| 1. |
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| 2. |
- Johansson Wensman, Jonas, et al.
(författare)
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Visualization of Borna Disease Virus Protein Interactions with Host Proteins using in situ Proximity Ligation Assay
- 2016
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Ingår i: British journal of virology. - : ResearchersLinks Ltd. - 2055-6128. ; 3:1, s. 11-23
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Tidskriftsartikel (refereegranskat)abstract
- Borna disease virus type 1 (BDV) comprises highly conserved neurotropic non-segmented negative strand RNA-virus variants causing neurological and behavioral disorders in a wide range of mammalian animals, possibly including humans. Viral persistence in the brain has been frequently observed, however, the exact mechanisms behind BDV’s ability to establish persistence despite a prominent immune response are not known. Here we have used in situ proximity ligation assay (in situ PLA), a selective tool for studying virus-host protein-protein interactions. BDV P (phosphoprotein) and N (nucleoprotein) have previously been reported to interact with several host proteins, thereby interfering with various signaling pathways. In this study, we focused on some of these interactions (BDV P-HMGB1, BDV N/P-Cdc2). First, we used rat glioma cell cultures persistently infected with a laboratory strain of BDV (C6BV) to establish the assay. Next, in situ PLA was applied to detect BDV P in brain tissues of infected animals. Finally, protein-protein interactions were visualized in both C6BV and brain tissues of experimentally as well as naturally infected animals (rat and horse, respectively). BDV proteins and their interactions with host proteins could be shown in cell cultures (HMGB1, Cdc2) and in brain tissues of rat (HMGB1, Cdc2) and horse (Cdc2 only) infected with BDV. In this study, we have for the first time directly visualized protein-protein interactions between BDV and its host, and thereby confirmed previous data to demonstrate findings in cell cultures to be applicable also in experimentally and naturally infected animals.
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| 3. |
- Andersson, C. David, et al.
(författare)
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Benefits of statistical molecular design, covariance analysis, and reference models in QSAR : a case study on acetylcholinesterase
- 2015
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Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 0920-654X .- 1573-4951. ; 29:3, s. 199-215
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Tidskriftsartikel (refereegranskat)abstract
- Scientific disciplines such as medicinal- and environmental chemistry, pharmacology, and toxicology deal with the questions related to the effects small organic compounds exhort on biological targets and the compounds' physicochemical properties responsible for these effects. A common strategy in this endeavor is to establish structure-activity relationships (SARs). The aim of this work was to illustrate benefits of performing a statistical molecular design (SMD) and proper statistical analysis of the molecules' properties before SAR and quantitative structure-activity relationship (QSAR) analysis. Our SMD followed by synthesis yielded a set of inhibitors of the enzyme acetylcholinesterase (AChE) that had very few inherent dependencies between the substructures in the molecules. If such dependencies exist, they cause severe errors in SAR interpretation and predictions by QSAR-models, and leave a set of molecules less suitable for future decision-making. In our study, SAR- and QSAR models could show which molecular sub-structures and physicochemical features that were advantageous for the AChE inhibition. Finally, the QSAR model was used for the prediction of the inhibition of AChE by an external prediction set of molecules. The accuracy of these predictions was asserted by statistical significance tests and by comparisons to simple but relevant reference models.
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| 4. |
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| 5. |
- Berg, Frenk van den, et al.
(författare)
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Results of the European collaborative project "Product Uniformity Control" to improve the inline sensing of mechanical properties and microstructure of automotive steels
- 2018
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Ingår i: e-Journal of Nondestructive Testing (eJNDT). - 1435-4934. ; 23:8
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Tidskriftsartikel (refereegranskat)abstract
- A European consortium consisting of four major steel manufacturers and ten academic technology institutes has conducted a research and development project, called “Product Uniformity Control“ (PUC) in the period 2013 to 2017. This project aimed to develop and improve non-destructive (inline) measurement techniques to characterise the (uniformity of the) microstructure of steel strip products. In this project, a multitude of strip steel samples from various stages of production have been collected from the four participating steel manufacturers. The samples have been characterised in various ways, namely on their (1) non-destructive measurement parameters using different techniques suited for inline evaluation, (2) fundamental ultrasonic and electromagnetic properties (wave speed, ultrasonic attenuation, magnetisation loops, coercive field), (3) tensile properties (stress-strain curves) and (4) microstructure (by optical micrographs and EBSD images). The correlations between these different characterisations will be addressed. Besides the experimental characterisation, a strong accent has been on modelling activities: during the project, fundamental models have been developed to describe, starting from 2D and 3D microstructures, the ultrasonic and magnetic properties, which are next used as input to sensor models that predict the output of the inline measurement systems. This contribution presents the recent results of experimental work, which underlines the importance of associated modelling studies for the interpretation of the measurement data for the benefit of inline characterisation of the mechanical properties complementary to traditional destructive tensile testing.
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| 6. |
- Berg, Lisa, et al.
(författare)
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Parental death during childhood and depression in young adults – a national cohort study
- 2016
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Ingår i: Journal of Child Psychology and Psychiatry. - : Wiley. - 0021-9630 .- 1469-7610. ; 57:9, s. 1092-1098
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThere are few prospective, population-based studies on childhood parental death and psychiatric disorders in adulthood, and previous findings are inconclusive. This study investigated the association between parental death from natural and external (suicides, accidents or homicides) causes before 18 years and the risk of clinical depression in young adults, in relation to age at loss and gender of both child and parent.MethodsIn this register-based study, a national cohort born in Sweden during 1973–1982 (n = 862,554) was followed with regard to hospital admissions and outpatient care for depression during 2006–2013. Multivariate Cox proportional hazards models were used to estimate the impact of parental death, taking sociodemographic and parental psychosocial covariates into account.ResultsMaternal death from natural causes was associated with a hazard ratio (HR) of outpatient care for depression of 1.19 [95% confidence interval (CI), 1.02–1.40] in men and 1.15 (1.01–1.31) in women, after adjustment for sociodemographic confounders, with similar effect sizes for paternal natural death. Death from external causes consistently had higher effect size compared with natural deaths, in particular in relation to risk of hospital admissions for depression where they were as high as HR 3.23 (2.38–4.38) for men, and 1.79 (1.30–2.47) for women after a loss of a mother. Losing a parent in preschool age, compared with losing a parent as a teenager, was associated with higher risks of both hospitalization (p = .006) and outpatient care (p = .001) for depression.ConclusionsThis study indicates that parental loss to death from natural causes during childhood is associated with a small increased risk of long-term consequences for psychological health. Children who lose their parents to death from external causes, that is suicides, accidents or homicides, and children losing a parent in young ages are, however, at particular risk and should be given priority in preventive interventions after parental loss.
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| 7. |
- Berg, Lisa, et al.
(författare)
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Parental death during childhood and violent crime in late adolescence to early adulthood : a Swedish national cohort study
- 2019
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Ingår i: Palgrave Communications. - : Springer Science and Business Media LLC. - 2055-1045. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Childhood parental death has been associated with adverse health, social and educational outcomes. Studies on long-term outcomes are in general scarce and there is little evidence on the long-term impact on anti-social behaviour. This study takes advantage of high-quality register data to investigate risk of violent crime in relation to childhood parental death in a large national cohort covering the entire Swedish population born in 1983–1993 (n = 1,103,656). The impact of parental death from external (suicides, accidents, homicides) and natural causes on risk for violent crime from age 15 to 20–30 years, considering multiple aspects of the rearing environment (including parental psychiatric disorders and criminal offending), was estimated through Cox regression. Unadjusted hazard ratios associated with parental death from external causes ranged between 2.20 and 3.49. For maternal and paternal death from external causes, adjusted hazard ratios were 1.26 (95% confidence intervals: 1.04–1.51) and 1.44 (95% confidence intervals: 1.32–1.57) for men, and 1.47 (95% confidence intervals: 1.05–2.06) and 1.51 (95% confidence intervals: 1.27–1.78) for women. With the exception of maternal death among women (hazard ratio 1.26, 95% confidence intervals: 1.03–1.53), parental death from natural causes was not associated with increased risks in adjusted models. The results underscore the importance of preventive interventions to prevent negative life-course trajectories, particularly when death is sudden and clustered with other childhood adversities.
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| 8. |
- Berg, Mikael
(författare)
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Complete genome of Avian coronavirus vaccine strains Ma5 and BR-I
- 2017
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Ingår i: Microbiology Resource Announcements. - 2576-098X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Avian coronavirus (AvCoV) is a ubiquitous multiple-serotype pathogen of poultry, and its control is mainly based on the use of vaccines. We report here the previously unknown full genomes of the Ma5 (27,652 nucleotides [nt]) and BR-I (27,618 nt) AvCoV vaccine strains of the GI-1 (Massachusetts) and GI-11 (Brazil) types.
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| 9. |
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| 10. |
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| 11. |
- Berg, Mikael, 1970-
(författare)
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Historielärares ämnesbiografier
- 2016
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Ingår i: Kulturell reproduktion i skola och nation. - Möklinta : Gidlunds förlag. - 9789178449613
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 12. |
- Berg, Mikael, et al.
(författare)
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Porcine Rubulavirus
- 2016
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Ingår i: Mononegaviruses of Veterinary Importance, Volume 2. - UK : CABI. - 9781780644172 ; , s. 106-113
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- This pig disease appeared in the early 1980s, but problems associated with the virus still remain. The dense population of pigs in the Mexican states of Michoacan, Jalisco and Guanajuato are the main focus of porcine rubulavirus may infection. The epidemiology of this disease is not fully clear. Bats may be a natural reservoir and may spread the virus to pigs, as has been reported for other emerging paramyxoviruses, and may explain why the virus seems to be localized. However, it is also clear that the virus circulates in pigs and so various trade precautions are important. In terms of viral genetic variation, the different isolates that have been found vary between years, but not extensively. In fact, some very recent isolates are very similar to old prototype isolates from the early 1980s. However, information on this is scarce and this needs to be studied in more detail. A least three genetic variants, based on the sequence of the haemagglutinine-neuraminidose gene, do circulate, but more may be found when the other genes and more isolates are studied. One obvious way to control this disease would be to develop an effective vaccine. There are some vaccine concepts that have been tested and can be put into field practice, and these are described and discussed in this chapter.
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| 13. |
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| 14. |
- Berg, Mikael, et al.
(författare)
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Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA)
- 2017
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Coronaviruses are of major importance for both animal and human health. With the emergence of novel coronaviruses such as SARS and MERS, the need for fast genome characterisation is ever so important. Further, in order to understand the influence of quasispecies of these viruses in relation to biology, techniques for deep-sequence and full-length viral genome analysis are needed. In the present study, we compared the efficiency of two sequence-independent approaches [sequence-independent single primer amplification (SISPA) and single primer isothermal amplification (SPIA, represented by the Ovation kit)] coupled with high throughput sequencing to generate the full-length genome of bovine coronavirus (BCoV) from a nasal swab. Both methods achieved high genome coverage (100% for SPIA and 99% for SISPA), however, there was a clear difference in the percentage of reads that mapped to BCoV. While approximately 45% of the Ovation reads mapped to BCoV (sequence depth of 169-284 944), only 0.07% of the SISPA reads (sequence depth of 0-249) mapped to the reference genome. Although BCoV was the focus of the study we also identified a bovine rhinitis B virus (BRBV) in the data sets. The trend for this virus was similar to that observed for BCoV regarding Ovation vs. SISPA, but with fewer sequences mapping to BRBV due to a lower amount of this virus. In summary, the SPIA approach used in this study produced coverage of the entire BCoV (high copy number) and BRBV (low copy number) and a high sequence/genome depth compared to SISPA. Although this is a limited study, the results indicate that the Ovation method could be a preferred approach for full genome sequencing if a low copy number of viral RNA is expected and if high sequence depth is desired.
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| 15. |
- Berg, Mikael, Universitetslektor, 1970-, et al.
(författare)
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Studieresa till Auschwitz : Elevers perspektivtagande i arbetet med förintelsen
- 2018
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Ingår i: SO-didaktik. - 2002-4525. ; :5, s. 8-19
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Inom historiedidaktiken är begreppet perspektivtagande centralt för förståelsen av ett historiskt fenomen. I den här artikeln tas utgångspunkt i en studieresa till Auschwitz för att undersöka med vilka kunskaper elever försöker skapa förståelse. Resultatet visar att eleverna anänder sig av olika emotioner och ämneskunskaper i sin strävan att tolka sin intryck från studiebesöket.
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| 16. |
- Berg, Mikael
(författare)
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The complete genome of Avian coronavirus D274 strain
- 2018
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Ingår i: Microbiology Resource Announcements. - 2576-098X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Avian coronavirus, the causative agent of avian infectious bronchitis, occurs as multiple genotypes and lineages, and full genomes are not available for the majority of them. This paper reports the (previously unknown) complete genome sequence of strain D274 of this virus (27,599 nucleotides), isolated from chickens in The Netherlands in 1979.
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| 17. |
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| 18. |
- Berg, Mikael
(författare)
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Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus
- 2019
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Ingår i: Infection, Genetics and Evolution. - : Elsevier BV. - 1567-1348 .- 1567-7257. ; 74
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Tidskriftsartikel (refereegranskat)abstract
- Several Avianparamyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and coworkers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world.
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| 19. |
- Bielack, Stefan S, et al.
(författare)
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Methotrexate, Doxorubicin, and Cisplatin (MAP) Plus Maintenance Pegylated Interferon Alfa-2b Versus MAP Alone in Patients With Resectable High-Grade Osteosarcoma and Good Histologic Response to Preoperative MAP: First Results of the EURAMOS-1 Good Response Randomized Controlled Trial
- 2015
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Ingår i: Journal of Clinical Oncology. - 1527-7755. ; 33:20, s. 2279-2287
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Tidskriftsartikel (refereegranskat)abstract
- Purpose EURAMOS-1, an international randomized controlled trial, investigated maintenance therapy with pegylated interferon alfa-2b (IFN-α-2b) in patients whose osteosarcoma showed good histologic response (good response) to induction chemotherapy. Patients and Methods At diagnosis, patients age ≤ 40 years with resectable high-grade osteosarcoma were registered. Eligibility after surgery for good response random assignment included ≥ two cycles of preoperative MAP (methotrexate, doxorubicin, and cisplatin), macroscopically complete surgery of primary tumor, < 10% viable tumor, and no disease progression. These patients were randomly assigned to four additional cycles MAP with or without IFN-α-2b (0.5 to 1.0 μg/kg per week subcutaneously, after chemotherapy until 2 years postregistration). Outcome measures were event-free survival (EFS; primary) and overall survival and toxicity (secondary). Results Good response was reported in 1,041 of 2,260 registered patients; 716 consented to random assignment (MAP, n = 359; MAP plus IFN-α-2b, n = 357), with baseline characteristics balanced by arm. A total of 271 of 357 started IFN-α-2b; 105 stopped early, and 38 continued to receive treatment at data freeze. Refusal and toxicity were the main reasons for never starting IFN-α-2b and for stopping prematurely, respectively. Median IFN-α-2b duration, if started, was 67 weeks. A total of 133 of 268 patients who started IFN-α-2b and provided toxicity information reported grade ≥ 3 toxicity during IFN-α-2b treatment. With median follow-up of 44 months, 3-year EFS for all 716 randomly assigned patients was 76% (95% CI, 72% to 79%); 174 EFS events were reported (MAP, n = 93; MAP plus IFN-α-2b, n = 81). Hazard ratio was 0.83 (95% CI, 0.61 to 1.12; P = .214) from an adjusted Cox model. Conclusion At the preplanned analysis time, MAP plus IFN-α-2b was not statistically different from MAP alone. A considerable proportion of patients never started IFN-α-2b or stopped prematurely. Long-term follow-up for events and survival continues.
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| 20. |
- Blomström, Anne-Lie, et al.
(författare)
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Genome Sequence of a Bovine Rhinitis B Virus Identified in Cattle in Sweden
- 2017
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Ingår i: Genome Announcements. - 2169-8287. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- A bovine rhinitis B virus, identified in a calf from Sweden, was genetically characterized. The complete polyprotein was recovered, and phylogenetic analysis showed that this virus has the highest similarity to a bovine rhinitis B virus previously identified in Mexico.
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| 21. |
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| 22. |
- Blomström, Anne-Lie, et al.
(författare)
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Viral Metagenomic Analysis Displays the Co-Infection Situation in Healthy and PMWS Affected Pigs
- 2016
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- The development of high-throughput sequencing technologies have allowed the possibility to investigate and characterise the entire microbiome of individuals, providing better insight to the complex interaction between different microorganisms. This will help to understand how the microbiome influence the susceptibility of secondary agents and development of disease. We have applied viral metagenomics to investigate the virome of lymph nodes from Swedish pigs suffering from the multifactorial disease postweaning multisystemic wasting syndrome (PMWS) as well as from healthy pigs. The aim is to increase knowledge of potential viruses, apart from porcine circovirus type 2 (PCV2), involved in PMWS development as well as to increase knowledge on the virome of healthy individuals. In healthy individuals, a diverse viral flora was seen with several different viruses present simultaneously. The majority of the identified viruses were small linear and circular DNA viruses, such as different circoviruses, anelloviruses and bocaviruses. In the pigs suffering from PMWS, PCV2 sequences were, as expected, detected to a high extent but other viruses were also identified in the background of PCV2. Apart from DNA viruses also RNA viruses were identified, among them were a porcine pestivirus showing high similarity to a recently (in 2015) discovered atypical porcine pestivirus in the US. Majority of the viruses identified in the background of PCV2 in PMWS pigs could also be identified in the healthy pigs. PCV2 sequences were also identified in the healthy pigs but to a much lower extent than in PMWS affected pigs. Although the method used here is not quantitative the very clear difference in amount of PCV2 sequences in PMWS affected pigs and healthy pigs most likely reflect the very strong replication of PCV2 known to be a hallmark of PMWS. Taken together, these findings illustrate that pigs appear to have a considerable viral flora consisting to a large extent of small single-stranded and circular DNA viruses. Future research on these types of viruses will help to better understand the role that these ubiquitous viruses may have on health and disease of pigs. We also demonstrate for the first time, in Europe, the presence of a novel porcine pestivirus.
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| 23. |
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| 24. |
- Cholleti, Harindranath, et al.
(författare)
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Genetic characterization of a novel picorna-like virus in Culex spp. Mosquitoes from Mozambique
- 2018
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Ingår i: Virology Journal. - : Springer Science and Business Media LLC. - 1743-422X. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Mosquitoes are the potential vectors for a variety of viruses that can cause diseases in the human and animal populations. Viruses in the order Picornavirales infect a broad range of hosts, including mosquitoes. In this study, we aimed to characterize a novel picorna-like virus from the Culex spp. of mosquitoes from the Zambezi Valley of Mozambique.& para;& para;Methods: The extracted RNA from mosquito pools was pre-amplified with the sequence independent single primer amplification (SISPA) method and subjected to high-throughput sequencing using the Ion Torrent platform. Reads that are classified as Iflaviridae, Picornaviridae and Dicistroviridae were assembled by CodonCode Aligner and SPAdes. Gaps between the viral contigs were sequenced by PCR. The genomic ends were analyzed by 5' and 3' RACE PCRs. The ORF was predicted with the NCBI ORF finder. The conserved domains were identified with ClustalW multiple sequence alignment, and a phylogenetic tree was built with MEGA. The presence of the virus in individual mosquito pools was detected by RT-PCR assay.& para;& para;Results: A near full-length viral genome (9740 nt) was obtained in Culex mosquitoes that encoded a complete ORF (3112 aa), named Culex picorna-like virus (CuPV-1). The predicted ORF had 38% similarity to the Hubei picorna-like virus 35. The sequence of the conserved domains, Helicase-Protease-RNA-dependent RNA polymerase, were identified by multiple sequence alignment and found to be at the 3' end, similar to iflaviruses. Phylogenetic analysis of the putative RdRP amino acid sequences indicated that the virus clustered with members of the Iflaviridae family. CuPV-1 was detected in both Culex and Mansonia individual pools with low infection rates.& para;& para;Conclusions: The study reported a highly divergent, near full-length picorna-like virus genome from Culex spp. mosquitoes from Mozambique. The discovery and characterization of novel viruses in mosquitoes is an initial step, which will provide insights into mosquito-virus interaction mechanisms, genetic diversity and evolution.
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| 25. |
- Cholleti, Harindranath, et al.
(författare)
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Vector-borne viruses and their detection by viral metagenomics
- 2018
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Ingår i: Infection Ecology & Epidemiology. - : Informa UK Limited. - 2000-8686. ; 8
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Forskningsöversikt (refereegranskat)abstract
- Arthropods, such as mosquitoes and ticks, are important vectors for different viruses (so called vector-borne viruses), some of which cause a significant number of human and animal deaths every year as well as affect public health worldwide. Dengue virus, yellow fever virus, chikungunya virus, Japanese encephalitis virus, tick-borne encephalitis virus and Zika virus are just a few examples of important vector-borne viruses. The majority of all vector-borne viruses have an RNA genome, which routinely undergo genetic modifications. The changes in the genome, apart from the environmental issues, can also influence the spread of viruses to new habitats and hosts and lead to the emergence of novel viruses, which may become a threat to public health. Therefore, it is important to investigate the viruses circulating in arthropod vectors to understand their diversity, host range and evolutionary history as well as to predict new emerging pathogens. The choice of detection method is important, as most of the methods can only detect viruses that have been previously well described. Viral metagenomics is a useful tool to simultaneously identify all the viruses present in a sample, including novel viruses. This review describes vector-borne viruses, their maintenance and emergence in nature, and detection using viral metagenomics.
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