| 1. |
- Andersson, Jan O, et al.
(författare)
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A century of typhus, lice and Rickettsia
- 2000
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Ingår i: Research in Microbiology. - : EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER. - 0923-2508 .- 1769-7123. ; 151:2, s. 143-150
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Tidskriftsartikel (refereegranskat)abstract
- At the beginning of the 20th century, it was discovered at the Pasteur Institute in Tunis that epidemic typhus is transmitted by the human body louse. The complete genome sequence of its causative agent, Rickettsia prowazekii, was determined at Uppsala University in Sweden at the end of the century. In this mini-review, we discuss insights gained from the genome sequence of this fascinating and deadly organism.
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| 2. |
- Andersson, Jan O, et al.
(författare)
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Genome degradation is an ongoing process in Rickettsia
- 1999
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Ingår i: Molecular biology and evolution. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038 .- 1537-1719. ; 16:9, s. 1178-1191
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- To study reductive evolutionary processes in bacterial genomes, we examine sequences in the Rickettsia genomes which are unconstrained by selection and evolve as pseudogenes, one of which is the metK gene, which codes for AdoMet synthetase. Here, we sequenced the metK gene and three surrounding genes in eight different species of the genus Rickettsia. The metK gene was found to contain a high incidence of deletions in six lineages, while the three genes in its surroundings were functionally conserved in all eight lineages. A more drastic example of gene degradation was identified in the metK downstream region, which contained an open reading frame in Rickettsia felis. Remnants of this open reading frame could be reconstructed in five additional species by eliminating sites of frameshift mutations and termination codons. A detailed examination of the two reconstructed genes revealed that deletions strongly predominate over insertions and that there is a strong transition bias for point mutations which is coupled to an excess of GC-to-AT substitutions. Since the molecular evolution of these inactive genes should reflect the rates and patterns of neutral mutations, our results strongly suggest that there is a high spontaneous rate of deletions as well as a strong mutation bias toward AT pairs in the Rickettsia genomes. This may explain the low genomic G + C content (29%), the small genome size (1.1 Mb), and the high noncoding content (24%), as well as the presence of several pseudogenes in the Rickettsia prowazekii genome.
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| 3. |
- Andersson, Jan O, et al.
(författare)
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Genomic rearrangements during evolution of the obligate intracellular parasite Rickettsia prowazekii as inferred from an analysis of 52015 bp nucleotide sequence
- 1997
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Ingår i: Microbiology. - 1350-0872 .- 1465-2080. ; 143:8, s. 2783-2795
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In this study a description is given of the sequence and analysis of 52 kb from the 1.1 Mb genome of Rickettsia prowazekii, a member of the alpha-Proteobacteria. An investigation was made of nucleotide frequencies and amino acid composition patterns of 41 coding sequences, distributed in 10 genomic contigs, of which 32 were found to have putative homologues in the public databases. Overall, the coding content of the individual contigs ranged from 59 to 97%, with a mean of 81%. The genes putatively identified included genes involved in the biosynthesis of nucleotides, macromolecules and cell wall structures as well as citric acid cycle component genes. In addition, a putative identification was made of a member of the regulatory response family of two-component signal transduction systems as well as a gene encoding haemolysin. For one gene, the homologue of metK, an internal stop codon was discovered within a region that is otherwise highly conserved. Comparisons with the genomic structures of Escherichia coli, Haemophilus influenzae and Bacillus subtilis have revealed several atypical gene organization patterns in the R. prowazekii genome. For example, R. prowazekii was found to have a unique arrangement of genes upstream of dnaA in a region that is highly conserved among other microbial genomes and thought to represent the origin of replication of a primordial replicon. The results presented in this paper support the hypothesis that the R. prowazekii genome is a highly derived genome and provide examples of gene order structures that are unique for the Rickettsia.
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| 4. |
- Andersson, Jan O, et al.
(författare)
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Insights into the evolutionary process of genome degradation
- 1999
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Ingår i: Current Opinion in Genetics and Development. - 0959-437X .- 1879-0380. ; 9:6, s. 664-671
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Tidskriftsartikel (refereegranskat)abstract
- Studies of noncoding and pseudogene sequence diversity, particularly in Rickettsia, have begun to reveal the basic principles of genome degradation in microorganisms. Increasingly, studies of genes and genomes suggest that there has been an extensive amount of horizontal gene transfer among microorganisms. As this inflow of genetic material does not seem generally to have resulted in genome size expansions, however, degenerative processes must be at the very least as widespread as horizontal gene transfer. The basic principles of gene degradation and elimination that are being explored in Rickettsia are likely to be of major importance for our understanding of how microbial genomes evolve.
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| 5. |
- Andersson, Jan O, et al.
(författare)
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Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes
- 2001
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Ingår i: Molecular biology and evolution. - 0737-4038 .- 1537-1719. ; 18:5, s. 829-839
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Tidskriftsartikel (refereegranskat)abstract
- Studies of neutrally evolving sequences suggest that differences in eukaryotic genome sizes result from different rates of DNA loss. However, very few pseudogenes have been identified in microbial species, and the processes whereby genes and genomes deteriorate in bacteria remain largely unresolved. The typhus-causing agent, Rickettsia prowazekii, is exceptional in that as much as 24% of its 1.1-Mb genome consists of noncoding DNA and pseudogenes. To test the hypothesis that the noncoding DNA in the R. prowazekii genome represents degraded remnants of ancestral genes, we systematically examined all of the identified pseudogenes and their flanking sequences in three additional Rickettsia species. Consistent with the hypothesis, we observe sequence similarities between genes and pseudogenes in one species and intergenic DNA in another species. We show that the frequencies and average sizes of deletions are larger than insertions in neutrally evolving pseudogene sequences. Our results suggest that inactivated genetic material in the Rickettsia genomes deteriorates spontaneously due to a mutation bias for deletions and that the noncoding sequences represent DNA in the final stages of this degenerative process.
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| 6. |
- Andersson, Pia, et al.
(författare)
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Oral health and nutritional status in a group of geriatric rehabilitation patients
- 2002
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Ingår i: Scandinavian Journal of Caring Sciences. - : Wiley-Blackwell. - 0283-9318 .- 1471-6712. ; 16:3, s. 311-318
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Tidskriftsartikel (refereegranskat)abstract
- The aims of this study were to evaluate the oral health status and nutritional status in a group of geriatric rehabilitation patients, and to analyse the relationship between these two parameters. Nurses at the ward performed structured assessments of oral and nutritional status using the Revised Oral Assessment Guide and the Subjective Global Assessment form in 223 newly admitted patients. Most oral health problems were found among patients who stayed longer at the hospital and were more dependent on help as compared with the healthier patients. Thirty-four per cent of the patients were either severely undernourished, at risk or suspected to be undernourished (UN). Oral health problems were more common among UN patients (p < 0.0005) compared with well-nourished patients. The most frequent oral health problem was found on teeth or dentures (48%). Problems related to the tongue and lips were also common among UN patients (56 and 44%, respectively). Oral health status was correlated (r = 0.32) to nutritional status. Problems with swallowing had the strongest association to the nutritional status (OR 6.05; 95% CI 2.41-15.18). This study demonstrated that poor oral health status was related to undernourishment.
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| 7. |
- Andersson, Siv GE, et al.
(författare)
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The genome sequence of Rickettsia prowazekii and the origin of mitochondria
- 1998
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 396:6707, s. 133-140
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Tidskriftsartikel (refereegranskat)abstract
- We describe here the complete genome sequence (1,111,523 base pairs) of the obligate intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus. This genome contains 834 protein-coding genes. The functional profiles of these genes show similarities to those of mitochondrial genes: no genes required for anaerobic glycolysis are found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R. prowazekii. In effect, ATP production in Rickettsia is the same as that in mitochondria. Many genes involved in the biosynthesis and regulation of biosynthesis of amino acids and nucleosides in free-living bacteria are absent from R. prowazekii and mitochondria. Such genes seem to have been replaced by homologues in the nuclear (host) genome. The R. prowazekii genome contains the highest proportion of non-coding DNA (24%) detected so far in a microbial genome. Such non-coding sequences may be degraded remnants of 'neutralized' genes that await elimination from the genome. Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondria than is any other microbe studied so far.
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| 8. |
- Backhaus, Erik, et al.
(författare)
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Antimicrobial susceptibility of invasive pneumococcal isolates from a region in south-west Sweden 1998-2001.
- 2007
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Ingår i: Scandinavian journal of infectious diseases. - : Informa UK Limited. - 0036-5548 .- 1651-1980. ; 39:1, s. 19-27
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Tidskriftsartikel (refereegranskat)abstract
- Invasive disease caused by antibiotic resistant pneumococci is a worldwide problem. All invasive pneumococcal strains in an area of south-west Sweden with 1.7 million inhabitants were collected prospectively during 1998-2001. Minimum inhibitory concentrations (MICs) were determined by E-test and correlated to serotypes and clinical characteristics. Of 827 strains, 744 (90%) were susceptible (S) to all agents tested and 83 (10%) were indeterminate (I) or resistant (R) to at least 1 agent. 22 isolates (2.7%) were I to penicillin (MIC >0.06 to < or = 1.0 mg/l), but none were R (MIC >1.0 mg/l). Numbers and proportions of decreased susceptibility against other agents tested were as follows: erythromycin R: 30 (3.6%), clindamycin R: 6 (0.7%), tetracycline R: 16 (1.9%), moxifloxacin R: 1 (0.1%), cotrimoxazole I: 17 (2%) and R: 31(4%). Non-susceptibility to at least 1 agent was not correlated with age, clinical manifestation, underlying diseases and outcome. The serotype distribution differed between non-susceptible and susceptible strains. The serotypes in the 7-valent pneumococcal conjugate vaccine covered 42% of all infections and 73% of those caused by non-susceptible strains. In conclusion, the impact of antibiotic resistance in invasive pneumococcal disease remains limited in south-west Sweden.
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| 9. |
- Dyrhage, Karl
(författare)
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Multi-omics investigation into bacterial evolution
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The focus of this thesis is the investigation of the evolution and cellular processes of Tuwongella immobilis and Apilactobacillus kunkeei, two bacterial species with different levels of genomic and cellular complexity, using a multi-omics approach.In the first study we examined the proteome of T. immobilis with LC-MS/MS after fractionation by differential solubilisation, yielding fractions corresponding to the cytoplasm, inner membrane, and outer membrane. The experiment was repeated with Escherichia coli and the results were compared. T. immobilis had five times as many predicted cytoplasmic proteins in the most hydrophobic fraction as E. coli. Among these are innovations in the Planctomycetota lineage and protein families that have undergone recent paralogisation followed by domain shuffling, including many enzymes related to information processing.The remaining three studies dealt with honeybee symbiont A. kunkeei. In the first of these, we sequenced and compared the chromosomal and extrachromosomal content of 102 novel A. kunkeei strains. We found that A. kunkeei has an open pangenome and an active set of transposable elements. Within the population we discovered three plasmids between 19.5 and 32.9 kb, one of which codes for enzymes involved in the synthesis of the antimicrobial compound kunkecin A which inhibits growth of the bee pathogen Melisococcus plutonius.In the next study we collected transcriptomic, proteomic, and metabolomic data from two growth phases from A. kunkeei strain A1401 and mapped the results to a metabolic pathway model. Enzymes involved in fermentation of fructose were highly expressed during the exponential growth phase. Enzymes involved in UMP biosynthesis were upregulated during stationary phase, as were protein involved in stress response and detoxification.The last study concerned the secretome of A. kunkeei. We characterised two types of extracellular particles from A. kunkeei strains A1401 and A0901. One type of particle was found to be proteinaceous, while the other type constituted membrane vesicles containing RNA. Comparison of transcriptomic data from the membrane vesicles and whole cells showed that the packing of the RNA was largely untargeted, but with a bias towards highly expressed mRNAs. We suggest that the cell uses membrane vesicles as a mechanism to get rid of superfluous mRNAs after rapid-response overexpression.Together these studies provide insights into the processes driving evolution in T. immobilis and A. kunkeei, and generate several testable hypotheses for future studies.
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| 10. |
- Fuxelius, Hans-Henrik, 1968-
(författare)
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Methods and Applications in Comparative Bacterial Genomics
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Comparative studies of bacterial genomes, now counting in the hundreds, generate massive amounts of information. In order to support a systematic and efficient approach to genomic analyses, a database driven system with graphic visualization of genomic properties was developed - GenComp. The software was applied to studies of obligate intracellular bacteria. In all studies, ORFs were extracted and grouped into ORF-families. Based on gene order synteny, orthologous clusters of core genes and variable spacer ORFs were identified and extracted for alignments and computation of substitution frequencies. The software was applied to the genomes of six Chlamydia trachomatis strains to identify the most rapidly evolving genes. Five genes were chosen for genotyping, and close to a 3-fold higher discrimination capacity was achieved than that of serotypes. With GenComp as the backbone, a massive comparative analysis were performed on the variable gene set in the Rickettsiaceae, which includes Rickettsia prowazekii and Orientia tsutsugamushi, the agents of epidemic and scrub typhus, respectively. O. tsutsugamushi has the most exceptional bacterial genome identified to date; the 2.2 Mb genome is 200-fold more repeated than the 1.1 Mb R. prowazekii genome due to an extensive proliferation of conjugative type IV secretion systems and associated genes. GenComp identified 688 core genes that are conserved across 7 closely related Rickettsia genomes along with a set of 469 variably present genes with homologs in other species. The analysis indicates that up to 70% of the extensively degraded and variably present genes represent mobile genetic elements and genes putatively acquired by horizontal gene transfer. This explains the paradox of the high pseudogene load in the small Rickettsia genomes. This study demonstrates that GenComp provides an efficient system for pseudogene identification and may help distinguish genes from spurious ORFs in the many pan-genome sequencing projects going on worldwide.
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| 11. |
- Ye, Weihua, et al.
(författare)
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Folded Alpha Helical Putative New Proteins from Apilactobacillus kunkeei
- 2024
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Ingår i: Journal of Molecular Biology. - : Elsevier. - 0022-2836 .- 1089-8638. ; 436:6
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Tidskriftsartikel (refereegranskat)abstract
- The emergence of new proteins is a central question in biology. Most tertiary protein folds known to date appear to have an ancient origin, but it is clear from bioinformatic analyses that new proteins continuously emerge in all organismal groups. However, there is a paucity of experimental data on new proteins regarding their structure and biophysical properties. We performed a detailed phylogenetic analysis and identified 48 putative open reading frames in the honeybee -associated bacterium Apilactobacillus kunkeei for which no or few homologs could be identified in closely -related species, suggesting that they could be relatively new on an evolutionary time scale and represent recently evolved proteins. Using circular dichroism-, fluorescence- and nuclear magnetic resonance (NMR) spectroscopy we investigated six of these proteins and show that they are not intrinsically disordered, but populate alpha -helical dominated folded states with relatively low thermodynamic stability (0-3 kcal/mol). The NMR and biophysical data demonstrate that small new proteins readily adopt simple folded conformations suggesting that more complex tertiary structures can be continuously re -invented during evolution by fusion of such simple secondary structure elements. These findings have implications for the general view on protein evolution, where de novo emergence of folded proteins may be a common event.
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| 12. |
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| 13. |
- Alsmark, Cecilia M., et al.
(författare)
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The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae
- 2004
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 101:26, s. 9716-9721
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Tidskriftsartikel (refereegranskat)abstract
- We present the complete genomes of two human pathogens, Bartonella quintana (1,581,384 bp) and Bartonella henselae (1,931,047 bp). The two pathogens maintain several similarities in being transmitted by insect vectors, using mammalian reservoirs, infecting similar cell types (endothelial cells and erythrocytes) and causing vasculoproliferative changes in immunocompromised hosts. A primary difference between the two pathogens is their reservoir ecology. Whereas B. quintana is a specialist, using only the human as a reservoir, B. henselae is more promiscuous and is frequently isolated from both cats and humans. Genome comparison elucidated a high degree of overall similarity with major differences being B. henselae specific genomic islands coding for filamentous hemagglutinin, and evidence of extensive genome reduction in B. quintana, reminiscent of that found in Rickettsia prowazekii. Both genomes are reduced versions of chromosome I from the highly related pathogen Brucella melitensis. Flanked by two rRNA operons is a segment with similarity to genes located on chromosome II of B. melitensis, suggesting that it was acquired by integration of megareplicon DNA in a common ancestor of the two Bartonella species. Comparisons of the vector-host ecology of these organisms suggest that the utilization of host-restricted vectors is associated with accelerated rates of genome degradation and may explain why human pathogens transmitted by specialist vectors are outnumbered by zoonotic agents, which use vectors of broad host ranges.
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| 14. |
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| 15. |
- Andersson, Agneta, et al.
(författare)
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Fatty acid composition of skeletal muscle reflects dietary fat compositionin humans
- 2002
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Ingår i: American Journal of Clinical Nutrition. - 0002-9165 .- 1938-3207. ; 76:6, s. 1222-1229
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Tidskriftsartikel (refereegranskat)abstract
- Background: It is still unknown whether the fatty acid composition of human skeletal muscle lipids is directly influenced by the fat composition of the diet.Objective: We investigated whether the fatty acid composition of the diet is reflected in the fatty acid profile of skeletal muscle phospholipids and triacylglycerols.Design: Thirty-two healthy adults (25 men and 7 women) included in a larger controlled, multicenter dietary study were randomly assigned to diets containing a high proportion of either saturated fatty acids (SFAs) [total fat, 36% of energy; SFAs, 18% of energy; monounsaturated fatty acids (MUFAs), 10% of energy] or MUFAs (total fat, 35% of energy; SFAs, 9% of energy; MUFAs, 19% of energy) for 3 mo. Within each diet group, there was a second random assignment to supplementation with fish oil capsules [containing 3.6 g n−3 fatty acids/d; 2.4 g eicosapentaenoic acid (20:5n−3) and docosahexaenoic acid (22:6n−3)] or placebo. A muscle biopsy sample was taken from the vastus lateralis muscle after the diet period. Parallel analyses of diet and supplementation effects were performed.Results: The proportions of myristic (14:0), pentadecanoic (15:0), heptadecanoic (17:0), and palmitoleic (16:1n−7) acids in the skeletal muscle phospholipids were higher and the proportion of oleic acid (18:1n−9) was lower in the SFA group than in the MUFA group. The proportion of total n−3 fatty acids in the muscle phospholipids was ≈2.5 times higher, with a 5 times higher proportion of eicosapentaenoic acid (20:5n−3), in subjects supplemented with n−3 fatty acids than in those given placebo. Similar differences were observed in the skeletal muscle triacylglycerols.Conclusion: The fatty acid composition of skeletal muscle lipids reflects the fatty acid composition of the diet in healthy men and women.
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| 16. |
- Andersson, Agneta, et al.
(författare)
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Key role of phosphorus and nitrogen in regulating cyanobacterial community composition in the northern Baltic Sea
- 2015
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Ingår i: Estuarine, Coastal and Shelf Science. - : Elsevier BV. - 0272-7714 .- 1096-0015. ; 164, s. 161-171
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Tidskriftsartikel (refereegranskat)abstract
- Despite cyanobacteria being a key phytoplankton group in the Baltic Sea, the factors governing their community structure are still poorly understood. Here, we studied the occurrence of the orders Chroococcales, Oscillatoriales and Nostocales, and potentially explanatory variables at five locations in the northern Baltic Sea from June September, 1998-2012. Cyanobacteria constituted 1-36% of the total phytoplankton biomass along the north south gradient. In the Bothnian Bay, Chroococcales and Oscillatoriales dominated the cyanobacterial community, whereas in the Bothnian Sea and northern Baltic Proper, Nostocales was the dominant group. The dominance of Chroococcales was coupled to low salinity and low total phosphorus, whereas Oscillatoriales correlated with high total nitrogen and low salinity. Nostocales correlated to high total phosphorus, inorganic phosphorus and salinity. Chroococcales showed an increase over time in the offshore Bothnian Bay, whereas Nostocales increased in the coastal Bothnian Sea and coastal Baltic Proper. The increase of Nostocales in the coastal Bothnian Sea was explained by a rise in total phosphorus and decrease in dissolved inorganic nitrogen compared to an increase of total nitrogen and phosphorus in the coastal Baltic Proper. No significant trends were observed in the cyanobacterial community in the offshore Bothnian Sea and the offshore northern Baltic Proper. We concluded that Chroococcales may be a useful indicator for increased phosphorus levels in waters with low phosphorus concentrations, whereas Nostocales could be used as a quality indicator for increasing phosphorus concentrations in waters with low inorganic N/P ratios (< 20), such as in the coastal Bothnian Sea and Baltic Proper.
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| 17. |
- Andersson, Agneta, et al.
(författare)
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Mer fosfor ger mer cyanobakterier i norra Östersjön
- 2013
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Ingår i: Havet. - : Havsmiljöinstitutet. ; , s. 51-54
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Forskningsöversikt (övrigt vetenskapligt/konstnärligt)abstract
- I flera områden i norra Östersjön har cyanobakterierna ökat under de senaste tio till femton åren. I Bottenhavets och Egentliga Östersjöns kustområden ökar de kvävefixerande cyanobakterierna. I Bottenvikens utsjö är det den småcelliga och kolonibildande gruppen Chroococcales som blir fler. Förändringarna beror i flera fall på ökande halter av fosfor.
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| 18. |
- Andersson, Agneta, et al.
(författare)
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Metabarcoding vs Microscopy - comparison of methods to monitor phytoplankton communities
- 2023
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Ingår i: ACS - ES & T Water. - : American Chemical Society (ACS). - 2690-0637. ; 3:8, s. 2671-2680
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Phytoplankton are used worldwide to monitor environmental status in aquatic systems. Long-time series of microscopy-analyzed phytoplankton are available from many monitoring stations. The microscopy-method is however time consuming and has short-comings. DNA metabarcoding has been suggested as an alternative method, but the consistency between different methods need further investigation. We performed a comparative study of microscopy and metabarcoding analyzing micro- and nanophytoplankton. For metabarcoding, 25-1000 ml seawater were filtered, DNA extracted and the 18S and 16S rRNA gene amplicons sequenced. For microscopy, based on the Utermöhl method we evaluated the use of three metrics: abundance, biovolume and carbon biomass. At the genus, species, and unidentified taxa level, metabarcoding generally showed higher taxonomic diversity than microscopy, and diversity was already captured at the lowest filtration volume tested, 25 ml. Metabarcoding and microscopy displayed relatively similar distribution pattern at the group level. The results showed that the relative abundances of the 18S rRNA amplicon at the group level best fitted the microscopy carbon biomass metric. The results are promising for implementing DNA metabarcoding as a complement to microscopy in phytoplankton monitoring, especially if databases would be improved and group level indexes could be applied to classify the environmental state of water bodies.
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| 19. |
- Andersson, Agneta, et al.
(författare)
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Oförändrad insulinkänslighet och lipidperoxidation efter ökat intag av fullkornsprodukter hos friska män och kvinnor.
- 2006
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Ingår i: Livsmedelsforskardagarna.
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Konferensbidrag (populärvet., debatt m.m.)abstract
- Flertalet epidemilogiska studier har visat positiva hälsoeffekter av ett högt intag av fullkornsprodukter. Framförallt är en minska risk för hjärtinfarkt/sjukdom visad, och datatalar även för en minskad risk för typ 2 diabetes. Mekanismerna bakom fullkornets positiva effekter är dock fortfarande oklara. Såväl en förbättrad insulinkänslighet som en minskad förekomst av lipidperoxidation och inflammation har föreslagits, vilket vi därför önskade undersöka i denna studie.I en randomiserad cross-over design deltog 30 lätt överviktiga (BMI 282) kvinnor (n=22) och män (n=8). Under två på varandra följande 6 veckors perioder fick deltagarna antingen cerealieprodukter med fullkorn eller utan fullkorn. En standardiserad mängd (3 skivor mjukt bröd, 2 skivor hårt bröd, 1 portion musli/gryn och 1 portion pasta/ris) inkluderades dagligen i deras vanliga kost. Perifer insulinkänslighet mättes med euglykemisk hyperinsulinemisk clampteknik. Lipidperoxidationsmarkören 8-iso-PGF2 mättes i urin och inflammationsmarkörerna CRP och IL-6 mättes i plasma. Kostinterventionen monitorerades med hjälp av vägda kostregisteringar och dagboksnoteringar.Kostregistreringarna bekräftade ett högre intag av fiber och flertalet mineralämnen under fullkornsperioden jämfört med icke-fullkornsperioden. Vi fann dock ingen förbättring av insulinkänsligheten och inte heller någon förändring av lipidperoxidation eller inflammationsmarkörer.Att ersätta icke-fullkorns produkter med fullkorn under en 6 veckors period hos vuxna lätt överviktiga friska män och kvinnor gav således ingen mätbar effekt på vare sig insulinkänslighet, lipidperoxidation eller inflammationsmarkörer. Frågan om vilka mekanismerna som ligger bakom de positiva hälsoeffekterna av fullkornsprodukter kvarstår och längre koststudier på deltagare med varierande metaboltstatus behövs.
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| 20. |
- Andersson, Agneta, et al.
(författare)
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Strategi för kontrollerande övervakning av Bottenhavets vattendistrikt
- 2008
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Ett pelagialprogram har tagits fram för övervakning i relativt opåverkade referensområden i kustvattentyperna 16 t.o.m.19 i Bottemhavet. Programmet bör kunna ligga till grund för uppföljning av internationella, nationella och regionala miljömål samt följa upp ekologisk status. Den rumsliga variationen samt mellanårsvariationen hos pelagiala variabler i Bottenhavsområdet har använts som utgångspunkt för att beräkna provtagningsbehovet. Det föreslagna programmet innebär att mellan 48 och 60 provtagningar årsperiod, varefter ekologisk status kan bedömas. Designen gör det möjligt att med 80 % säkerhet bedöma ekologisk status med mätdata som ligger minst 20 % från klassgränserna. Mätprogrammet är designat för provtagningar -årsperiod. Stationer har slumpats ut i de olika typerna, och förslag på årliga provtagningslokaler anges i rapporten. Eftersom djupet vid de olika stationerna varierar, bör de flesta pelagiala variablerna provtas vid ett diskret djup i övre delen av vattenmassan, t.ex. 1 m djup. Av vetenskapliga och ekonomiska skäl är det viktigt att pelagialprogrammet samordnas för hela Bottenhavet.För mjukbottenfauna bedöms det befintliga integrerade programmet för trendanalys i Bottenhavet kunna tillgodose Vattendirektivets behov för kontrollerande övervakning i distriktet. Detta under förutsättning att Sundsvallsbuktens program fortsätter och att de nya nationella och regionala provtagningsområdena i södra Bottenhavet (Gräsö) etableras och drivs. Dimensioneringen av nuvarande nationellt och regionalt bottenfaunaprogram och områdesövervakning men har även visat sig vara väl anpassat för bedömningar inom ramen för Vattendirektivet. Enligt bedömningsgrunden bör minst 5 stationer användas för klassning av ekologisk status. Dessa stationer måste dock inte ligga inom samma vattenförekomst, utan kan vara lokaliserade i angränsande vattenförekomster. Den ekologiska statusen för mjukbottenfauna i enskilda vattenförekomster klassas genom extrapolering med hjälp av data från närbelägna områden med liknande bottenmiljö och påverkansgrad.Befintlig fiskebeståndsövervakning föreslås fortlöpa för att möjliggöra uppföljning av förändringar. En utökning av antalet övervakningsområden föreslås dock för att upprätta minst ett referensområde per inre och yttre kustvattentyp. En kombination av stratifierad och slumpmässig övervakning av fiskebestånden enligt nuvarande strategi föreslås, där djupintervallen stratifieras medan stationerna slumpas ut i respektive djupintervall.Provfiske och provtagning för miljögiftsanalys av fisk bör samordnas till samma provtagningstillfälle. Vidare bör den modell för samfinansiering och samordning som idag tillämpas av kustlänen i Bottniska viken för övervakning av fiskbestånd, samt och miljögiftsövervakning av fisk, fortlöpa även framöver.De ämnen som ingår i det pågående nationella programmet för miljögifter i fisk bör mätas även i de nya föreslagna områdena. När EU:s dotterdirektiv för prioriterade ämnen är beslutat och Vattenmyndigheterna fastställt miljökvalitetsnormer för särskilda förorenande ämnen, bör en översyn göras och ytterligare ämnen som är aktuella för Bottenhavet införlivas i övervakningsprogrammet. Miljögiftsövervakning i fisk bedöms kunna mätas med ett maximalt avstånd på 75 km mellan stationsområdena. Bedömning och extrapolera mätvärdena.För samtliga delprogram har en grova uppskattningar av kostnader för genomförandet gjorts.
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| 21. |
- Andersson, Agneta, et al.
(författare)
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Whole-grain foods do not affect insulin sensitivity or markers of lipid peroxidation and inflammation in healthy, moderately overweight subjects
- 2007
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Ingår i: Journal of Nutrition. - 0022-3166 .- 1541-6100. ; 137:6, s. 1401-1407
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Tidskriftsartikel (refereegranskat)abstract
- High intakes of whole grain foods are inversely related to the incidence of coronary heart diseases and type 2 diabetes, but the mechanisms remain unclear. Our study aimed to evaluate the effects of a diet rich in whole grains compared with a diet containing the same amount of refined grains on insulin sensitivity and markers of lipid peroxidation and inflammation. In a randomized crossover study, 22 women and 8 men (BMI 28 +/- 2) were given either whole-grain or refined-grain products (3 bread slices, 2 crisp bread slices, 1 portion muesli, and 1 portion pasta) to include in their habitual daily diet for two 6-wk periods. Peripheral insulin sensitivity was determined by euglycemic hyperinsulinemic clamp tests. 8-Iso-prostaglandin F(2alpha) (8-iso PGF(2alpha)), an F(2)-isoprostane, was measured in the urine as a marker of lipid peroxidation, and highly sensitive C-reactive protein and IL-6 were analyzed in plasma as markers of inflammation. Peripheral insulin sensitivity [mg glucose . kg body wt(-1) . min(-1) per unit plasma insulin (mU/L) x 100] did not improve when subjects consumed whole-grain products (6.8 +/- 3.0 at baseline and 6.5 +/- 2.7 after 6 wk) or refined products (6.4 +/- 2.9 and 6.9 +/- 3.2, respectively) and there were no differences between the 2 periods. Whole-grain consumption also did not affect 8-iso-PGF(2alpha) in urine, IL-6 and C-reactive protein in plasma, blood pressure, or serum lipid concentrations. In conclusion, substitution of whole grains (mainly based on milled wheat) for refined-grain products in the habitual daily diet of healthy moderately overweight adults for 6-wk did not affect insulin sensitivity or markers of lipid peroxidation and inflammation.
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| 22. |
- Andersson, Agneta, et al.
(författare)
-
Ökat intag av fullkornsprodukter. Effekter på insulinkänslighet, lipidperoxidation och inflammationsmarkörer?
- 2006
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Ingår i: Svenska Läkarsällskapets Riksstämma.
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Konferensbidrag (populärvet., debatt m.m.)abstract
- Bakgrund: Flertalet epidemiologiska studier har visat positiva hälsoeffekter av ett högt intag av fullkornsprodukter. Framförallt är en minskad risk för hjärtinfarkt/sjukdom visad, men data talar även för en minskad risk för typ 2 diabetes. Mekanismerna bakom fullkornets positiva effekter är dock fortfarande oklara. Såväl en förbättrad insulinkänslighet som en minskad förekomst av lipidperoxidation och inflammation har föreslagits, vilket vi önskade undersöka i denna studie.Metod: I en randomiserad cross-over design deltog 30 lätt överviktiga (BMI 282) kvinnor (n=22) och män (n=8). Under två på varandra följande 6-veckors perioder fick deltagarna antingen cerealieprodukter med fullkorn eller utan fullkorn. En standardiserad mängd (3 skivor mjukt bröd, 2 skivor hårt bröd, 1 portion musli/gryn och 1 portion pasta/ris) inkluderades dagligen i deras vanliga kost. Perifer insulinkänslighet mättes med euglykemisk hyperinsulinemisk clampteknik. Lipidperoxidationsmarkören 8-iso-PGF2 mättes i urin och inflammationsmarkörerna CRP och IL-6 mättes i plasma. Kostinterventionen monitorerades med hjälp av vägda kostregisteringar och dagboksnoteringar.Resultat: Kostregistreringarna bekräftade ett högre intag av fiber och flertalet mineralämnen under fullkornsperioden jämfört med icke-fullkornsperioden. Vi fann dock ingen förbättring av insulinkänsligheten och inte heller någon förändring av lipidperoxidation eller inflammationsmarkörer.Sammanfattning: Att ersätta icke-fullkorns produkter med fullkorn under en 6-veckors period hos vuxna lätt överviktiga friska män och kvinnor gav ingen mätbar effekt på insulinkänslighet, lipidperoxidation eller inflammationsmarkörer. Frågan om vilka mekanismerna som ligger bakom de positiva hälsoeffekterna av fullkornsprodukter kvarstår och längre koststudier på deltagare med varierande metaboltstatus behövs.
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| 23. |
- Andersson, Evert, et al.
(författare)
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On the environmental performance of a high-speed train
- 2014
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Ingår i: International Journal of Rail transportation. - : Taylor & Francis Group. - 2324-8378 .- 2324-8386. ; 2:1, s. 59-66
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Tidskriftsartikel (refereegranskat)abstract
- Environmental performance is one of the major considerations of future high-speed trains. Two main issues have been closely investigated in the Green Train programme, namely (1) energy use and (2) external noise. Analysis, development and testing in the Green Train programme have focused primarily on speeds up to 250 km/h, although the energy issues have also been studied at top speeds up to 320 km/h. The energy use is estimated for both long-distance trains with few stops and for fast regional services with relatively tight underway stops. These estimations result in an energy use of 46–62 Wh per passenger-km – or 30–40 Wh per seat-km – accounted as electricity taken from the public electric power grid. Improved aerodynamic performance, efficient space utilization, electric regenerative brakes, eco-driving advice and improved energy efficiency in the propulsion system make this possible. Trackside noise has also been analysed and tested in the programme. In order to maintain the same or lower noise level at 250 km/h as at lower speeds with current trains, a number of measures are proposed. These include bogie skirts, wheel absorbers and careful aerodynamic design of the front area and of all protruding objects. In sensitive residential areas, further improvement may be achieved with rail absorbers or low trackside screens.
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| 24. |
- Andersson, Gun, et al.
(författare)
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A chance to live: Women's experiences of living with a colostomy after rectal cancer surgery
- 2010
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Ingår i: International Journal of Nursing Practice. - 1322-7114 .- 1440-172X. ; 16:6, s. 603-608
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to describe women's experience of living with a colostomy after rectal cancer surgery. Interviews with five women about their experiences were subjected to thematic content analysis. The findings showed that receiving a cancer diagnosis gave rise to thoughts about life and death. For the women to feel comfortable, the information and health-care measures need to focus on supporting them through the entire process, also when the treatment is completed. After the surgery, the women adjusted to living with colostomy and carried on as before the cancer diagnosis, but they constantly worried about leakage or flatulence. The women were happy to have survived the cancer and this realization helped them to accept and have a good life with colostomy. In conclusion, women with colostomy because of rectal surgery need specific rehabilitation and nursing care that focuses on adjustment to temporary or permanent changes in life.
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| 25. |
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| 26. |
- Andersson, Gerhard, 1966-, et al.
(författare)
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Memories of significant episodes in child psychotherapy : An autobiographical memory approach
- 2006
-
Ingår i: Psychology and Psychotherapy. - 1476-0835 .- 2044-8341. ; 79:2, s. 229-236
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Tidskriftsartikel (refereegranskat)abstract
- In this study, child psychotherapists (N = 31) were asked to retrieve emotionally valenced therapy episodes by using an autobiographical memory approach, with cue words to elicit specific therapy episodes (e.g. irritated, ashamed, loving, and elated). One group of teachers for the disabled (N = 10) and one group of music therapists (N = 9) were also tested and served as comparison groups. Results showed that all participants were able to retrieve memories of episodes. When asked to rate each memory, negative memories were returned to less often, and overall positive memories were rated as more easy to recall and more vivid. Memories derived from positive cue words were also judged to have a more positive compared with negative importance for outcome. Surprisingly, memories derived from the cue word irritated were seen as having more positive than negative importance for outcome. Finally, we checked memory specificity for each memory derived. A high degree of specificity was found overall (72-88%). In conclusion, cue words might be a useful way to generate specific memories of therapy episodes in future research. © 2006 The British Psychological Society.
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| 27. |
- Andersson, Hannah, et al.
(författare)
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Oral Administration of Lactobacillus plantarum 299v Reduces Cortisol Levels in Human Saliva during Examination Induced Stress : A Randomized, Double-Blind Controlled Trial
- 2016
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Ingår i: International Journal of Microbiology. - : Hindawi Publishing Corporation. - 1687-918X .- 1687-9198. ; 2016
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Tidskriftsartikel (refereegranskat)abstract
- Objective. To clarify the effect of Lactobacillus plantarum 299v on the salivary cortisol and salivary IgA levels in young adults under examination stress. Design. Forty-one students with an upcoming academic exam were included in a randomized double-blind, placebo-controlled study. The probiotic bacteria or the placebo product was administered in capsules once a day during 14 days. Saliva was collected and a perceived stress test was filled out at each sampling occasion. Saliva was collected for cortisol analysis by Electrochemiluminescence Immunoassay (ECLI) and salivary IgA was analysed by Enzyme-Linked Immunosorbent Assay (ELISA). Abundance of lactobacilli was evaluated by cultivation of saliva on selective medium and identification of L. plantarum 299v was done on randomly selected colonies by a random amplification of polymorphic DNA (RAPD) typing. Results. A significant difference in cortisol levels was found between the treatment group and the placebo group (P < 0.05), together with a significant increase in levels of lactobacilli in the treatment group compared with the placebo group (P < 0.001). No significant changes were found for salivary IgA. Conclusion. A probiotic bacterium with ability to reduce symptoms of irritable bowel syndrome (IBS) prohibited increased levels of the stress marker cortisol during the examination period. The registration number of the study is NCT02974894, and the study is registered at ClinicalTrials.gov.
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| 28. |
- Andersson, Kristina E, et al.
(författare)
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Diverse effects of oats on cholesterol metabolism in C57BL/6 mice correlate with expression of hepatic bile acid-producing enzymes.
- 2013
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Ingår i: European Journal of Nutrition. - : Springer Science and Business Media LLC. - 1436-6215 .- 1436-6207. ; 52:7, s. 1755-1769
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: We previously reported that two substrains of C57BL/6 mice respond differently to oats with respect to reduction in plasma cholesterol. Analysis of this difference might offer clues to mechanisms behind the cholesterol-lowering effect of oats. Here, we address the possible roles of hepatic steroid metabolism and the intestinal microbiota in this respect. METHODS: Female C57BL/6 mice were fed an atherogenic diet with oat bran (27 %) or control fibres for 4 weeks. RESULTS: C57BL/6 NCrl mice responded to oat bran with 19 ± 1 % (P < 0.001) lower plasma cholesterol, 40 ± 5 % (P < 0.01) higher excretion of bile acids and increased expression of the bile acid-producing hepatic enzymes CYP7A1 and CYP8B1, but none of these effects were found in C57BL/6JBomTac mice. However, on control diet, C57BL/6JBomTac had tenfold higher expression of CYP7A1 and levels of hepatic cholesterol esters than C57BL/6NCrl mice. Plasma levels of fructosamine indicated improved glycemic control by oat bran in C57BL/6NCrl but not in C57BL/6JBomTac. C57BL/6JBomTac had higher intestinal microbiota diversity, but lower numbers of Enterobacteriaceae, Akkermansia and Bacteroides Fragilis than C57BL/6NCrl mice. Oat bran increased bacterial numbers in both substrains. Microbiota diversity was reduced by oats in C57BL/6JBomTac, but unaffected in C57BL/6NCrl. CONCLUSIONS: Our data do not support a connection between altered microbiota diversity and reduced plasma cholesterol, but the bacterial composition in the intestine may influence the effects of added fibres. The cholesterol-lowering properties of oats involve increased production of bile acids via the classical pathway with up-regulation of CYP7A1 and CYP8B1. Altered cholesterol or bile acid metabolism may interfere with the potential of oats to reduce plasma cholesterol.
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| 29. |
- Andersson, Mona, 1939-
(författare)
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The early childhood environment rating scale (ECERS) as a tool in evaluating and improving quality in preschools
- 1999
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Author and title: Andersson Mona: The Early Childhood Environment Rating Scale (ECERS) as a Tool in Evaluating and Improving Quality in Preschools. Key words: Preschool, preschool classroom, environmental quality, consciousness, process quality, self evaluation, standardization, validity, reliability, quasi-experiment.This is an empirical study exploring the use of the Early Childhood Environment Rating Scale (ECERS) for the evaluation of environmental quality in preschools.A standardization of the ECERS to Swedish preschools has been carried out. The procedures and findings of this standardization include several tests performed to ensure that the Swedish version of the ECERS would be both valid and reliable.The main hypothesis in this study is that the ECERS can be used to improve environmental quality. This hypothesis was tested in a quasi-experiment. Three separate samples in different preschools were chosen: a Control group, an Information group and an Intervention group. These three groups were evaluated by an independent evaluator before and after the study. The Control group received no information about the ECERS. The Information group as well as the Intervention group received information about the possibility of using the ECERS as a means for the staff to improve quality. In addition, the Intervention group was allowed extra resources such as two hours a month for discussions concerning the results of individual evaluations made by the staff in each classroom.The findings showed an improvement in environmental quality, in the Information group from a mean value of 3.8 to 4.6. In the Intervention group the improvement was even more substantial, from 3.2 to 4.7 whereas the Control group showed a small improvement of 4.1 to 4.3. A statistical sign test of significance was carried out. The changes in the Control group were not significant, while the changes in the Information as well as the Intervention groups were found to be significant at the 95 percent level. It seems as if the hypothesis, that the use of the ECERS could improve environmental quality in preschools, is verified.In supplementary questionnaires and interviews, it was documented that preschool teachers could make better use of their potential competence as they became more conscious of it through the use of the ECERS.
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| 30. |
- Andersson, Siv Folkhammar, et al.
(författare)
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Arthritis management in primary care : A study of physiotherapists' current practice, educational needs and adherence to national guidelines
- 2017
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Ingår i: Musculoskeletal Care. - Chichester : John Wiley & Sons. - 1478-2189 .- 1557-0681. ; 15:4, s. 333-340
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: With an increasing number of patients with osteoarthritis (OA) and rheumatoid arthritis (RA) in primary care, our aim was to investigate arthritis-related practice in physiotherapy and to study adherence to evidence-based care.METHODS: Seventy physiotherapists (PTs) working in primary care were emailed a questionnaire to investigate current practice and the number of roles assumed by PTs, the degree of confidence, educational needs and adherence to national guidelines in managing patients with OA or RA. Interventions supported by national guidelines were compared with reports of treatment modalities in the questionnaire.RESULTS: Sixty-four (91%) PTs responded, and they reported a higher degree of confidence in assessment, treatment and education of patients with OA than for those with RA (p < 0.001). The total number of roles assumed by the PTs was higher in the management of OA than for RA (p < 0.001). PTs who assumed a greater number of roles also reported a stronger degree of confidence in assessing OA (p = 0.036). Those who assumed fewer roles also reported less confidence in RA treatment (p = 0.045). Recommendations in the guidelines were followed by the majority of PTs for eight of 11 treatment modalities in OA and for six of six in RA.CONCLUSIONS: PTs reported a lower degree of confidence and the assumption of fewer roles in managing patients with RA compared with OA. There was good adherence to the national guidelines for almost all the treatment modalities listed. Even so, the results indicate a need for education, especially in chronic inflammatory arthritis care.
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| 31. |
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| 32. |
- Andersson, Siv G E, et al.
(författare)
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Comparative genomics of microbial pathogens and symbionts.
- 2002
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Ingår i: Bioinformatics. - 1367-4803 .- 1367-4811. ; 18 Suppl 2, s. S17-
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Tidskriftsartikel (refereegranskat)abstract
- We are interested in quantifying the contribution of gene acquisition, loss, expansion and rearrangements to the evolution of microbial genomes. Here, we discuss factors influencing microbial genome divergence based on pair-wise genome comparisons of closely related strains and species with different lifestyles. A particular focus is on intracellular pathogens and symbionts of the genera Rickettsia, Bartonella and BUCHNERA: Extensive gene loss and restricted access to phage and plasmid pools may provide an explanation for why single host pathogens are normally less successful than multihost pathogens. We note that species-specific genes tend to be shorter than orthologous genes, suggesting that a fraction of these may represent fossil-orfs, as also supported by multiple sequence alignments among species. The results of our genome comparisons are placed in the context of phylogenomic analyses of alpha and gamma proteobacteria. We highlight artefacts caused by different rates and patterns of mutations, suggesting that atypical phylogenetic placements can not a priori be taken as evidence for horizontal gene transfer events. The flexibility in genome structure among free-living microbes contrasts with the extreme stability observed for the small genomes of aphid endosymbionts, in which no rearrangements or inflow of genetic material have occurred during the past 50 millions years (1). Taken together, the results suggest that genomic stability correlate with the content of repeated sequences and mobile genetic elements, and thereby indirectly with bacterial lifestyles.
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| 33. |
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| 34. |
- Andersson, Siv G. E.
(författare)
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Stress management strategies in single bacterial cells
- 2016
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 113:15, s. 3921-3923
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 35. |
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| 36. |
- Andersson, Siv, et al.
(författare)
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On the origin of mitochondria: a genomics perspective.
- 2003
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Ingår i: Philosophical Transactions of the Royal Society B: Biological Sciences. - : The Royal Society. - 1471-2970. ; 358:1429, s. 165-177
-
Tidskriftsartikel (refereegranskat)abstract
- The availability of complete genome sequence data from both bacteria and eukaryotes provides information about the contribution of bacterial genes to the origin and evolution of mitochondria. Phylogenetic analyses based on genes located in the mitochondrial genome indicate that these genes originated from within the f-proteobacteria. A number of ancestral bacterial genes have also been transferred from the mitochondrial to the nuclear genome, as evidenced by the presence of orthologous genes in the mitochondrial genome in some species and in the nuclear genome of other species. However, a multitude of mitochondrial proteins encoded in the nucleus display no homology to bacterial proteins, indicating that these originated within the eukaryotic cell subsequent to the acquisition of the endosymbiont. An analysis of the expression patterns of yeast nuclear genes coding for mitochondrial proteins has shown that genes predicted to be of eukaryotic origin are mainly translated on polysomes that are free in the cytosol whereas those of putative bacterial origin are translated on polysomes attached to the mitochondrion. The strong relationship with f-proteobacterial genes observed for some mitochondrial genes, combined with the lack of such a relationship for others, indicates that the modern mitochondrial proteome is the product of both reductive and expansive processes.
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| 37. |
- Andersson, Siv
(författare)
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The bacterial world gets smaller
- 2006
-
Ingår i: Science. - 0036-8075 .- 1095-9203. ; 314:5797, s. 259-260
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Forskningsöversikt (övrigt vetenskapligt/konstnärligt)
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| 38. |
- Ardell, David H., et al.
(författare)
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TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA sythetase
- 2006
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 34:3, s. 893-904
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Tidskriftsartikel (refereegranskat)abstract
- We present TFAM, an automated, statistical method to classify the identity of tRNAs. TFAM, currently optimized for bacteria, classifies initiator tRNAs and predicts the charging identity of both typical and atypical tRNAs such as suppressors with high confidence. We show statistical evidence for extensive variation in tRNA identity determinants among bacterial genomes due to variation in overall tDNA base content. With TFAM we have detected the first case of eukaryotic-like tRNA identity rules in bacteria. An alpha-proteobacterial clade encompassing Rhizobiales, Caulobacter crescentus and Silicibacter pomeroyi, unlike a sister clade containing the Rickettsiales, Zymomonas mobilis and Gluconobacter oxydans, uses the eukaryotic identity element A73 instead of the highly conserved prokaryotic element C73. We confirm divergence of bacterial histidylation rules by demonstrating perfect covariation of alpha-proteobacterial tRNA(His) acceptor stems and residues in the motif IIb tRNA-binding pocket of their histidyl-tRNA synthetases (HisRS). Phylogenomic analysis supports lateral transfer of a eukaryotic-like HisRS into the alpha-proteobacteria followed by in situ adaptation of the bacterial tDNA(His) and identity rule divergence. Our results demonstrate that TFAM is an effective tool for the bioinformatics, comparative genomics and evolutionary study of tRNA identity.
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| 39. |
- Attitalla, Idress H., 1969-
(författare)
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Biological and Molecular Characteristics of Microorganism-Stimulated Defence Response in Lycopersicon esculentum –L
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Microorganisms, including two fungi, Phytophthora cryptogea and Fusarium oxysporum strain Fo-(IMI 386351), and one bacterium, Pesudomonas sp. strain MF30, were tested for their abilities to stimulate plant defence responses in tomato (Lycopersicon esculentum –L.) and to serve as effective biocontrol agents (Bs). The study included in vivo and in vitro characterization of biological attributes of the microorganisms, pertaining to their abilities to stimulate plant immunity against a fungal pathogen, Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of tomato wilt disease. Using Lycopersicon esculentum –L. as a model plant for examining some fundamental elements of the plant-microorganism interaction, the study reveals and clarifies some aspects of the close association and the complexity of such systems. For each B, the results revealed a B-distinct plant-microorganism interaction, which included systemic induced resistance (SIR). A phylogenetic analyses of the partial sequences of two Fo-(IMI 386351) genes, a mitochondrial small subunit ribosomal DNA (mtSSU rDNA) and the nuclear translation elongation factor 1α (EF-1α), provided phylogenetic trees confirming that Fo-(IMI 386351) might be a member of Fol or of F. oxysporum f. sp. melonis, which have polyphyletic evolutionary origins. RFLP analysis (mtDNA), suggested that Fo-(IMI 386351) probably belongs to Fol. For routine and accurate differentiation between two morphologically indistinguishable F. oxysporum formae speciales strains, F. oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicis-lycopersici, a molecular method (mtDNA RFLP analysis) was developed, and its usefulness for such differentiation was compared with that of two other methods: isozyme analysis and an osmotic method, revealed with high performance liquid chromatography (HPLC). The HPLC-spectra of Fo-(IMI 386351) had an extra peak for the two tested fractions, indicating that activation of the observed plant defence mechanism could have been at least partially the result of one of the products of the eliciting microbe. Preliminary results obtained by nuclear magnetic resonance spectrometry of those fractions suggest that the extra peak probably represents an oligosaccharide, which may have acted as a mobile signal and triggered the plant defence mechanisms. We concluded that (1) our three tested microorganisms are able to stimulate plant defence mechanisms by triggering SIR (plant immunity), (2) the complexity and elaborateness of evolved plant-microbe interactions involving plant defence can, at least in some cases, be observed and studied in the laboratory, and (3) molecular tools can be a powerful means for identifying fungal strains and for clarifying their taxonomical relationships.
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| 40. |
- Batut, Jacques, et al.
(författare)
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The evolution of chronic infection strategies in the α-proteobacteria
- 2004
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Ingår i: Nature Reviews Microbiology. - : Springer Science and Business Media LLC. - 1740-1526 .- 1740-1534. ; 2, s. 933-945
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Forskningsöversikt (refereegranskat)abstract
- Many of the -proteobacteria establish long-term, often chronic, interactions with higher eukaryotes. These interactions range from pericellular colonization through facultative intracellular multiplication to obligate intracellular lifestyles. A common feature in this wide range of interactions is modulation of host-cell proliferation, which sometimes leads to the formation of tumour-like structures in which the bacteria can grow. Comparative genome analyses reveal genome reduction by gene loss in the intracellular -proteobacterial lineages, and genome expansion by gene duplication and horizontal gene transfer in the free-living species. In this review, we discuss -proteobacterial genome evolution and highlight strategies and mechanisms used by these bacteria to infect and multiply in eukaryotic cells.
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| 41. |
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| 42. |
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| 43. |
- Berglund, Eva C., et al.
(författare)
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Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents
- 2010
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11, s. 152-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Rodents represent a high-risk reservoir for the emergence of new human pathogens. The recent completion of the 2.3 Mb genome of Bartonella grahamii, one of the most prevalent blood-borne bacteria in wild rodents, revealed a higher abundance of genes for host-cell interaction systems than in the genomes of closely related human pathogens. The sequence variability within the global B. grahamii population was recently investigated by multi locus sequence typing, but no study on the variability of putative host-cell interaction systems has been performed. Results: To study the population dynamics of B. grahamii, we analyzed the genomic diversity on a whole-genome scale of 27 B. grahamii strains isolated from four different species of wild rodents in three geographic locations separated by less than 30 km. Even using highly variable spacer regions, only 3 sequence types were identified. This low sequence diversity contrasted with a high variability in genome content. Microarray comparative genome hybridizations identified genes for outer surface proteins, including a repeated region containing the fha gene for filamentous hemaggluttinin and a plasmid that encodes a type IV secretion system, as the most variable. The estimated generation times in liquid culture medium for a subset of strains ranged from 5 to 22 hours, but did not correlate with sequence type or presence/absence patterns of the fha gene or the plasmid. Conclusion: Our study has revealed a geographic microstructure of B. grahamii in wild rodents. Despite near-identity in nucleotide sequence, major differences were observed in gene presence/absence patterns that did not segregate with host species. This suggests that genetically similar strains can infect a range of different hosts.
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| 44. |
- Berglund, Eva Caroline
(författare)
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Genome Evolution and Host Adaptation in Bartonella
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Bacteria of the genus Bartonella infect the red blood cells of a wide range of wild and domestic mammals and are transmitted between hosts by blood-sucking insects. Although most Bartonella infections are asymptomatic, the genus contains several human pathogens. In this work, host adaptation and host switches in Bartonella have been studied from a genomic perspective, with special focus on the acquisition and evolution of genes involved in host interactions. As part of this study, the complete genome of B. grahamii isolated from a Swedish wood mouse was sequenced. A genus-wide comparison revealed that rodent-associated Bartonella species, which have rarely been associated with human disease, have the largest genomes and the largest number of host-adaptability genes. Analysis of known and putative genes for host interactions identified several families of autotransporters as horizontally transferred to the Bartonella ancestor, with a possible role both during early host adaptation and subsequent host shifts. In B. grahamii, the association of a gene transfer agent (GTA) and phage-derived run-off replication of a large genomic segment was demonstrated for the first time. Among all acquisitions to the Bartonella ancestor, the only well conserved gene clusters are those that encode the GTA and contain the origin of the run-off replication. This conservation, along with a high density of host-adaptability genes in the amplified region suggest that the GTA provides a strong selective advantage, possibly by increasing recombination frequencies of host-adaptability genes, thereby facilitating evasion of the host immune system and colonization of new hosts. B. grahamii displays stronger geographic pattern and higher recombination frequencies than the cat-associated B. henselae, probably caused by different lifestyles and/or population sizes of the hosts. The genomic diversity of B. grahamii is markedly lower in Europe and North America than in Asia, possibly an effect of reduced host variability in these areas following the latest ice age.
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| 45. |
- Berglund, Eva C., et al.
(författare)
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Rapid diversification by recombination in Bartonella grahamii from wild rodents in Asia contrasts with low levels of genomic divergence in Northern Europe and America
- 2010
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 19:11, s. 2241-2255
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Tidskriftsartikel (refereegranskat)abstract
- Bartonella is a genus of vector-borne bacteria that infect the red blood cells of mammals, and includes several human-specific and zoonotic pathogens. Bartonella grahamii has a wide host range and is one of the most prevalent Bartonella species in wild rodents. We studied the population structure, genome content and genome plasticity of a collection of 26 B. grahamii isolates from 11 species of wild rodents in seven countries. We found strong geographic patterns, high recombination frequencies and large variations in genome size in B. grahamii compared with previously analysed cat- and human-associated Bartonella species. The extent of sequence divergence in B. grahamii populations was markedly lower in Europe and North America than in Asia, and several recombination events were predicted between the Asian strains. We discuss environmental and demographic factors that may underlie the observed differences.
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| 46. |
- Berglund, Eva C., et al.
(författare)
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Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii
- 2009
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Ingår i: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 5:7, s. e1000546-
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Tidskriftsartikel (refereegranskat)abstract
- The genus Bartonella comprises facultative intracellular bacteria adapted to mammals, including previously recognized and emerging human pathogens. We report the 2,341,328 bp genome sequence of Bartonella grahamii, one of the most prevalent Bartonella species in wild rodents. Comparative genomics revealed that rodent-associated Bartonella species have higher copy numbers of genes for putative host-adaptability factors than the related human-specific pathogens. Many of these gene clusters are located in a highly dynamic region of 461 kb. Using hybridization to a microarray designed for the B. grahamii genome, we observed a massive, putatively phage-derived run-off replication of this region. We also identified a novel gene transfer agent, which packages the bacterial genome, with an over-representation of the amplified DNA, in 14 kb pieces. This is the first observation associating the products of run-off replication with a gene transfer agent. Because of the high concentration of gene clusters for host-adaptation proteins in the amplified region, and since the genes encoding the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize that these systems are driven by selection. We propose that the coupling of run-off replication with gene transfer agents promotes diversification and rapid spread of host-adaptability factors, facilitating host shifts in Bartonella.
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| 47. |
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| 48. |
- Bisch, Gaelle, et al.
(författare)
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Genome Evolution of Bartonellaceae Symbionts of Ants at the Opposite Ends of the Trophic Scale
- 2018
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 10:7, s. 1687-1704
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Tidskriftsartikel (refereegranskat)abstract
- Many insects rely on bacterial symbionts to supply essential amino acids and vitamins that are deficient in their diets, but metabolic comparisons of closely related gut bacteria in insects with different dietary preferences have not been performed. Here, we demonstrate that herbivorous ants of the genus Dolichoderus from the Peruvian Amazon host bacteria of the family Bartonellaceae, known for establishing chronic or pathogenic infections in mammals. We detected these bacteria in all studied Dolichoderus species, and found that they reside in the midgut wall, that is, the same location as many previously described nutritional endosymbionts of insects. The genomic analysis of four divergent strains infecting different Dolichoderus species revealed genes encoding pathways for nitrogen recycling and biosynthesis of several vitamins and all essential amino acids. In contrast, several biosynthetic pathways have been lost, whereas genes for the import and conversion of histidine and arginine to glutamine have been retained in the genome of a closely related gut bacterium of the carnivorous ant Harpegnathos saltator. The broad biosynthetic repertoire in Bartonellaceae of herbivorous ants resembled that of gut bacteria of honeybees that likewise feed on carbohydrate-rich diets. Taken together, the broad distribution of Bartonellaceae across Dolichoderus ants, their small genome sizes, the specific location within hosts, and the broad biosynthetic capability suggest that these bacteria are nutritional symbionts in herbivorous ants. The results highlight the important role of the host nutritional biology for the genomic evolution of the gut microbiota-and conversely, the importance of the microbiota for the nutrition of hosts.
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| 49. |
- Björkholm, Patrik, et al.
(författare)
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Mitochondrial genomes are retained by selective constraints on protein targeting
- 2015
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 112:33, s. 10154-10161
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Tidskriftsartikel (refereegranskat)abstract
- Mitochondria are energy-producing organelles in eukaryotic cells considered to be of bacterial origin. The mitochondrial genome has evolved under selection for minimization of gene content, yet it is not known why not all mitochondrial genes have been transferred to the nuclear genome. Here, we predict that hydrophobic membrane proteins encoded by the mitochondrial genomes would be recognized by the signal recognition particle and targeted to the endoplasmic reticulum if they were nuclear-encoded and translated in the cytoplasm. Expression of the mitochondrially encoded proteins Cytochrome oxidase subunit 1, Apocytochrome b, and ATP synthase subunit 6 in the cytoplasm of HeLa cells confirms export to the endoplasmic reticulum. To examine the extent to which the mitochondrial proteome is driven by selective constraints within the eukaryotic cell, we investigated the occurrence of mitochondrial protein domains in bacteria and eukaryotes. The accessory protein domains of the oxidative phosphorylation system are unique to mitochondria, indicating the evolution of new protein folds. Most of the identified domains in the accessory proteins of the ribosome are also found in eukaryotic proteins of other functions and locations. Overall, one-third of the protein domains identified in mitochondrial proteins are only rarely found in bacteria. We conclude that the mitochondrial genome has been maintained to ensure the correct localization of highly hydrophobic membrane proteins. Taken together, the results suggest that selective constraints on the eukaryotic cell have played a major role in modulating the evolution of the mitochondrial genome and proteome.
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| 50. |
- Björkholm, Patrik, et al.
(författare)
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Why mitochondria need a genome revisited
- 2017
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Ingår i: FEBS Letters. - : WILEY-BLACKWELL. - 0014-5793 .- 1873-3468. ; 591:1, s. 65-75
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we experimentally address the debate about why functional transfer of mitochondrial genes to the nucleus has been halted in some organismal groups and why cytosolic expression of mitochondrial proteins has proven remarkably difficult. By expressing all 13 human mitochondrial-encoded genes with strong mitochondrial-targeting sequences in the cytosol of human cells, we show that all proteins, except ATP8, are transported to the endoplasmic reticulum (ER). These results confirm and extend previous findings based on three mitochondrial genes lacking mitochondrial-targeting sequences that also were relocated to the ER during cytosolic expression. We conclude that subcellular protein targeting constitutes a major barrier to functional transfer of mitochondrial genes to the nuclear genome.
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