the ED. In receiver-operating-characteristics (ROC) analysis, copeptin had an incremental predictive value compared to NEWS alone (P = 0.002). Conclusions: Emergency physicians decisions to admit patients with chest pain and/or breathlessness from the ED to a ward are related to age, O-2 saturation, heart rate, NEWS category, and copeptin. As an independent predictive marker for admission, early analysis of copeptin might be beneficial when improving patient pathways at the ED.
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| 33. |
- Dillman, Karen L., et al.
(författare)
-
New records, range extensions and nomenclatural innovations for lichens and lichenicolous fungi from Alaska, USA
- 2012
-
Ingår i: Herzogia. - : Herzogia. - 0018-0971. ; 25:2, s. 177-210
-
Tidskriftsartikel (refereegranskat)abstract
- New records, range extensions and nomenclatural innovations for lichens and lichenicolous fungi from Alaska, U.S.A. - Herzogia 25: 177-210. Surveys of lichens and lichenicolous fungi have been taking place in the U.S. state of Alaska for more than 160 years, but until now assessing the full extent of their diversity has been hampered by the lack of a comprehensive and synonymized baseline inventory. In this paper we will begin to redress this by resolving outstanding nomenclatural issues and providing voucher data for a forthcoming catalog of Alaskan lichens, specifically: 1) synonymization,and/or resolution of status of species previously reported from Alaska, with emphasis on Alaskan types; 2) species new to the Alaska lichen biota; and 3) biogeographically significant new records from within Alaska. We report 91 species new to the flora of Alaska, including 65 lichens, three saprophytic calicioid fungi and 23 lichenicolous fungi. Of these, we report thirteen species, Biatora sphaeroidiza, Biatorella conspurcans, Chaenothecopsis arthoniae, Collemopsidium foveolatum, Dactylospora frigida, Halospora discrepans, Lecanora bryopsora, Opegrapha geographicola, Peltigera lyngei, Petractis clausa, Protoblastenia cyclospora, Thelocarpon impressellum and Usnea cylindrica as new to North America. In addition, Arthonia pruinata and Flavocetraria minuscula are new to Canada and Adelococcus alpestris new to the United States. We further place the following five names into synonymy: Lecania disceptans (Nyl.) Lynge [= Halecania alpivaga (Th.Fr.) M.Mayrhofer], Lecidea pallidella Nyl. [= Lecania subfuscula (Nyl.) S.Ekman], Lempholemma triptodes (Nyl.) Zahlbr. Leciophysma finmarkicum Th.Fr.), Polyblastia obtenta (Nyl.) Lynge [= Sporodictyon terrestre (Th.Fr.) S.Savic & Tibell], and Verrucaria pernigrata Nyl. [= Protothelenella sphinctrinoides (Nyl.) H.Mayrhofer & Poelt]. We propose restoring the long overlooked taxon Polyblastia exalbida (Nyl.) Zahlbr., currently known only from Alaska, to the North American lichen checklist. Finally, we propose the new combination Puttea caesia (Fr.) M.Svensson & T.Sprib. to replace Lecidea symmictella Nyl., which becomes a synonym.
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| 34. |
- Dupont, Chris L., et al.
(författare)
-
Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
- 2014
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:2, s. e89549-
-
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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| 35. |
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| 36. |
- Ekman, Carl Johan, et al.
(författare)
-
A History of Psychosis in Bipolar Disorder is Associated With Gray Matter Volume Reduction.
- 2017
-
Ingår i: Schizophrenia bulletin. - : Oxford University Press (OUP). - 1745-1701 .- 0586-7614. ; 43:1, s. 99-107
-
Tidskriftsartikel (refereegranskat)abstract
- Psychotic symptoms are prevalent in schizophrenia, bipolar disorder, and other psychiatric and neurological disorders, yet the neurobiological underpinnings of psychosis remain obscure. In the last decade, a large number of magnetic resonance imaging studies have shown differences in local gray matter volume between patients with different psychiatric syndromes and healthy controls. Few studies have focused on the symptoms, which these syndromes are constituted of. Here, we test the association between psychosis and gray matter volume by using a sample of 167 subjects with bipolar disorder, with and without a history of psychosis, and 102 healthy controls. Magnetic resonance images were analyzed on group level using a voxel-wise mass univariate analysis (Voxel-Based Morphometry). We found that patients with a history of psychosis had smaller gray matter volume in left fusiform gyrus, the right rostral dorsolateral prefrontal cortex, and the left inferior frontal gyrus compared with patients without psychosis and with healthy controls. There was no volume difference in these areas between the no-psychosis group and healthy controls. These areas have previously been structurally and functionally coupled to delusions and hallucinations. Our finding adds further evidence to the probability of these regions as key areas in the development of psychotic symptoms.
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| 37. |
- Ekman, Elisabet, 1953-, et al.
(författare)
-
Attitudes among hospital physicians to the reporting of adverse drug reactions in Sweden
- 2009
-
Ingår i: European Journal of Clinical Pharmacology. - Berlin Heidelberg : Springer. - 0031-6970 .- 1432-1041. ; 65, s. 613-618
-
Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: This study was designed to investigate attitudes to and incentive for reporting adverse drug reactions (ADRs) in general and towards nurses as reporters of ADRs in particular in a sample of hospital physicians.METHOD: A questionnaire was sent to 1,201 randomly selected hospital physicians.RESULTS: The main factors for the decision to report an ADR were the severity of the reaction, a reaction to a new drug, and an unusual reaction. The most important factor for refraining from reporting was that the reaction was well known. There were no significant differences between males and females or between age groups in these aspects. A majority were positive or neutral to nurses as reporters. Only 6% stated that their willingness to report ADRs would be affected in a negative way if nurses were involved in the program for reporting.CONCLUSIONS: The results of this survey showed that inclusion of hospital nurses as reporters will not decrease the reporting rate from the physicians.
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| 38. |
- Ekman, Elisabet, et al.
(författare)
-
Awareness among nurses about reporting of adverse drug reactions in Sweden
- 2012
-
Ingår i: Drug, Healthcare and Patient Safety. - 1179-1365. ; 4, s. 61-66
-
Tidskriftsartikel (refereegranskat)abstract
- Background: The purpose of this study was to investigate awareness among nurses regarding their new role as reporters of adverse drug reactions in Sweden and factors that may influence reporting by nurses.Methods: In 2007, all nurses were included in the adverse drug reaction reporting scheme in Sweden. A questionnaire was sent to 753 randomly selected nurses in September 2010.Results: Of the 453 (60%) responding nurses, 265 (58%) were aware that nurses were included in the reporting of adverse drug reactions. Sixty-one nurses (14%) stated that they had reported an adverse drug reaction. Fifteen percent (n = 70) of the respondents had received training about reporting of adverse drug reactions. Almost one third of these (n = 21, 30%) had reported an adverse drug reaction on at least one occasion. Among nurses without training, a smaller proportion (n = 40, 11%, P < 0.05) had reported an adverse drug reaction on at least one occasion. The two factors considered most important by nurses for reporting were the severity of the adverse drug reaction and if the reaction was to a newly approved drug. A majority of the nurses (n = 397, 88%) were interested in a training course in pharmacology as part of their ongoing professional development. One third (32%) of all nurses stated that one reason for not reporting a suspected adverse drug reaction was that the physician responsible did not regard the reaction necessary to report.Conclusion: We found that more than half of the study population of nurses in Sweden were aware of their new role as reporters of adverse drug reactions, but few of the responding nurses had reported an adverse drug reaction. Given that training seems to be associated with high reporting frequency, we suggest more training in pharmacovigilance for nurses.
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| 39. |
- Ekman, Inger, 1952, et al.
(författare)
-
Person-centered care -ready for prime time.
- 2011
-
Ingår i: European Journal of Cardiovascular Nursing. - : Sage Publications. - 1474-5151 .- 1873-1953. ; 10:4, s. 248-251
-
Tidskriftsartikel (refereegranskat)abstract
- Long-term diseases are today the leading cause of mortality worldwide and are estimated to be the leading cause of disability by 2020. Person-centered care (PCC) has been shown to advance concordance between care provider and patient on treatment plans, improve health outcomes and increase patient satisfaction. Yet, despite these and other documented benefits, there are a variety of significant challenges to putting PCC into clinical practice. Although care providers today broadly acknowledge PCC to be an important part of care, in our experience we must establish routines that initiate, integrate, and safeguard PCC in daily clinical practice to ensure that PCC is systematically and consistently practiced, i.e. not just when we feel we have time for it. In this paper, we propose a few simple routines to facilitate and safeguard the transition to PCC. We believe that if conscientiously and systematically applied, they will help to make PCC the focus and mainstay of care in long-term illness.
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| 40. |
- Ekman, Jan, et al.
(författare)
-
TIME - en gemensam informationsutbytesplattform för järnvägstransportbranschen
- 2006. - 5
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- TIME står för Train Information Management Environment. TIME är ett tänkt övergripande informationssystem för Järnväg. Viktiga aspekter hos TIME är utformningen av en plattform för kommunikation mellan aktörerna i järnvägstransportbranschen och information mellan fordon och system med en fast plats. TIME gäller alla delar i ett informationssystem, hur data produceras och processas, infrastruktur för information och principer för datalagring och informationsutbyte samt funktioner och tjänster baserade på denna information. TIME avser t.ex. att medverka till att samverkan mellan järnvägstransportbranschens aktörer fungerar bra, dessa aktörers egen verksamhet blir effektiv och att kunder till järnvägen och andra som beror av järnvägen erhåller rätt information.
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| 41. |
- Ekman, Martin, et al.
(författare)
-
Cellular and functional specificity among ferritin-like proteins in the multicellular cyanobacterium Nostoc punctiforme.
- 2014
-
Ingår i: Environmental Microbiology. - Oxford : Wiley-Blackwell. - 1462-2912 .- 1462-2920. ; 16:3, s. 829-844
-
Tidskriftsartikel (refereegranskat)abstract
- Ferritin-like proteins constitute a remarkably heterogeneous protein family, including ferritins, bacterioferritins and Dps proteins. The genome of the filamentous heterocyst-forming cyanobacterium Nostoc punctiforme encodes five ferritin-like proteins. In the present paper, we report a multidimensional characterization of these proteins. Our phylogenetic and bioinformatics analyses suggest both structural and physiological differences among the ferritin-like proteins. The expression of these five genes responded differently to hydrogen peroxide treatment, with a significantly higher rise in transcript level for Npun_F3730 as compared with the other four genes. A specific role for Npun_F3730 in the cells tolerance against hydrogen peroxide was also supported by the inactivation of Npun_F3730, Npun_R5701 and Npun_R6212; among these, only the ΔNpun_F3730 strain showed an increased sensitivity to hydrogen peroxide compared with wild type. Analysis of promoter-GFP reporter fusions of the ferritin-like genes indicated that Npun_F3730 and Npun_R5701 were expressed in all cell types of a diazotrophic culture, while Npun_F6212 was expressed specifically in heterocysts. Our study provides the first comprehensive analysis combining functional differentiation and cellular specificity within this important group of proteins in a multicellular cyanobacterium.
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| 42. |
- Ekman, Martin, 1971-
(författare)
-
Cyanobacteria in symbiosis with plants : Protein patterns and regulatory mechanisms
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cyanobacteria belonging to the heterocystous genus Nostoc, capable of oxygenic photosynthesis and nitrogen fixation via the enzyme nitrogenase, may form symbiotic associations with plants. In these associations most of the N2 fixed by the symbiotic cyanobacteria (cyanobiont) is transferred to the host, which in turn supplies the cyanobiont with fixed carbon. By using a proteomic approach adapted for investigating unsequenced organisms, adaptations of the cyanobiont to symbiotic conditions within the angiosperm Gunnera, for which each generation needs to be newly infected, and the water fern Azolla, which is in permanent association with its cyanobiont, were investigated. Despite morphological and physiological modifications of the cyanobionts, many basic functions appear to be intact in symbiosis compared to when free-living, as indicated by similar protein levels. Some differences were identified however, and in the view of parallel studies on photoautotrophic and heterotrophic growth of free-living cyanobacteria, these indicated that cellular functions were focused on N2 fixation and the associated heterocyst specific metabolism, and also reflected a mainly heterotrophic growth. Stress responses were induced in both cyanobionts, while surface adaptations mainly in that of Gunnera, possibly a reflection of its intracellular location in combination with the microaerobic and dark conditions inside the Gunnera glands. The heterocyst envelope was reduced, which may be involved in ammonia release. The level of nitrogenase was considerably higher in the Azolla cyanobiont, potentially reflecting a co-evolution with its host plant. The results also indicate that the Azolla cyanobiont may be classified as a new genus. Probably induced by oxygen, some nitrogenase in the Azolla cyanobiont carried a post-translational modification, located within a specific peptide corresponding to the part of nitrogenase that is ADP-ribosylated in certain other N2-fixing bacteria. However, the modification, with a mass of 300-400 Da, was not identified. The regulation behind heterocyst differentiation, N2-fixation and N-assimilation in symbiosis was also investigated. The mechanisms involving the regulatory proteins NtcA and HetR appear to be intact in symbiosis but distinctly upregulated, generating the higher heterocyst frequencies observed. This upregulation may be induced by a high C:N ratio in symbiosis or a plant effector molecule. These results also indicate that glutamine synthetase levels are reduced in symbiosis by a separate, but unknown mechanism. A sugar uptake regulator located near the hrm hormogonium repressing operon may be involved in carbohydrate uptake in the Gunnera symbiosis. Expression of isoenzymes of glyceraldehyde-3-phosphate dehydrogenase and fructose-1,6-bisphosphatase and a possible redox regulation of certain enzymes may be involved in regulation of metabolic pathways in symbiotic as well as in free-living cyanobacteria. Potential host-induced mechanisms responsible for cyanobiont adaptations, other than the environment offered in symbiosis, remain to be identified.
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| 43. |
- Ekman, M J, et al.
(författare)
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6-minute walk test before and after a weight reduction program in obese subjects.
- 2013
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Ingår i: Obesity. - : Wiley. - 1930-739X .- 1930-7381. ; 21:3, s. 236-243
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Tidskriftsartikel (refereegranskat)abstract
- Weight loss and physical activity have shown favorable effects on risks associated with obesity. It is therefore of interest to evaluate exercise capacity and related co-morbidities in obese patients. We present data from obese subjects evaluated by the 6-minute walk test (6MWT) before and after a 7.3 (6.1-8.2) month weight reduction program. 251 subjects completed the test at baseline (BMI 40.6 [36.9-44.6] kg/m(2) ) and 129 (51.4 %) repeated the test after intervention (BMI 35.6 [31.2-38.5] kg/m(2) ). The six minute walking distance (6MWD) at baseline (535 [480-580] m) and at follow up (599 [522-640] m) correlated to several cardiovascular risk markers. Age, weight, height, resting heart rate, smoking status, fP-glucose and use of ß-blockers explained 43 % of the variance in predicted 6MWD at baseline. The effect of smoking status, fP-glucose, ß-blockers and resting heart rate lost significance at follow up. Presence of diabetes and the metabolic syndrome had a negative influence on 6MWD but did not affect the impact of intervention based on percentage increase in walking distance. Gender had no impact on 6MWD. Reported pain during the test was common but decreased after intervention (57.0 % vs. 28.7 %, p<0.001). In conclusion, the 6MWT may be used to evaluate intervention success beyond kilogram weight loss in obese subjects. We present formulas to predict 6MWD and the effect of weight loss on walking distance in clinical practice. Pain is a common problem which has to be considered when giving advice on exercise as a part of weight loss intervention.
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| 44. |
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| 45. |
- Ekman, Martin, et al.
(författare)
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Metabolic Adaptations in a H-2 Producing Heterocyst-Forming Cyanobacterium : Potentials and Implications for Biological Engineering
- 2011
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 10:4, s. 1772-1784
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Tidskriftsartikel (refereegranskat)abstract
- Nostoc punctiforme ATCC 29133 is a photoautotrophic cyanobacterium with the ability to fix atmospheric nitrogen and photoproduce hydrogen through the enzyme nitrogenase. The H-2 produced is reoxidized by an uptake hydrogenase. Inactivation of the uptake hydrogenase in N. punctiforme leads to increased H-2 release but unchanged rates of N-2 fixation, indicating redirected metabolism. System-wide understanding of the mechanisms of this metabolic redirection was obtained using complementary quantitative proteomic approaches, at both the filament and the heterocyst level. Of the total 1070 identified and quantified proteins, 239 were differentially expressed in the uptake hydrogenase mutant (NHM5) as compared to wild type. Our results indicate that the inactivation of uptake hydrogenase in N. punctiforme changes the overall metabolic equilibrium, affecting both oxygen reduction mechanisms in hetcrocysts as well as processes providing reducing equivalents for metabolic functions such as N-2 fixation. We identify specific metabolic processes used by NHM5 to maintain a high rate of N-2 fixation, and thereby potential targets for further improvement of nitrogenase based H-2 photogeneration. These targets include, but are not limited to, components of the oxygen scavenging capacity and cell envelope of heterocysts and proteins directly or indirectly involved in reduced carbon transport from vegetative cells to heterocysts.
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| 46. |
- Ekman, Martin, et al.
(författare)
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Protein expression profiles in an endosymbiotic cyanobacterium revealed by a proteomic approach
- 2006
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Ingår i: Molecular Plant-Microbe Interactions. - 0894-0282 .- 1943-7706. ; 19:11, s. 1251-1261
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Tidskriftsartikel (refereegranskat)abstract
- Molecular mechanisms behind adaptations in the cyano-bacterium (Nostoc sp.) to a life in endosymbiosis with plants are still not clarified, nor are the interactions between the partners. To get further insights, the proteome of a Nostoc strain, freshly isolated from the symbiotic gland tissue of the angiosperm Gunnera manicata Linden, was analyzed and compared with the proteome of the same strain when free-living. Extracted proteins were separated by two-dimensional gel electrophoresis and were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry combined with tandem mass spectrometry. Even when the higher percentage of differentiated cells (heterocysts) in symbiosis was compensated for, the majority of the proteins detected in the symbiotic cyanobacteria were present in the free-living counterpart, indicating that most cellular processes were common for both stages. However, differential expression profiling revealed a significant number of proteins to be down-regulated or missing in the symbiotic stage, while others were more abundant or only expressed in symbiosis. The differential protein expression was primarily connected to i) cell envelope-associated processes, including proteins involved in exopolysaccharide synthesis and surface and membrane associated proteins, ii) to changes in growth and metabolic activities (C and N), including upregulation of nitrogenase and proteins involved in the oxidative pentose phosphate pathway and downregu-lation of Calvin cycle enzymes, and iii) to the dark, micro-aerobic conditions offered inside the Gunnera gland cells, including changes in relative phycobiliprotein concentrations. This is the first comprehensive analysis of proteins in the symbiotic state.
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| 47. |
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