| 1. |
- Iqbal, Mudassir, et al.
(författare)
-
Natural variation of root lesion nematode antagonism in the biocontrol fungus Clonostachys rosea and identification of biocontrol factors through genome-wide association mapping
- 2020
-
Ingår i: Evolutionary applications. - : Wiley. - 1752-4571. ; 13, s. 2264-2283
-
Tidskriftsartikel (refereegranskat)abstract
- Biological control is a promising approach to reduce plant diseases caused by nematodes to ensure high productivity in agricultural production. Large-scale analyses of genetic variation in fungal species used for biocontrol can generate knowledge regarding interaction mechanisms that can improve efficacy of biocontrol applications. In this study, we performed a genome-wide association study (GWAS) for in vitro antagonism against the root lesion nematode Pratylenchus penetrans in 53 previously genome re-sequenced strains of the biocontrol fungus Clonostachys rosea. Nematode mortality in C. rosea potato dextrose broth (PDB) culture filtrates was highly variable and showed continuous variation (p < .001) between strains, indicating a polygenic inheritance. Twenty-one strains produced culture filtrates with higher (p <= .05) nematode mortality compared with the PDB control treatment, while ten strains lowered (p <= .05) the mortality. The difference in in vitro antagonism against P. penetrans correlated with antagonism against the soybean cyst nematode Heterodera glycines, indicating lack of host specificity in C. rosea. An empirical Bayesian multiple hypothesis testing approach identified 279 single nucleotide polymorphism markers significantly (local false sign rate < 10(-10)) associated with the trait. Genes present in the genomic regions associated with nematicidal activity included several membrane transporters, a chitinase and genes encoding proteins predicted to biosynthesize secondary metabolites. Gene deletion strains of the predicted nonribosomal peptide synthetase genes nps4 and nps5 were generated and showed increased (p <= .001) fungal growth and conidiation rates compared to the wild type. Deletion strains also exhibited reduced (p < .001) nematicidal activity and reduced (p <= .05) biocontrol efficacy against nematode root disease and against fusarium foot rot on wheat. In summary, we show that the GWAS approach can be used to identify biocontrol factors in C. rosea, specifically the putative nonribosomal peptide synthetases NPS4 and NPS5.
|
|
| 2. |
- Andersson, Viktor, 1983, et al.
(författare)
-
Algae-based biofuel production as part of an industrial cluster
- 2014
-
Ingår i: Biomass and Bioenergy. - : Elsevier BV. - 1873-2909 .- 0961-9534. ; 71, s. 113-124
-
Tidskriftsartikel (refereegranskat)abstract
- This paper presents a study on the production of biofuels from algae cultivated in municipal wastewater in Gothenburg, Sweden. A possible biorefinery concept is studied based on two cases; Case A) combined biodiesel and biogas production, and Case B) only biogas production. The cases are compared in terms of product outputs and impact on global CO2 emissions mitigation. The area efficiency of the algae-based biofuels is also compared with other biofuel production routes. The study investigates the collaboration between an algae cultivation, biofuel production processes, a wastewater treatment plant and an industrial cluster for the purpose of utilizing material flows and industrial excess heat between the actors. This collaboration provides the opportunity to reduce the CO2 emissions from the process compared to a stand-alone operation. The results show that Case A is advantageous to Case B with respect to all studied factors. It is found that the algae-based biofuel production routes investigated in this study has higher area efficiency than other biofuel production routes. The amount of algae-based biofuel possible to produce corresponds to 31 MWfuel for Case A and 26 MWfuel in Case B.
|
|
| 3. |
|
|
| 4. |
- Arnrup, K, et al.
(författare)
-
Classification of dental behavior management problems among children.
- 2007
-
Ingår i: Poster presentation at the 85th General Session & Exhibition of the IADR, New Orleans, LA, USA, March 21-24, 2007..
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Objectives: This study aimed to further investigate the heterogeneity within the group of children referred for specialist treatment because of dental behavior management problems (DBMP). A specific aim was to evaluate the validity of a previously reported cluster structure in another DBMP study group. Methods: 177 child dental patients, aged 4 to 12 at referral to a specialist pediatric dental clinic in Göteborg, Sweden, were classified into subgroups according to their personal characteristics. Cluster structure was described and compared to previously reported findings in a DBMP study group of same-aged child dental patients in Örebro, Sweden (n=74). Parental assessments of children's dental and general fear, temperament and behavior were made pre-treatment. The children also performed a vocabulary test. Data were analyzed mainly with a person-based approach using sequences of cluster analyses. Results: Classification into five different subgroups was judged the best representation of the Göteborg study group data, while four groups had been defined in Örebro. The new clusters partly paralleled the previous and were labeled (I) Extrovert, outgoing, (II) Highly fearful, multiple problems, (III) Highly fearful, (IV) Moderately fearful, externalizing, impulsive and (V) Moderately fearful, inhibited. Cluster profile II describes severe dental fear and general temperamental and behavioral problems of internalizing as well as externalizing character. Such combined problems were not clearly revealed in the Örebro cluster structure. Conclusion: The contention that children with dental behavior management problems (DBMP) comprise a heterogeneous group was strengthened. Similar, although not identical, clusters of children showing DBMP were identified in this replication study. Apart from different levels of dental fear, varying temperamental and behavioral characteristics need to be taken into consideration to better match treatment for these patients
|
|
| 5. |
- Bergius, Marianne, 1950, et al.
(författare)
-
Prediction of prolonged pain experiences during orthodontic treatment
- 2008
-
Ingår i: American Journal of Orthodontics and Dentofacial Orthopedics. - : Elsevier BV. - 1097-6752 .- 0889-5406. ; 133:3
-
Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: In this study, we investigated prolonged pain reactions in teenage orthodontic patients during a common orthodontic treatment. The aim was to examine factors predicting pain at the end of a follow-up week after placement of elastic separators. METHODS: Fifty-five patients (ages, 12-18 years) were included. Baseline assessments were made of perceived intensity of general and dental pain experiences, motivation for treatment, dental anxiety, and personality factors (self-esteem and temperament). Pain intensity was assessed on a visual analog scale, and pain medications were recorded. The patients were separated into pain and no-pain groups according to pain experiences at day 7. RESULTS: The pain group (mainly girls) had significantly higher ratings of treatment pain than in the non-pain group at all times measured except for the treatment day. Bivariate and multiple logistic regressions showed significant predictive power from motivation, dental anxiety, activity temperament, and vaccination pain. CONCLUSIONS: In this adolescent patient sample, low motivation for orthodontic treatment, high ratings of vaccination pain, elevated dental anxiety level, and low activity temperament characterized patients reporting pain 1 week after the elastic separators were placed.
|
|
| 6. |
- Broberg, Magnus, et al.
(författare)
-
A Method for Bounding the Minimal Completion Time in Multiprocessors
- 2002
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The cluster systems used today usually prohibit that a running process on one node is reallocated to another node. A parallel program developer thus has to decide how processes should be allocated to the nodes in the cluster. Finding an allocation that results in minimal completion time is NP-hard and (non-optimal) heuristic algorithms have to be used. One major drawback with heuristics is that we do not know if the result is close to optimal or not. In this paper we present a method for finding a guaranteed minimal completion time for a given program. The method can be used as a bound that helps the user to determine when it is worth-while to continue the heuristic search. Based on some parameters derived from the program, as well as some parameters describing the hardware platform, the method produces the minimal completion time bound. The method includes an aggressive branch-and-bound algorithm that has been shown to reduce the search space to 0.0004%. A practical demonstration of the method is presented using a tool that automatically derives the necessary program parameters and produces the bound without the need for a multiprocessor. This makes the method accessible for practitioners.
|
|
| 7. |
- Broberg, Magnus, et al.
(författare)
-
A Tool for Binding Threads to Processors
- 2001
-
Konferensbidrag (refereegranskat)abstract
- Many multiprocessor systems are based on distributed shared memory. It is often important to statically bind threads to processors in order to avoid remote memory access, due to performance. Finding a good allocation takes long time and it is hard to know when to stop searching for a better one. It is sometimes impossible to run the application on the target machine. The developer needs a tool that finds the good allocations without the target multiprocessor. We present a tool that uses a greedy algorithm and produces allocations that are more than 40% faster (in average) than when using a binpacking algorithm. The number of allocations to be evaluated can be reduced by 38% with a 2% performance loss. Finally, an algorithm is proposed that is promising in avoiding local maxima.
|
|
| 8. |
- Broberg, Magnus, et al.
(författare)
-
An Allocation Strategy Using Shadow-processors and Simulation Technique
- 2001
-
Konferensbidrag (refereegranskat)abstract
- Efficient performance tuning of parallel programs for multiprocessors is often hard. When it comes to assigning threads to processors there is not much support from commercial operating systems, like the Solaris operating system. The only known value is, in best case, the total execution time of each thread. The developer is left to the bin packing algorithm with no knowledge about the interactions and dependencies between the threads. The bin packing algorithm assigns, in the worst case, the threads to the processors such that the program will have the longest possible execution time. A simple example of such a program is shown. We present here a way of retrieving more information and a test mechanism that makes it possible to compare two different assignments of threads on processors also with regard to the interactions and dependencies between the threads. Also an algorithm is proposed that gives the best assignment of threads to processors in the case above where the bin packing algorithm gave the worst possible assignment. The algorithm uses shadow-processors and requires more processors than on the target machine during some allocation steps. Thus, a simulation tool like the one presented here must be used.
|
|
| 9. |
|
|
| 10. |
- Broberg, Martin, et al.
(författare)
-
Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales)
- 2021
-
Ingår i: Evolutionary applications. - : Wiley. - 1752-4571. ; 14, s. 476-497
-
Tidskriftsartikel (refereegranskat)abstract
- Various strains of the mycoparasitic fungal speciesClonostachys roseaare used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy ofC. roseain biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction betweenC. roseaand plant pathogenic fungi. Here, we determined the genome sequences of 11Clonostachysstrains, representing five species inClonostachyssubgenusBionectria, and performed a comparative genomic analysis with the aim to identify gene families evolving under selection for gene gains or losses. Several gene families predicted to encode proteins involved in biosynthesis of secondary metabolites, including polyketide synthases, nonribosomal peptide syntethases and cytochrome P450s, evolved under selection for gene gains (p <= .05) in theBionectriasubgenus lineage. This was accompanied with gene copy number increases (p <= .05) in ATP-binding cassette (ABC) transporters and major facilitator superfamily (MFS) transporters predicted to contribute to drug efflux. MostClonostachysspecies were also characterized by high numbers of auxiliary activity (AA) family 9 lytic polysaccharide monooxygenases, AA3 glucose-methanol-choline oxidoreductases and additional carbohydrate-active enzyme gene families with putative activity (or binding) towards xylan and rhamnose/pectin substrates. Particular features of theC. roseagenome included expansions (p <= .05) of the ABC-B4 multidrug resistance transporters, the ABC-C5 multidrug resistance-related transporters and the 2.A.1.3 drug:H + antiporter-2 MFS drug resistance transporters. The ABC-G1 pleiotropic drug resistance transporter geneabcG6inC. roseawas induced (p <= .009) by exposure to the antifungalFusariummycotoxin zearalenone (1121-fold) and various fungicides. Deletion ofabcG6resulted in mutants with reduced (p < .001) growth rates on media containing the fungicides boscalid, fenhexamid and iprodione. Our results emphasize the role of biosynthesis of, and protection against, secondary metabolites inClonostachyssubgenusBionectria.
|
|
