| 1. |
- Öhrman, Caroline, et al.
(författare)
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Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis
- 2021
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Ingår i: Microorganisms. - : MDPI. - 2076-2607. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.
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| 2. |
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| 3. |
- Berman, David S., et al.
(författare)
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Holographic Noncommutativity
- 2000
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Ingår i: J. High Energy Phys. ; 05, s. 002-
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Brijs, Jeroen, et al.
(författare)
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The final countdown: Continuous physiological welfare evaluation of farmed fish during common aquaculture practices before and during harvest
- 2018
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486 .- 1873-5622. ; 495, s. 903-911
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Tidskriftsartikel (refereegranskat)abstract
- Welfare of farmed fish has become of increasing concern for consumers, producers, interest groups and authorities. To improve fish welfare, it is necessary to find indicators that can identify stressful situations early enough so that an intervention can take place before detrimental effects occur. By using heart rate bio-loggers in freely swimming rainbow trout (Oncorhynchus mykiss), combined with plasma cortisol levels and a range of haematological and blood chemistry parameters, we assessed the severity of stress responses induced by a range of common aquaculture practices before and during harvest. Following surgery, transportation and reintroduction with conspecifics in the sea cage, it took similar to 4 days for heart rate to stabilize and for a clear circadian rhythm in heart rate to emerge (i.e. average circadian fluctuation in heart rate of similar to 25 to 27 beats min(-1)). The presence or absence of this circadian rhythm in heart rate could inform researchers in the aquaculture industry whether or not specific farming routines induce unnecessary and prolonged stress. The elevations in heart rate caused by common farming practises such as crowding and transportation (e.g. heart rate increased by similar to 8 and 9 beats min-1 above what would normally be expected for that time of day, respectively) corresponded well with increases in plasma cortisol levels. Stressful farming practises or events (indicated by elevated plasma cortisol levels) such as air exposure during brailing and aquatic hypoxia triggered a hypoxic bradycardia until fish were released back into oxygenated water whereupon heart rate significantly increased to repay the accumulated oxygen debt. Repeated stress induced by multiple farming practises (i.e. combined stressors of crowding, brailing and transportation) clearly had a cumulative and long-lasting effect as heart rate peaked at similar to 25 beats min(-1) above what would normally be expected for that time of day. Heart rate also remained significantly elevated by similar to 9 beats min(-1) the following morning, suggesting that if rainbow trout need to be subjected to multiple stressors during consequtive days, it is recommended that sufficient time for recovery is provided between stressors. This study demonstrates that heart rate monitoring can be useful to assess stress levels of freely swimming fish in sea cages. Moreover, the use of implantable bio-loggers opens up a broad range of possible applications that will allow researchers to investigate the effects of environmental and/or anthropogenic stressors on the welfare of fish under conditions more realistic to the aquaculture industry.
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| 5. |
- Callier, Myriam D., et al.
(författare)
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Attraction and repulsion of mobile wild organisms to finfish and shellfish aquaculture: A review
- 2018
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Ingår i: Reviews in Aquaculture. - : Wiley. - 1753-5123 .- 1753-5131. ; 10:4, s. 924-949
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Tidskriftsartikel (refereegranskat)abstract
- © 2017 Wiley Publishing Asia Pty Ltd. Knowledge of aquaculture-environment interactions is essential for the development of a sustainable aquaculture industry and efficient marine spatial planning. The effects of fish and shellfish farming on sessile wild populations, particularly infauna, have been studied intensively. Mobile fauna, including crustaceans, fish, birds and marine mammals, also interact with aquaculture operations, but the interactions are more complex and these animals may be attracted to (attraction) or show an aversion to (repulsion) farm operations with various degrees of effects. This review outlines the main mechanisms and effects of attraction and repulsion of wild animals to/from marine finfish cage and bivalve aquaculture, with a focus on effects on fisheries-related species. Effects considered in this review include those related to the provision of physical structure (farm infrastructure acting as fish aggregating devices (FADs) or artificial reefs (ARs), the provision of food (e.g. farmed animals, waste feed and faeces, fouling organisms associated with farm structures) and some farm activities (e.g. boating, cleaning). The reviews show that the distribution of mobile organisms associated with farming structures varies over various spatial (vertical and horizontal) and temporal scales (season, feeding time, day/night period). Attraction/repulsion mechanisms have a variety of direct and indirect effects on wild organisms at the level of individuals and populations and may have implication for the management of fisheries species and the ecosystem in the context of marine spatial planning. This review revealed considerable uncertainties regarding the long-term and ecosystem-wide consequences of these interactions. The use of modelling may help better understand consequences, but long-term studies are necessary to better elucidate effects.
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| 6. |
- Eriksson, Johan, 1987, et al.
(författare)
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Solute Concentrations in the Matrix of Zirconium Alloys Studied by Atom Probe Tomography
- 2023
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Ingår i: ASTM Special Technical Publication. - 0066-0558. ; STP1645, s. 149-172
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Konferensbidrag (refereegranskat)abstract
- This work indicates that the matrix content of the alloying elements iron, chromium, and nickel in as-produced commercial Zircaloy-2-type materials is lower than what has been indicated by many previous studies. Atom probe tomography in voltage pulse mode was used to study the matrix content of solutes in Zircaloy-2 of type LK3/L and a similar model alloy, called Alloy 2, of the same heat treatment. Both alloys were analyzed in the as-produced state and after reactor exposure. In the as-produced materials, the concentrations of iron, chromium, and nickel were all below the detection limits of around 10 wt. ppm. After reactor exposure, these alloying elements were observed to reside in clusters at loops, and the matrix content (including clusters) of iron had increased to about 1,200 wt. ppm in the fueled region of the rod and to about half that value in the plenum region. The chromium content in the fueled region was approximately 100 wt. ppm, and the nickel content was approximately 200 wt. ppm. In the plenum region, the content of these elements was lower. However, due to an uneven distribution of clusters, there was a wide scatter in the measured concentrations in the irradiated materials. Additionally, the matrix concentrations of solute elements in (nonirradiated) Zircaloy-2 were investigated for a series of samples subjected to a annealing at 770◦C followed by cooling at different rates. From these measurements, the solubilities at 770◦C were estimated to be around 65 wt. ppm for chromium, at least 37 wt. ppm for iron, and below 9 wt. ppm for nickel. Slow cooling resulted in virtually no iron, chromium, or nickel in the matrix. The concentration of aluminum in the matrix was observed to be between 10 and 20 wt. ppm for all a-annealed samples and for the as-produced materials of commercial heat treatment.
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| 7. |
- Eriksson, Karolina Ida Anna, et al.
(författare)
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Association between Legionella species and humic substances during early summer in the northern Baltic Sea
- 2023
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Ingår i: Frontiers in Marine Science. - : Frontiers Media S.A.. - 2296-7745. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Climate change is projected to cause alterations in northern coastal systems, including humification and intensified nutrient loads, which can lead to ecosystem imbalances and establishment of new bacterial species. Several potential pathogens, such as different species of Legionella, hide in the environment between infections, some by living inside protozoan host cells. Knowledge about the occurrence of Legionella in natural waters is missing, which disable risk assessments of exposure. We performed a study of the species diversity of Legionella in the northern Baltic Sea (Gulf of Bothnia) during early summer to map their occurrence and to identify possible environmental drivers. We detected Legionella and potential protozoan hosts along gradients of the Gulf of Bothnia. We also for the first time present third generation full-length 16S rRNA amplicon sequencing (Nanopore) to resolve environmental species classification of Legionella, with a method suitable to study all bacteria. Our data show that full length 16S rRNA sequences is sufficient to resolve Legionella while the standard short Illumina sequences did not capture the entire diversity. For accurate species classification of Legionella, harmonization between the Nanopore classification methods is still needed and the bias toward the well-studied Legionella pneumophila need to be resolved. Different Legionella species occurred both in the Bothnian Sea and in the Bothnian Bay and their abundance were linked to humic substances and low salinity. The relative abundance of Legionella was higher in the humic-rich northern waters of the Bothnian Bay. The link between Legionella species and humic substances may be indirect via promotion of the heterotrophic microbial food web, allowing Legionella species and similar bacteria to establish. Humic substances are rich in iron, which has been shown crucial for growth of Legionella species and other pathogens. Considering climate change projections in this regional area, with increased humification and freshwater inflow, this bacterial niche containing potential pathogens might become more widespread in the future Baltic Sea. This study demonstrates the significance of DNA sequencing to monitor public health relevant bacteria like Legionella species in the environment. Including sequencing of bacteria and protozoa in the environmental monitoring programs could be used to identify ecosystem imbalances, which enable appropriate responses to emerging diseases.
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| 8. |
- Eriksson, Karolina I. A., 1991-
(författare)
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Bacteria that escape predation : waterborne pathogens and their relatives
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The hidden presence of opportunistic bacterial pathogens in the environment evokes concerns about emerging diseases, especially in the light of climate change. The co-evolution of bacteria and their predators (protozoa) has led to bacterial defence strategies of which some contribute to the ability of bacteria to cause disease. To increase our understanding of the interplay between bacteria, protozoa, land use, and climate scenarios in Nordic brackish and freshwater, four studies were designed. The first study explored the co-occurrence patterns between predation resistant bacteria (PRB) and bacterivorous protozoa in a coastal area in the northern Baltic Sea. The results showed higher PRB diversity in the bays and freshwater inlets, than in the offshore waters. Further, genotype specific interactions between protozoa and bacteria were identified. The second study focused on Legionella species diversity and their association with humic substances and low salinity, potentially facilitated through the promotion of the heterotrophic microbial food web or by iron availability. The third study examined the impact of intensified land use on bacterial taxa abundance and community composition in lake inflows, demonstrating indirect downstream effects on water quality. Factors such as pastures, fields, farms, aluminium, iron, and humic substances were linked to increased Legionella abundance. The fourth study exposed aquatic organisms to climate change scenarios, causing eutrophication or brownification with elevated iron levels. Pseudomonas aeruginosa were found to be especially persistent to iron, likely linked to the same mechanism that enables survival in protozoan cells. This trait was shared with other observed intracellular pathogens and uncultured species, who showed elevated resilience to brownification and ability to survive outside host cells. These findings identified complex relationships, which improve our understanding of the intricate dynamics that shape aquatic ecosystems, and highlight the importance of considering multiple factors in managing water resources and maintaining ecosystem health. Human activities including intensified land use can have far-reaching consequences, jeopardizing the pristine nature of water bodies and escalate the presence of environmental and opportunistic bacterial pathogens.
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| 9. |
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| 10. |
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| 11. |
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| 12. |
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| 13. |
- Gilljam, Mikael, 1957, et al.
(författare)
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Politik på hemmaplan. Tiotusen fullmäktigeledamöter tycker om politik och demokrati
- 2010
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- I Sverige har kommuner och landsting ett huvudansvar för en stor del av den offentliga politiken. Den demokratiska makten ligger där i händerna på cirka 14 000 folkvalda ledamöter i kommun- och landstingsfullmäktige. I ett demokratiskt perspektiv är det av största vikt för medborgarna att känna till vilken politik dessa folkvalda vill föra. De folkvalda har också stora kunskaper om hur de politiska institutionerna fungerar i praktiken och vilka problem och möjligheter som demokratiska reformer skulle innebära. Även på dessa områden är det intressant att få veta hur våra folkvalda tycker och tänker. Under 2008-2009 genomförde vi Kommun- och landstingsfullmäktigeundersökningen, en enkät till samtliga folkvalda politiker på kommunal och regional nivå i Sverige. Enkäten besvarades av nära 10 000 fullmäktigeledamöter. Undersökningen är den absolut största i sitt slag som genomförts i Sverige. I boken Politik på hemmaplan redovisar vi hur Sveriges fullmäktigeledamöter ställer sig i en rad politiska sakfrågor och hur de tycker att demokratin i kommuner och landsting fungerar och bör fungera. I boken redovisas också hur ledamöterna ser på nya politiska organisationsformer, protester och hot mot politiker, partipolitiska konflikter och social representation. I många av dessa frågor har den partipolitiska tillhörigheten stor betydelse, men vi finner också belägg för att politikernas sociala bakgrund spelar roll för deras ställningstaganden liksom huruvida de tillhör den regerande majoriteten eller oppositionen.
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| 14. |
- Gilljam, Mikael, 1957, et al.
(författare)
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Representationsprinciper i riksdag och kommun
- 2010
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Ingår i: Martin Brothén & Sören Holmberg: Folkets representanter. En bok om riksdagsledamöter och politisk representation i Sverige.. - Göteborg : Statsvetenskapliga institutionen, Göteborgs universitet. - 9789161815302 ; , s. 35-64
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 15. |
- Huyben, David, et al.
(författare)
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Haematological and intestinal health parameters of rainbow trout are influenced by dietary live yeast and increased water temperature
- 2019
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Ingår i: Fish and Shellfish Immunology. - : Elsevier BV. - 1050-4648 .- 1095-9947. ; 89, s. 525-536
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Tidskriftsartikel (refereegranskat)abstract
- Live yeast may be a sustainable protein source in salmonid diets while exhibiting a probiotic effect to counteract environmental stressors, such as increased water temperature that is being exacerbated by climate change. The objective of this study was to evaluate the effects of feeding a high dietary inclusion of live yeast and increased water temperature on growth, haematological and intestinal physiology of rainbow trout. For six weeks, 129 g fish in 16 tanks (n = 4) were fed either a diet based on fishmeal or based on live yeast (214 g kg −1 of diet or 7.6 log CFU g −1 of Saccharomyces cerevisiae) that replaced 40% of fishmeal protein while fish were reared in water temperatures of either 11 °C (cold) or 18 °C (warm). Fish weights, caudal blood and proximal and distal intestines were collected and analysed. Fish fed live yeast resulted in reduced growth (SGR and WG) and higher FCR, while growth in cold and warm water was similar despite differences in TGC. However, increased mortality, plasma cortisol, and intestinal oedema and villous damage indicated fish reared in warm water were subjected to chronic stress. Temperature had a significant effect on haematocrit and red blood cell counts that resulted in significantly higher haemoglobin levels in fish kept in warm water attributed to an elevated oxygen demand. In the proximal intestine, increased temperature resulted in reduced expression of pro-inflammatory cytokines, e.g. TNFα and IL8, that were further reduced in fish fed live yeast. In addition, feeding live yeast reduced gene expression of CLD6 involved in gut barrier function, which suggests that the level of yeast was too high and masked any beneficial effects on fish health. In conclusion, feeding a high inclusion of live yeast reduced fish growth and expression of intestinal genes, while increasing the temperature from 11 to 18 °C subjected fish to chronic stress that restricted growth, suppressed innate immunity and induced intestinal damage. Replacing 40% of fishmeal protein with live yeast did not counteract negative effects caused by increased temperature, thus alternative strategies need to be explored and implemented to protect the growth and health of rainbow trout from seasonal and long-term rises in water temperature. © 2019
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| 16. |
- Jernberg, Tomas, et al.
(författare)
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Impact of ischaemic heart disease severity and age on risk of cardiovascular outcome in diabetes patients in Sweden : A nationwide observational study
- 2019
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Ingår i: BMJ Open. - : BMJ. - 2044-6055. ; 9:4
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Tidskriftsartikel (refereegranskat)abstract
- Objectives To compare short-term cardiovascular (CV) outcome in type 2 diabetes (T2D) patients without ischaemic heart disease (IHD), with IHD but no prior myocardial infarction (MI), and those with prior MI; and assess the impact on risk of age when initiating first-time glucose-lowering drug (GLD). Design Cohort study linking morbidity, mortality and medication data from Swedish national registries. Participants First-time users of GLD during 2007-2016. Outcomes Predicted cumulative incidence for the CV outcome (MI, stroke and CV mortality) was estimated. A Cox model was developed where age at GLD start and CV risk was modelled. Results 260 070 first-time GLD users were included, 221 226 (85%) had no IHD, 16 294 (6%) had stable IHD-prior MI and 22 550 (9%) had IHD+MI. T2D patients without IHD had a lower risk of CV outcome compared with the IHD populations (±prior MI), (3-year incidence 4.78% vs 5.85% and 8.04%). The difference in CV outcome was primarily driven by a relative greater MI risk among the IHD patients. For T2D patients without IHD, an almost linear association between age at start of GLD and relative risk was observed, whereas in IHD patients, the younger (<60 years) patients had a relative greater risk compared with older patients. Conclusions T2D patients without IHD had a lower risk of the CV outcome compared with the T2D populations with IHD, primarily driven by a greater risk of MI. For T2D patients without IHD, an almost linear association between age at start of GLD and relative risk was observed, whereas in IHD patients, the younger patients had a relative greater risk compared with older patients. Our findings suggest that intense risk prevention should be the key strategy in the management of T2D patients, especially for younger patients.
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| 17. |
- Jokipii-Lukkari, Soile, et al.
(författare)
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NorWood : a gene expression resource for evo-devo studies of conifer wood development
- 2017
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 216:2, s. 482-494
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Tidskriftsartikel (refereegranskat)abstract
- The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development.RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks.Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies.The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.
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| 18. |
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| 19. |
- Kellgren, Therese, et al.
(författare)
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Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215
- 2024
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Ingår i: BMC Microbiology. - : BioMed Central (BMC). - 1471-2180. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings.Results: We completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination’s role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30–50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2.Conclusions: This study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings.
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| 20. |
- Knudsen, David, et al.
(författare)
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Dietary soya saponins increase gut permeability and play a key role in the onset of soyabean-induced enteritis in Atlantic salmon ( Salmo salar L.).
- 2008
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Ingår i: The British journal of nutrition. - 0007-1145. ; 100:1, s. 120-9
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Tidskriftsartikel (refereegranskat)abstract
- Saponins are naturally occurring amphiphilic molecules and have been associated with many biological activities. The aim of the present study was to investigate whether soya saponins trigger the onset of soyabean-induced enteritis in Atlantic salmon (Salmo salar L.), and to examine if dietary soya saponins increase the epithelial permeability of the distal intestine in Atlantic salmon. Seven experimental diets containing different levels of soya saponins were fed to seawater-adapted Atlantic salmon for 53 d. The diets included a fishmeal-based control diet, two fishmeal-based diets with different levels of added soya saponins, one diet containing 25% lupin kernel meal, two diets based on 25% lupin kernel meal with different levels of added soya saponins, and one diet containing 25% defatted soyabean meal. The effect on intestinal morphology, intestinal epithelial permeability and faecal DM content was examined. Fish fed 25% defatted soyabean meal displayed severe enteritis, whereas fish fed 25% lupin kernel meal had normal intestinal morphology. The combination of soya saponins and fishmeal did not induce morphological changes but fish fed soya saponins in combination with lupin kernel meal displayed significant enteritis. Increased epithelial permeability was observed in fish fed 25% defatted soyabean meal and in fish fed soya saponin concentrate independent of the protein source in the feed. The study demonstrates that soya saponins, in combination with one or several unidentified components present in legumes, induce an inflammatory reaction in the distal intestine of Atlantic salmon. Soya saponins increase the intestinal epithelial permeability but do not, per se, induce enteritis.
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| 21. |
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| 22. |
- Liu, Lijun, et al.
(författare)
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A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus
- 2015
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Ingår i: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 82:5, s. 887-898
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Tidskriftsartikel (refereegranskat)abstract
- Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.
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| 23. |
- Mayweg, David, 1986, et al.
(författare)
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Formation of pure zirconium islands inside c-component loops in high-burnup fuel cladding
- 2024
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Ingår i: Journal of Nuclear Materials. - 0022-3115. ; 597
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Tidskriftsartikel (refereegranskat)abstract
- High-burnup Zr-based nuclear fuel claddings exhibit accelerated irradiation growth, corrosion and hydrogen pick-up, all correlated with the emergence of c-component dislocation loops. We made use of sub-nm-resolution atom probe tomography to characterize the nanoscale chemistry of c-loops in fuel cladding from boiling water reactor operation. We found segregation of Fe, Ni and Sn to dislocation lines and depletion of Sn and O inside the loops, resulting in nearly pure Zr islands. We also observed nucleation of suboxide inside one c-loop, pointing to a possible mechanism of accelerated in-reactor corrosion. Such Zr-islands might also promote hydride precipitation and associated degradation.
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| 24. |
- Netotea, Sergiu, et al.
(författare)
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ComPlEx : conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa
- 2014
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15, s. 106-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Divergence in gene regulation has emerged as a key mechanism underlying species differentiation. Comparative analysis of co-expression networks across species can reveal conservation and divergence in the regulation of genes. Results: We inferred co-expression networks of A. thaliana, Populus spp. and O. sativa using state-of-the-art methods based on mutual information and context likelihood of relatedness, and conducted a comprehensive comparison of these networks across a range of co-expression thresholds. In addition to quantifying gene-gene link and network neighbourhood conservation, we also applied recent advancements in network analysis to do cross-species comparisons of network properties such as scale free characteristics and gene centrality as well as network motifs. We found that in all species the networks emerged as scale free only above a certain co-expression threshold, and that the high-centrality genes upholding this organization tended to be conserved. Network motifs, in particular the feed-forward loop, were found to be significantly enriched in specific functional subnetworks but where much less conserved across species than gene centrality. Although individual gene-gene co-expression had massively diverged, up to similar to 80% of the genes still had a significantly conserved network neighbourhood. For genes with multiple predicted orthologs, about half had one ortholog with conserved regulation and another ortholog with diverged or non-conserved regulation. Furthermore, the most sequence similar ortholog was not the one with the most conserved gene regulation in over half of the cases. Conclusions: We have provided a comprehensive analysis of gene regulation evolution in plants and built a web tool for Comparative analysis of Plant co-Expression networks (ComPlEx, http:// complex. plantgenie. org/). The tool can be particularly useful for identifying the ortholog with the most conserved regulation among several sequence-similar alternatives and can thus be of practical importance in e. g. finding candidate genes for perturbation experiments.
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| 25. |
- Rosenqvist, Tage, et al.
(författare)
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Succession of bacterial biofilm communities following removal of chloramine from a full-scale drinking water distribution system
- 2023
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Ingår i: npj Clean Water. - 2059-7037. ; 2023:6
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Tidskriftsartikel (refereegranskat)abstract
- Monochloramine is used to regulate microbial regrowth in drinking water distribution systems (DWDS) but produces carcinogenic disinfection byproducts and constitutes a source of energy for nitrifying bacteria. This study followed biofilm-dispersed microbial communities of a full-scale DWDS distributing ultrafiltered water over three years, before and after removal of monochloramine. Communities were described using flow cytometry and amplicon sequencing, including full-length 16S rRNA gene sequencing. Removal of monochloramine increased total cell counts by up to 440%. Increased abundance of heterotrophic bacteria was followed by emergence of the predatory bacteria Bdellovibrio, and a community potentially metabolizing small organic compounds replaced the nitrifying core community. No increased abundance of Mycobacterium or Legionella was observed. Co-occurrence analysis identified a network of Nitrosomonas, Nitrospira, Sphingomonas and Hyphomicrobium, suggesting that monochloramine supported this biofilm community. While some species expanded into the changed niche, no immediate biological risk to consumers was indicated within the DWDS.
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| 26. |
- Sandås, Kristofer, et al.
(författare)
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Nanometa Live : a user-friendly application for real-time metagenomic data analysis and pathogen identification
- 2024
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Ingår i: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 40:3
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Tidskriftsartikel (refereegranskat)abstract
- Summary: Nanometa Live presents a user-friendly interface designed for real-time metagenomic data analysis and pathogen identification utilizing Oxford Nanopore Technologies’ MinION and Flongle flow cells. It offers an efficient workflow and graphical interface for the visualization and interpretation of metagenomic data as it is being generated. Key features include automated BLAST validation, streamlined handling of custom Kraken2 databases, and a simplified graphical user interface for enhanced user experience. Nanometa Live is particularly notable for its capability to run without constant internet or server access once installed, setting it apart from similar tools. It provides a comprehensive view of taxonomic composition and facilitates the detection of user-defined pathogens or other species of interest, catering to both researchers and clinicians.Availability and implementation: Nanometa Live has been implemented as a local web application using the Dash framework with Snakemake handling the data processing. The source code is freely accessible on the GitHub repository at https://github.com/FOIBioinformatics/nanometa_live and it is easily installable using Bioconda. It includes containerization support via Docker and Singularity, ensuring ease of use, reproducibility, and portability.
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| 27. |
- Sundell, David, et al.
(författare)
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AspWood : High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula
- 2017
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Ingår i: The Plant Cell. - : Oxford University Press (OUP). - 1040-4651 .- 1532-298X. ; 29:7, s. 1585-1604
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Tidskriftsartikel (refereegranskat)abstract
- Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer elite varieties will benefit from improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated high-spatial-resolution RNA sequencing data spanning the secondary phloem, vascular cambium, and wood-forming tissues of Populus tremula. The transcriptome comprised 28,294 expressed, annotated genes, 78 novel protein-coding genes, and 567 putative long intergenic noncoding RNAs. Most paralogs originating from the Salicaceae whole-genome duplication had diverged expression, with the exception of those highly expressed during secondary cell wall deposition. Coexpression network analyses revealed that regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. A comparative analysis revealed that a majority of these modules are conserved in Picea abies. The high spatial resolution of our data enabled identification of novel roles for characterized genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. An associated web resource (AspWood, http://aspwood.popgenie.org) provides interactive tools for exploring the expression profiles and coexpression network.
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| 28. |
- Sundell, David, et al.
(författare)
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FlexTaxD : flexible modification of taxonomy databases for improved sequence classification
- 2021
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Ingår i: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811 .- 1460-2059. ; 37:21, s. 3932-3933
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Tidskriftsartikel (refereegranskat)abstract
- The Flexible Taxonomy Database framework provides a method for modification and merging official and custom taxonomic databases to create improved databases. Using such databases will increase accuracy and precision of existing methods to classify sequence reads.
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| 29. |
- Sundell, David, et al.
(författare)
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High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula
- 2016
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, however, efforts to engineer new, elite varieties are constrained by the lack of a comprehensive understanding of the transcriptional network underlying cambial growth and wood formation. We generated RNA Sequencing transcriptome data for four mature, wild-growing aspens (Populus tremula) from high-spatial-resolution tangential cryosection series spanning the secondary phloem, vascular cambium, expanding and secondary cell wall forming xylem cells, cell death zone and the previous years annual ring. The transcriptome comprised 28,294 expressed, previously annotated protein-coding genes, 78 novel protein-coding genes and 567 long intergenic non-coding RNAs. Most paralogs originating from the Salicaceae whole genome duplication had diverged expression, with the notable exception of those with high expression during secondary cell wall deposition. We performed co-expression network analysis to identify central transcriptional modules and associated several of these with known biological processes. This revealed previously uncharacterized complexity underlying the regulation of cambial growth and wood formation, with modules forming a continuum of activated processes across the tissues. The high spatial resolution suggested novel roles for known genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and components of lignification. The associated web resource (AspWood, http://aspwood.popgenie.org) integrates the data within a set of interactive tools for exploring the co-expression network of cambial growth and wood formation.
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| 30. |
- Sundell, David, 1984-
(författare)
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Novel resources enabling comparative regulomics in forest tree species
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Lignocellulosic plants are the most abundant source of terrestrial biomass and are one of the potential sources of renewable energy that can replace the use of fossil fuels. For a country such as Sweden, where the forest industry accounts for 10% of the total export, there would be large economical benefits associated with increased biomass yield. The availability of research on wood development conducted in conifer tree species, which represent the majority of the forestry in Sweden, is limited and the majority of research has been conducted in model angiosperm species such as Arabidopsis thaliana. However, the large evolutionary distance between angiosperms and gymnosperms limits the possibility to identify orthologous genes and regulatory pathways by comparing sequence similarity alone. At such large evolutionary distances, the identification of gene similarity is, in most cases, not sufficient and additional information is required for functional annotation. In this thesis, two high-spatial resolution datasets profiling wood development were processed; one from the angiosperm tree Populus tremula and the other from the conifer species Picea abies. These datasets were each published together with a web resource including tools for the exploration of gene expression, co-expression and functional enrichment of gene sets. One developed resource allows interactive, comparative co-expression analysis between species to identify conserved and diverged co-expression modules. These tools make it possible to identifying conserved regulatory modules that can focus downstream research and provide biologists with a resource to identify regulatory genes for targeted trait improvement.
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| 31. |
- Sundell, David, et al.
(författare)
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The Plant Genome Integrative Explorer Resource : PlantGenIE.org
- 2015
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 208:4, s. 1149-1156
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Tidskriftsartikel (refereegranskat)abstract
- Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, BLAST homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the COMPLEX resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.
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| 32. |
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| 33. |
- Svensson, Daniel, et al.
(författare)
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doepipeline : a systematic approach to optimizing multi-level and multi-step data processing workflows
- 2019
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Ingår i: BMC Bioinformatics. - : BioMed Central. - 1471-2105. ; 20:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Selecting the proper parameter settings for bioinformatic software tools is challenging. Not only will each parameter have an individual effect on the outcome, but there are also potential interaction effects between parameters. Both of these effects may be difficult to predict. To make the situation even more complex, multiple tools may be run in a sequential pipeline where the final output depends on the parameter configuration for each tool in the pipeline. Because of the complexity and difficulty of predicting outcomes, in practice parameters are often left at default settings or set based on personal or peer experience obtained in a trial and error fashion. To allow for the reliable and efficient selection of parameters for bioinformatic pipelines, a systematic approach is needed.Results: We present doepipeline, a novel approach to optimizing bioinformatic software parameters, based on core concepts of the Design of Experiments methodology and recent advances in subset designs. Optimal parameter settings are first approximated in a screening phase using a subset design that efficiently spans the entire search space, then optimized in the subsequent phase using response surface designs and OLS modeling. Doepipeline was used to optimize parameters in four use cases; 1) de-novo assembly, 2) scaffolding of a fragmented genome assembly, 3) k-mer taxonomic classification of Oxford Nanopore Technologies MinION reads, and 4) genetic variant calling. In all four cases, doepipeline found parameter settings that produced a better outcome with respect to the characteristic measured when compared to using default values. Our approach is implemented and available in the Python package doepipeline.Conclusions: Our proposed methodology provides a systematic and robust framework for optimizing software parameter settings, in contrast to labor- and time-intensive manual parameter tweaking. Implementation in doepipeline makes our methodology accessible and user-friendly, and allows for automatic optimization of tools in a wide range of cases. The source code of doepipeline is available at https://github.com/clicumu/doepipeline and it can be installed through conda-forge.
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| 34. |
- Tiukova, Ievgeniia, et al.
(författare)
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Adaptation of Dekkera bruxellensis to lignocellulose-based substrate
- 2014
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Ingår i: Biotechnology and applied biochemistry. - : Wiley. - 0885-4513 .- 1470-8744. ; 61:1, s. 51-57
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Tidskriftsartikel (refereegranskat)abstract
- Adaptation of Dekkera bruxellensis to lignocellulose hydrolysate was investigated. Cells of D. bruxellensis were grown for 72 and 192H in batch and continuous culture, respectively (adapted cells). Cultivations in semisynthetic medium were run as controls (nonadapted cells). To test the adaptation, cells from these cultures were reinoculated in the lignocellulose medium, and growth and ethanol production characteristics were monitored. Cells adapted to lignocellulose hydrolysate had a shorter lag phase, grew faster, and produced a higher ethanol concentration as compared with nonadapted cells. A stability test showed that after cultivation in rich medium, cells partially lost the adapted phenotype but still showed faster growth and higher ethanol production as compared with nonadapted cells. Because alcohol dehydrogenase genes have been described to be involved in the adaptation to furfural in Saccharomyces cerevisiae, an analogous mechanism of adaptation to lignocelluloses hydrolysate of D. bruxellensis was hypothesized. However, gene expression analysis showed that genes homologous to S. cerevisiae ADH1 were not involved in the adaptation to lignocelluloses hydrolysate in D. bruxellensis.
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