| 1. |
- Medema, M. H., et al.
(författare)
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Minimum Information about a Biosynthetic Gene cluster
- 2015
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Ingår i: Nature Chemical Biology. - : Springer Science and Business Media LLC. - 1552-4450 .- 1552-4469. ; 11:9, s. 625-631
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Forskningsöversikt (refereegranskat)abstract
- A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.
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| 2. |
- Chibueze, J. O., et al.
(författare)
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A MeerKAT, e-MERLIN, HESS, and Swift search for persistent and transient emission associated with three localized FRBs
- 2022
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press. - 0035-8711 .- 1365-2966. ; 515:1, s. 1365-1379
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Tidskriftsartikel (refereegranskat)abstract
- We report on a search for persistent radio emission from the one-off fast radio burst (11(B) 20190714A, as well as from two repeating FRBs, 20190711A and 20171019A, using the MeerKAT radio telescope. For FRB 20171019A, we also conducted simultaneous observations with the High-Energy Stereoscopic System (H.E.S.S.) in very high-energy gamma rays and searched for signals in the ultraviolet, optical, and X-ray bands. For this FRB, we obtain a UV flux upper limit of 1.39 x 10(-16) erg cm(-2) s(-1) angstrom(-1), X-ray limit of similar to 6.6 x 10(-14) erg cm(-2) s(-1) and a limit on the very high energy gamma-ray flux Phi(E > 120 GeV) < 1.7 x 10(-12) erg cm(-2) S-1. We obtain a radio upper limit of similar to 15 mu Jy beam(-1) for persistent emission at the locations of both FRBs 20190711A and 20171019A with MeerKAT. However, we detected an almost unresolved (ratio of integrated flux to peak flux is similar to 1.7 beam) radio emission, where the synthesized beam size was similar to 8 arcsec size with a peak brightness of similar to 53 mu Jy beam(-1) at MeerKAT and similar to 86 mu Jy beam(-1) at e-MERLIN, possibly associated with FRB 20190714A at z = 0.2365. This represents the first detection of persistent continuum radio emission potentially associated with a (as-yet) non- repeating FRB. If the association is confirmed, one of the strongest remaining distinction between repeaters and non-repeaters would no longer be applicable. A parallel search for repeat bursts from these FRBs revealed no new detections down to a fluence of 0.08 Jy ms for a 1 ms duration burst.
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| 3. |
- Wortman, J. R., et al.
(författare)
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The 2008 update of the Aspergillus nidulans genome annotation: A community effort
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 46, s. S2-S13
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Tidskriftsartikel (refereegranskat)abstract
- The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology. (C) 2009 Elsevier Inc. All rights reserved.
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| 4. |
- Adam, R. M., et al.
(författare)
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The XXL Survey: LI. Pressure profile and Y SZ -M scaling relation in three low-mass galaxy clusters at z∼1 observed with NIKA2
- 2024
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 684
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Tidskriftsartikel (refereegranskat)abstract
- Context. The thermodynamical properties of the intracluster medium (ICM) are driven by scale-free gravitational collapse, but they also reflect the rich astrophysical processes at play in galaxy clusters. At low masses (∼1014M) and high redshift (z≳1), these properties remain poorly constrained, observationally speaking, due to the difficulty in obtaining resolved and sensitive data. Aims. We aim to investigate the inner structure of the ICM as seen through the Sunyaev-Zel’dovich (SZ) effect in this regime of mass and redshift. We focused on the thermal pressure profile and the scaling relation between SZ flux and mass, namely the YSZ-M scaling relation. Methods. The three galaxy clusters XLSSC 072 (z=1.002), XLSSC 100 (z=0.915), and XLSSC 102 (z=0.969), with M500∼2×1014M, were selected from the XXL X-ray survey and observed with the NIKA2 millimeter camera to image their SZ signal. XMM-Newton X-ray data were used as a complement to the NIKA2 data to derive masses based on the YX-M relation and the hydrostatic equilibrium. Results. The SZ images of the three clusters, along with the X-ray and optical data, indicate dynamical activity related to merging events. The pressure profile is consistent with that expected for morphologically disturbed systems, with a relatively flat core and a shallow outer slope. Despite significant disturbances in the ICM, the three high-redshift low-mass clusters follow the YSZ-M relation expected from standard evolution remarkably well. Conclusions. These results indicate that the dominant physics that drives cluster evolution is already in place by z∼1, at least for systems with masses above M500∼1014M.
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| 5. |
- Ricci, M., et al.
(författare)
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The XXL Survey: XLIV. Sunyaev-Zel'dovich mapping of a low-mass cluster at z ∼1: A multi-wavelength approach
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 642
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Tidskriftsartikel (refereegranskat)abstract
- High-mass clusters at low redshifts have been intensively studied at various wavelengths. However, while more distant objects at lower masses constitute the bulk population of future surveys, their physical state remain poorly explored to date. In this paper, we present resolved observations of the Sunyaev-Zel'dovich (SZ) effect, obtained with the NIKA2 camera, towards the cluster of galaxies XLSSC 102, a relatively low-mass system (M500 ∼ 2 × 1014 M·) at z = 0.97 detected from the XXL survey. We combine NIKA2 SZ data, XMM-Newton X-ray data, and Megacam optical data to explore, respectively, the spatial distribution of the gas electron pressure, the gas density, and the galaxies themselves. We find significant offsets between the X-ray peak, the SZ peak, the brightest cluster galaxy, and the peak of galaxy density. Additionally, the galaxy distribution and the gas present elongated morphologies. This is interpreted as the sign of a recent major merging event, which induced a local boost of the gas pressure towards the north of XLSSC 102 and stripped the gas out of the galaxy group. The NIKA2 data are also combined with XXL data to construct the thermodynamic profiles of XLSSC 102, obtaining relatively tight constraints up to about ∼r500, and revealing properties that are typical of disturbed systems. We also explore the impact of the cluster centre definition and the implication of local pressure substructure on the recovered profiles. Finally, we derive the global properties of XLSSC 102 and compare them to those of high-mass-and-low-redshift systems, finding no strong evidence for non-standard evolution. We also use scaling relations to obtain alternative mass estimates from our profiles. The variation between these different mass estimates reflects the difficulty to accurately measure the mass of low-mass clusters at z ∼ 1, especially with low signal-to-noise ratio data and for a disturbed system. However, it also highlights the strength of resolved SZ observations alone and in combination with survey-like X-ray data. This is promising for the study of high redshift clusters from the combination of eROSITA and high resolution SZ instruments and will complement the new generation of optical surveys from facilities such as LSST and Euclid.
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| 6. |
- Engström, A E, et al.
(författare)
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Mechanical circulatory support with the Impella 5.0 device for postcardiotomy cardiogenic shock: a three-center experience
- 2013
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Ingår i: Minerva Cardioangiologica. - : Edizione Minerva Medica. - 0026-4725 .- 1827-1618. ; 61:5, s. 539-546
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Tidskriftsartikel (refereegranskat)abstract
- AIM:Postcardiotomy cardiogenic shock (PCCS) is associated with high mortality rates, despite full conventional treatment. Although the results of treatment with surgically implantable ventricular assist devices have been encouraging, the invasiveness of this treatment limits its applicability. Several less invasive devices have been developed, including the Impella system. The objective of this study was to describe our three-center experience with the Impella 5.0 device in the setting of PCCS.METHODS:From January 2004 through December 2010, a total of 46 patients were diagnosed with treatment-refractory PCCS and treated with the Impella 5.0 percutaneous left ventricular assist device at three european heart centers. Baseline and follow-up characteristics were collected retrospectively and entered into a dedicated database.RESULTS:Within the study cohort of 46 patients, mean logistic and additive EuroSCORES were 24 ± 19 and 10 ± 4. The majority of patients underwent coronary artery bypass grafting (48%) or combined surgery (33%). Half of all patients had been treated with an intra-aortic balloon pump before 5.0-implantation, 1 patient had been treated with an Impella 2.5 device. All patients were on mechanical ventilation and intravenous inotropes. The Kaplan-Meier estimate of overall 30-day survival was 39.5%.CONCLUSION:Thirty-day survival rates for patients with PCCS, refractory to aggressive conventional treatment and treated with the Impella 5.0 device, are comparable to those reported in studies evaluating surgically implantable VADs, whereas the Impella system is much less invasive. Therefore, mechanical circulatory support with the Impella 5.0 device is a suitable treatment modality for patients with severe PCCS.
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| 7. |
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| 8. |
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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. |
- Bracher, J. M., et al.
(författare)
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The Penicillium chrysogenum transporter PcAraT enables high-affinity, glucose-insensitive l-arabinose transport in Saccharomyces cerevisiae
- 2018
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Ingår i: Biotechnology for Biofuels. - : BioMed Central. - 1754-6834. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: l-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Its low-affinity uptake via the Saccharomyces cerevisiae Gal2 galactose transporter is inhibited by d-glucose. Especially at low concentrations of l-arabinose, uptake is an important rate-controlling step in the complete conversion of these feedstocks by engineered pentose-metabolizing S. cerevisiae strains. Results: Chemostat-based transcriptome analysis yielded 16 putative sugar transporter genes in the filamentous fungus Penicillium chrysogenum whose transcript levels were at least threefold higher in l-arabinose-limited cultures than in d-glucose-limited and ethanol-limited cultures. Of five genes, that encoded putative transport proteins and showed an over 30-fold higher transcript level in l-arabinose-grown cultures compared to d-glucose-grown cultures, only one (Pc20g01790) restored growth on l-arabinose upon expression in an engineered l-arabinose-fermenting S. cerevisiae strain in which the endogenous l-arabinose transporter, GAL2, had been deleted. Sugar transport assays indicated that this fungal transporter, designated as PcAraT, is a high-affinity (K m = 0.13 mM), high-specificity l-arabinose-proton symporter that does not transport d-xylose or d-glucose. An l-arabinose-metabolizing S. cerevisiae strain in which GAL2 was replaced by PcaraT showed 450-fold lower residual substrate concentrations in l-arabinose-limited chemostat cultures than a congenic strain in which l-arabinose import depended on Gal2 (4.2 × 10-3 and 1.8 g L-1, respectively). Inhibition of l-arabinose transport by the most abundant sugars in hydrolysates, d-glucose and d-xylose was far less pronounced than observed with Gal2. Expression of PcAraT in a hexose-phosphorylation-deficient, l-arabinose-metabolizing S. cerevisiae strain enabled growth in media supplemented with both 20 g L-1 l-arabinose and 20 g L-1 d-glucose, which completely inhibited growth of a congenic strain in the same condition that depended on l-arabinose transport via Gal2. Conclusion: Its high affinity and specificity for l-arabinose, combined with limited sensitivity to inhibition by d-glucose and d-xylose, make PcAraT a valuable transporter for application in metabolic engineering strategies aimed at engineering S. cerevisiae strains for efficient conversion of lignocellulosic hydrolysates.
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| 14. |
- Kerkhoven, Eduard, 1985, et al.
(författare)
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Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei
- 2013
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Ingår i: PLoS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 9:12, s. Art. no. e1003371-
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Tidskriftsartikel (refereegranskat)abstract
- Dynamic models of metabolism can be useful in identifying potential drug targets, especially in unicellular organisms. A model of glycolysis in the causative agent of human African trypanosomiasis, Trypanosoma brucei, has already shown the utility of this approach. Here we add the pentose phosphate pathway (PPP) of T. brucei to the glycolytic model. The PPP is localized to both the cytosol and the glycosome and adding it to the glycolytic model without further adjustments leads to a draining of the essential bound-phosphate moiety within the glycosome. This phosphate “leak” must be resolved for the model to be a reasonable representation of parasite physiology. Two main types of theoretical solution to the problem could be identified: (i) including additional enzymatic reactions in the glycosome, or (ii) adding a mechanism to transfer bound phosphates between cytosol and glycosome. One example of the first type of solution would be the presence of a glycosomal ribokinase to regenerate ATP from ribose 5-phosphate and ADP. Experimental characterization of ribokinase in T. brucei showed that very low enzyme levels are sufficient for parasite survival, indicating that other mechanisms are required in controlling the phosphate leak. Examples of the second type would involve the presence of an ATP:ADP exchanger or recently described permeability pores in the glycosomal membrane, although the current absence of identified genes encoding such molecules impedes experimental testing by genetic manipulation. Confronted with this uncertainty, we present a modeling strategy that identifies robust predictions in the context of incomplete system characterization. We illustrate this strategy by exploring the mechanism underlying the essential function of one of the PPP enzymes, and validate it by confirming the model predictions experimentally.
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| 15. |
- Kersten, Elin T G, et al.
(författare)
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Can a single dose response predict the effect of montelukast on exercise-induced bronchoconstriction?
- 2015
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Ingår i: Pediatric Pulmonology. - : Wiley. - 8755-6863.
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Tidskriftsartikel (refereegranskat)abstract
- Exercise-induced bronchoconstriction (EIB) can be prevented by a single dose of montelukast (MLK). The effect is variable, similar to the variable responsiveness observed after daily treatment with MLK. We hypothesized that the effect of a single MLK-dose (5 or 10 mg) on EIB could predict the clinical effectiveness of longer term once daily treatment.
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| 16. |
- Khalid, M., et al.
(författare)
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Genetic Risk of Autism Spectrum Disorder in a Pakistani Population
- 2020
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 11:10
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Tidskriftsartikel (refereegranskat)abstract
- Autism spectrum disorder (ASD) is a group of complex multifactorial neurodevelopmental and neuropsychiatric disorders in children characterized by impairment of communication and social interaction. Several genes with associated single nucleotide polymorphisms (SNPs) have been identified for ASD in different genetic association studies, meta-analyses, and genome-wide association studies (GWAS). However, associations between different SNPs and ASD vary from population to population. Four SNPs in genes CNTNAP2, EIF4E, ATP2B2, CACNA1C, and SNP rs4307059 (which is found between CDH9 and CDH10 genes) have been identified and reported as candidate risk factors for ASD. The aim of the present study was, for the first time, to assess the association of SNPs in these genes with ASD in the Pakistani population. PCR-based genotyping was performed using allele-specific primers in 93 ASD and 93 control Pakistani individuals. All genetic associations, genotype frequencies, and allele frequencies were computed as odds' ratios (ORs) using logistic regression with a threshold of p <= 0.01 to determine statistical significance. We found that the homozygous genotypes of mutant T alleles of CNTNAP2 and ATP2B2 were significantly associated with Pakistani ASD patients in unadjusted ORs (p < 0.01), but their significance score was lost in the adjusted model. Other SNPs such as rs4307059, rs17850950 of EIF4E, and rs1006737 of CACNA1C were not statistically significant. Based on this, we conclude that SNPs are not associated with, or are not the main cause of, autism in the Pakistani population, indicating the involvement of additional players, which need to be investigated in future studies in a large population size. One of the limitations of present study is its small sample size. However, this study, being the first on Pakistani ASD patients, may lay the foundations for future studies in larger samples.
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| 17. |
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| 18. |
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| 19. |
- Grijseels, S., et al.
(författare)
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Identification of the decumbenone biosynthetic gene cluster in penicillium decumbens and the importance for production of calbistrin
- 2018
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Ingår i: Fungal Biology and Biotechnology. - : Springer Science and Business Media LLC. - 2054-3085. ; 5:1, s. 1-17
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Tidskriftsartikel (refereegranskat)abstract
- Background: Filamentous fungi are important producers of secondary metabolites, low molecular weight molecules that often have bioactive properties. Calbistrin A is a secondary metabolite with an interesting structure that was recently found to have bioactivity against leukemia cells. It consists of two polyketides linked by an ester bond: a bicy-clic decalin containing polyketide with structural similarities to lovastatin, and a linear 12 carbon dioic acid structure. Calbistrin A is known to be produced by several uniseriate black Aspergilli, Aspergillus versicolor-related species, and Penicillia. Penicillium decumbens produces calbistrin A and B as well as several putative intermediates of the calbistrin pathway, such as decumbenone A-B and versiol. Results: A comparative genomics study focused on the polyketide synthase (PKS) sets found in three full genome sequence calbistrin producing fungal species, P. decumbens, A. aculeatus and A. versicolor, resulted in the identification of a novel, putative 13-membered calbistrin producing gene cluster (calA to calM). Implementation of the CRISPR/ Cas9 technology in P. decumbens allowed the targeted deletion of genes encoding a polyketide synthase (calA), a major facilitator pump (calB) and a binuclear zinc cluster transcription factor (calC). Detailed metabolic profiling, using UHPLC-MS, of the ∆calA (PKS) and ∆calC ( TF) strains confirmed the suspected involvement in calbistrin productions as neither strains produced calbistrin nor any of the putative intermediates in the pathway. Similarly analysis of the excreted metabolites in the ∆calB (MFC-pump) strain showed that the encoded pump was required for efficient export of calbistrin A and B. Conclusion: Here we report the discovery of a gene cluster (calA-M) involved in the biosynthesis of the polyketide calbistrin in P. decumbens. Targeted gene deletions proved the involvement of CalA (polyketide synthase) in the biosynthesis of calbistrin, CalB (major facilitator pump) for the export of calbistrin A and B and CalC for the transcriptional regulation of the cal-cluster. This study lays the foundation for further characterization of the calbistrin biosynthetic pathway in multiple species and the development of an efficient calbistrin producing cell factory.
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| 20. |
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| 21. |
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| 22. |
- Verhoeven, Maarten D., et al.
(författare)
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Laboratory evolution of a glucose-phosphorylation-deficient, arabinose-fermenting S. cerevisiae strain reveals mutations in GAL2 that enable glucose-insensitive L-arabinose uptake
- 2018
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Ingår i: FEMS yeast research (Print). - : Oxford University Press. - 1567-1356 .- 1567-1364. ; 18:6
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Tidskriftsartikel (refereegranskat)abstract
- Cas9-assisted genome editing was used to construct an engineered glucose-phosphorylation-negative S. cerevisiae strain, expressing the Lactobacillus plantarum L-arabinose pathway and the Penicillium chrysogenum transporter PcAraT. This strain, which showed a growth rate of 0.26 h(-1) on L-arabinose in aerobic batch cultures, was subsequently evolved for anaerobic growth on L-arabinose in the presence of D-glucose and D-xylose. In four strains isolated from two independent evolution experiments the galactose-transporter gene GAL2 had been duplicated, with all alleles encoding Gal2(N376T) or Gal(2N376I) substitutions. In one strain, a single GAL2 allele additionally encoded a Gal2(T89I) substitution, which was subsequently also detected in the independently evolved strain IMS0010. In C-14-sugar-transport assays, Gal2(N376S), Gal2(N376T) and Gal(2N376I) substitutions showed a much lower glucose sensitivity of L-arabinose transport and a much higher Km for D-glucose transport than wild-type Gal2. Introduction of the Gal2(N376I) substitution in a non-evolved strain enabled growth on L-arabinose in the presence of D-glucose. Gal2(N376T), T89I and Gal2(T89I) variants showed a lower K-m for L-arabinose and a higher K-m for D-glucose than wild-type Gal2, while reverting Gal2(N376T), T89I to Gal2(N376) in an evolved strain negatively affected anaerobic growth on L-arabinose. This study indicates that optimal conversion of mixed-sugar feedstocks may require complex 'transporter landscapes', consisting of sugar transporters with complementary kinetic and regulatory properties.
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| 23. |
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| 25. |
- Driessen, Peter P. J., et al.
(författare)
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Governance Strategies for Improving Flood Resilience in the Face of Climate Change
- 2018
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Ingår i: Water. - : MDPI. - 2073-4441. ; 10:11
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Tidskriftsartikel (refereegranskat)abstract
- Flooding is the most common of all natural disasters and accounts for large numbers of casualties and a high amount of economic damage worldwide. To be ‘flood resilient’, countries should have sufficient capacity to resist, the capacity to absorb and recover, and the capacity to transform and adapt. Based on international comparative research, we conclude that six key governance strategies will enhance ‘flood resilience’ and will secure the necessary capacities. These strategies pertain to: (i) the diversification of flood risk management approaches; (ii) the alignment of flood risk management approaches to overcome fragmentation; (iii) the involvement, cooperation, and alignment of both public and private actors in flood risk management; (iv) the presence of adequate formal rules that balance legal certainty and flexibility; (v) the assurance of sufficient financial and other types of resources; (vi) the adoption of normative principles that adequately deal with distributional effects. These governance strategies appear to be relevant across different physical and institutional contexts. The findings may also hold valuable lessons for the governance of climate adaptation more generally.
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| 26. |
- Farbru, E, et al.
(författare)
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EFNS guideline on diagnosis and management of post-polio syndrome. Report of an EFNS task force
- 2006
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Ingår i: European Journal of Neurology. - : Wiley. - 1351-5101 .- 1468-1331. ; 13:8, s. 795-801
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Tidskriftsartikel (refereegranskat)abstract
- Post-polio syndrome (PPS) is characterized by new or increased muscular weakness, atrophy, muscle pain and fatigue several years after acute polio. The aim of the article is to prepare diagnostic criteria for PPS, and to evaluate the existing evidence for therapeutic interventions. The Medline, EMBASE and ISI databases were searched. Consensus in the group was reached after discussion by e-mail. We recommend Halstead's definition of PPS from 1991 as diagnostic criteria. Supervised, aerobic muscular training, both isokinetic and isometric, is a safe and effective way to prevent further decline for patients with moderate weakness (Level B). Muscular training can also improve muscular fatigue, muscle weakness and pain. Training in a warm climate and non-swimming water exercises are particularly useful (Level B). Respiratory muscle training can improve pulmonary function. Recognition of respiratory impairment and early introduction of non-invasive ventilatory aids prevent or delay further respiratory decline and the need for invasive respiratory aid (Level C). Group training, regular follow-up and patient education are useful for the patients’ mental status and well-being. Weight loss, adjustment and introduction of properly fitted assistive devices should be considered (good practice points). A small number of controlled studies of potential-specific treatments for PPS have been completed, but no definitive therapeutic effect has been reported for the agents evaluated (pyridostigmine, corticosteroids, amantadine). Future randomized trials should particularly address the treatment of pain, which is commonly reported by PPS patients. There is also a need for studies evaluating the long-term effects of muscular training.
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| 27. |
- Guzman-Chavez, F., et al.
(författare)
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Mechanism and regulation of sorbicillin biosynthesis by Penicillium chrysogenum
- 2017
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Ingår i: Microbial Biotechnology. - : Wiley. - 1751-7907 .- 1751-7915. ; 10:4, s. 958-968
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Tidskriftsartikel (refereegranskat)abstract
- Penicillium chrysogenum is a filamentous fungus that is used to produce -lactams at an industrial scale. At an early stage of classical strain improvement, the ability to produce the yellow-coloured sorbicillinoids was lost through mutation. Sorbicillinoids are highly bioactive of great pharmaceutical interest. By repair of a critical mutation in one of the two polyketide synthases in an industrial P.chrysogenum strain, sorbicillinoid production was restored at high levels. Using this strain, the sorbicillin biosynthesis pathway was elucidated through gene deletion, overexpression and metabolite profiling. The polyketide synthase enzymes SorA and SorB are required to generate the key intermediates sorbicillin and dihydrosorbicillin, which are subsequently converted to (dihydro)sorbillinol by the FAD-dependent monooxygenase SorC and into the final product oxosorbicillinol by the oxidoreductase SorD. Deletion of either of the two pks genes not only impacted the overall production but also strongly reduce the expression of the pathway genes. Expression is regulated through the interplay of two transcriptional regulators: SorR1 and SorR2. SorR1 acts as a transcriptional activator, while SorR2 controls the expression of sorR1. Furthermore, the sorbicillinoid pathway is regulated through a novel autoinduction mechanism where sorbicillinoids activate transcription.
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| 30. |
- Lacas, Benjamin, et al.
(författare)
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Role of radiotherapy fractionation in head and neck cancers (MARCH) : an updated meta-analysis
- 2017
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Ingår i: The Lancet Oncology. - 1470-2045 .- 1474-5488. ; 18:9, s. 1221-1237
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Tidskriftsartikel (refereegranskat)abstract
- Background The Meta-Analysis of Radiotherapy in squamous cell Carcinomas of Head and neck (MARCH) showed that altered fractionation radiotherapy is associated with improved overall and progression-free survival compared with conventional radiotherapy, with hyperfractionated radiotherapy showing the greatest benefit. This update aims to confirm and explain the superiority of hyperfractionated radiotherapy over other altered fractionation radiotherapy regimens and to assess the benefit of altered fractionation within the context of concomitant chemotherapy with the inclusion of new trials. Methods For this updated meta-analysis, we searched bibliography databases, trials registries, and meeting proceedings for published or unpublished randomised trials done between Jan 1, 2009, and July 15, 2015, comparing primary or postoperative conventional fractionation radiotherapy versus altered fractionation radiotherapy (comparison 1) or conventional fractionation radiotherapy plus concomitant chemotherapy versus altered fractionation radiotherapy alone (comparison 2). Eligible trials had to start randomisation on or after Jan 1, 1970, and completed accrual before Dec 31, 2010; had to have been randomised in a way that precluded prior knowledge of treatment assignment; and had to include patients with non-metastatic squamous cell carcinoma of the oral cavity, oropharynx, hypopharynx, or larynx undergoing first-line curative treatment. Trials including a non-conventional radiotherapy control group, investigating hypofractionated radiotherapy, or including mostly nasopharyngeal carcinomas were excluded. Trials were grouped in three types of altered fractionation: hyperfractionated, moderately accelerated, and very accelerated. Individual patient data were collected and combined with a fixed-effects model based on the intention-to-treat principle. The primary endpoint was overall survival. Findings Comparison 1 (conventional fractionation radiotherapy vs altered fractionation radiotherapy) included 33 trials and 11 423 patients. Altered fractionation radiotherapy was associated with a significant benefit on overall survival (hazard ratio [HR] 0·94, 95% CI 0·90–0·98; p=0·0033), with an absolute difference at 5 years of 3·1% (95% CI 1·3–4·9) and at 10 years of 1·2% (−0·8 to 3·2). We found a significant interaction (p=0·051) between type of fractionation and treatment effect, the overall survival benefit being restricted to the hyperfractionated group (HR 0·83, 0·74–0·92), with absolute differences at 5 years of 8·1% (3·4 to 12·8) and at 10 years of 3·9% (−0·6 to 8·4). Comparison 2 (conventional fractionation radiotherapy plus concomitant chemotherapy versus altered fractionation radiotherapy alone) included five trials and 986 patients. Overall survival was significantly worse with altered fractionation radiotherapy compared with concomitant chemoradiotherapy (HR 1·22, 1·05–1·42; p=0·0098), with absolute differences at 5 years of −5·8% (−11·9 to 0·3) and at 10 years of −5·1% (−13·0 to 2·8). Interpretation This update confirms, with more patients and a longer follow-up than the first version of MARCH, that hyperfractionated radiotherapy is, along with concomitant chemoradiotherapy, a standard of care for the treatment of locally advanced head and neck squamous cell cancers. The comparison between hyperfractionated radiotherapy and concomitant chemoradiotherapy remains to be specifically tested. Funding Institut National du Cancer; and Ligue Nationale Contre le Cancer.
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| 33. |
- Mangnus, Astrid C., et al.
(författare)
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Envisioning alternatives in pre-structured urban sustainability transformations: Too late to change the future?
- 2022
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Ingår i: Cities. - : Elsevier BV. - 0264-2751. ; 120
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Tidskriftsartikel (refereegranskat)abstract
- In the governance of urban sustainability transformations, participatory futures practices are increasingly popular. Yet there is a rising awareness that the success or failure of these practices depends on how they are staged and the context in which they are conducted. These contextual factors are often less than ideal, and futures practices take place at the crossroads of many pre-determined agendas and priorities. We distinguish four factors that shape the effects of participatory futures practices: 1) how the institutional landscape constrains or enables a project aimed at urban sustainability transformations; 2) the participatory culture surrounding the project; 3) the project design; and 4) the futures methods applied. We assess these factors in three cities within the European H2020 IRIS Smart Cities project. In each city, project members participated in sessions where they designed citizen engagement using a futures methodology: the novel Scope and Ladder models. Each city reflects a different combination of the four contextual factors. We find that space for exploration and re-imagining can be found and optimized under imperfect conditions. Drawing on the results of the three cases, we conclude with a set of recommendations for the funders, project members and futures organizers of urban sustainability transformation projects.
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| 34. |
- Mózsik, László, et al.
(författare)
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CRISPR-based transcriptional activation tool for silent genes in filamentous fungi
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Filamentous fungi are historically known to be a rich reservoir of bioactive compounds that are applied in a myriad of fields ranging from crop protection to medicine. The surge of genomic data available shows that fungi remain an excellent source for new pharmaceuticals. However, most of the responsible biosynthetic gene clusters are transcriptionally silent under laboratory growth conditions. Therefore, generic strategies for activation of these clusters are required. Here, we present a genome-editing-free, transcriptional regulation tool for filamentous fungi, based on the CRISPR activation (CRISPRa) methodology. Herein, a nuclease-defective mutant of Cas9 (dCas9) was fused to a highly active tripartite activator VP64-p65-Rta (VPR) to allow for sgRNA directed targeted gene regulation. dCas9-VPR was introduced, together with an easy to use sgRNA “plug-and-play” module, into a non-integrative AMA1-vector, which is compatible with several filamentous fungal species. To demonstrate its potential, this vector was used to transcriptionally activate a fluorescent reporter gene under the control of the penDE core promoter in Penicillium rubens. Subsequently, we activated the transcriptionally silent, native P. rubens macrophorin biosynthetic gene cluster by targeting dCas9-VPR to the promoter region of the transcription factor macR. This resulted in the production of antimicrobial macrophorins. This CRISPRa technology can be used for the rapid and convenient activation of silent fungal biosynthetic gene clusters, and thereby aid in the identification of novel compounds such as antimicrobials.
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| 35. |
- Mózsik, László, et al.
(författare)
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Modular synthetic biology toolkit for filamentous fungi
- 2021
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Ingår i: ACS Synthetic Biology. - : American Chemical Society (ACS). - 2161-5063. ; 10:11, s. 2850-2861
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Tidskriftsartikel (refereegranskat)abstract
- Filamentous fungi are highly productive cell factories, often used in industry for the production of enzymes and small bioactive compounds. Recent years have seen an increasing number of synthetic-biology-based applications in fungi, emphasizing the need for a synthetic biology toolkit for these organisms. Here we present a collection of 96 genetic parts, characterized in Penicillium or Aspergillus species, that are compatible and interchangeable with the Modular Cloning system. The toolkit contains natural and synthetic promoters (constitutive and inducible), terminators, fluorescent reporters, and selection markers. Furthermore, there are regulatory and DNA-binding domains of transcriptional regulators and components for implementing different CRISPR-based technologies. Genetic parts can be assembled into complex multipartite assemblies and delivered through genomic integration or expressed from an AMA1-sequence-based, fungal-replicating shuttle vector. With this toolkit, synthetic transcription units with established promoters, fusion proteins, or synthetic transcriptional regulation devices can be more rapidly assembled in a standardized and modular manner for novel fungal cell factories.
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| 36. |
- Mózsik, László, et al.
(författare)
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Synthetic control devices for gene regulation in Penicillium chrysogenum
- 2019
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Ingår i: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 18:1, s. 203-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Orthogonal, synthetic control devices were developed for Penicillium chrysogenum, a model filamentous fungus and industrially relevant cell factory. In the synthetic transcription factor, the QF DNA-binding domain of the transcription factor of the quinic acid gene cluster of Neurospora crassa is fused to the VP16 activation domain. This synthetic transcription factor controls the expression of genes under a synthetic promoter containing quinic acid upstream activating sequence (QUAS) elements, where it binds. A gene cluster may demand an expression tuned individually for each gene, which is a great advantage provided by this system. RESULTS: The control devices were characterized with respect to three of their main components: expression of the synthetic transcription factors, upstream activating sequences, and the affinity of the DNA binding domain of the transcription factor to the upstream activating domain. This resulted in synthetic expression devices, with an expression ranging from hardly detectable to a level similar to that of highest expressed native genes. The versatility of the control device was demonstrated by fluorescent reporters and its application was confirmed by synthetically controlling the production of penicillin. CONCLUSIONS: The characterization of the control devices in microbioreactors, proved to give excellent indications for how the devices function in production strains and conditions. We anticipate that these well-characterized and robustly performing control devices can be widely applied for the production of secondary metabolites and other compounds in filamentous fungi.
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| 37. |
- Mózsik, László, et al.
(författare)
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Synthetic control devices for gene regulation in Penicillium chrysogenum
- 2020
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Synthetic biology aims at controlled gene regulation that can lead to increased production of chemicals and pharmaceuticals. In this work synthetic control devices were developed for Penicillium chrysogenum, a model filamentous fungus and industrially relevant cell factory.
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| 38. |
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| 39. |
- Pohl, Carsten, et al.
(författare)
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Genome editing in penicillium chrysogenum using cas9 ribonucleoprotein particles
- 2018
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Ingår i: Methods in Molecular Biology. - New York, NY : Springer New York. - 1940-6029 .- 1064-3745. ; 1772, s. 213-232
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Several CRISPR/Cas9 tools have been recently established for precise genome editing in a wide range of filamentous fungi. This genome editing platform offers high flexibility in target selection and the possibility of introducing genetic deletions without the introduction of transgenic sequences. This chapter describes an approach for the transformation of Penicillium chrysogenum protoplasts with preassembled ribonucleoprotein particles (RNPs) consisting of purified Cas9 protein and in vitro transcribed single guide RNA (sgRNA) for the deletion of genome sequences or their replacement with alternative sequences. This method is potentially transferable to all fungal strains where protoplasts can be obtained from.
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| 40. |
- Reimann, Julia, et al.
(författare)
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Regulation of archaella expression by the FHA and von Willebrand domain-containing proteins ArnA and ArnB in Sulfolobus acidocaldarius
- 2012
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Ingår i: Molecular Microbiology. - : Wiley. - 0950-382X .- 1365-2958. ; 86:1, s. 24-36
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Tidskriftsartikel (refereegranskat)abstract
- The ability of microorganisms to sense and respond to sudden changes in their environment is often based on regulatory systems comprising reversible protein phosphorylation. The archaellum (former: archaeal flagellum) is used for motility in Archaea and therefore functionally analogous to the bacterial flagellum. In contrast with archaellum-mediated movement in certain members of the Euryarchaeota, this process, including its regulation, remains poorly studied in crenarchaeal organisms like Sulfolobus species. Recently, it was shown in Sulfolobus acidocaldarius that tryptone limiting conditions led to the induction of archaella expression and assembly. Here we have identified two proteins, the FHA domain-containing protein ArnA and the vWA domain-containing protein ArnB that are involved in regulating archaella expression in S. acidocaldarius. Both proteins are phosphorylated by protein kinases in vitro and interact strongly in vivo. Phenotypic analyses revealed that these two proteins are repressors of archaella expression. These results represent the first step in understanding the networks that underlie regulation of cellular motility in Crenarchaeota and emphasize the importance of protein phosphorylation in the regulation of cellular processes in the Archaea.
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| 41. |
- Triyanti, Annisa, et al.
(författare)
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Clarifying and strengthening the role of law and governance in climate scenario frameworks
- 2023
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Ingår i: Earth System Governance. - 2589-8116. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- Shared socio-economic pathways (SSPs) and shared policy assumptions (SPAs) are lauded as a common basis for climate scenario research across disciplines, yet they lack essential legal and governance elements that are indispensable when assessing future development pathways. This article sets out to address this shortcoming by explaining the interrelated but distinct features of law and governance and their downplayed roles in climate scenario research. We explore the extent to which legal and govsternance features are included in the current SSP and SPA development process and then suggest that the substance of legal and governance features in climate scenario frameworks could be enriched in four ways, by: 1) identifying the nuances of legal and policy objectives; 2) assessing the effectiveness of institutions and instruments; 3) integrating the assessment of the flexibility and adaptability of legal and governance systems into the projection of long-term pathways; and 4) responding to the urgent need to integrate climate and energy justice while still cautiously considering normative principles to be opportunities and challenges. We further argue that future climate scenario frameworks should consider law and governance at multiple scales and in distinct contexts to improve the usability, applicability, and reliability of the integrated pathways. Finally, in order to project future risks, this article suggests improvement regarding the processes, including inter- and transdisciplinary inclusion that can potentially be considered when furthering climate scenario frameworks that enhance understanding of the complex, uncertain future and the long-term consequences of certain decisions.
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| 42. |
- Viggiano, Annarita, et al.
(författare)
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Pathway for the biosynthesis of the pigment chrysogine by Penicillium chrysogenum
- 2018
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Ingår i: Applied and Environmental Microbiology. - 1098-5336 .- 0099-2240. ; 84:4
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Tidskriftsartikel (refereegranskat)abstract
- Chrysogine is a yellow pigment produced by Penicillium chrysogenum and other filamentous fungi. Although the pigment was first isolated in 1973, its biosynthetic pathway has so far not been resolved. Here, we show that deletion of the highly expressed nonribosomal peptide synthetase (NRPS) gene Pc21g12630 (chyA) resulted in a decrease in the production of chrysogine and 13 related compounds in the culture broth of P. chrysogenum. Each of the genes of the chyAcontaining gene cluster was individually deleted, and corresponding mutants were examined by metabolic profiling in order to elucidate their function. The data suggest that the NRPS ChyA mediates the condensation of anthranilic acid and alanine into the intermediate 2-(2-aminopropanamido)benzoic acid, which was verified by feeding experiments of a ΔchyA strain with the chemically synthesized product. The remainder of the pathway is highly branched, yielding at least 13 chrysogine-related compounds.
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| 43. |
- Wienicke, Frederik J., et al.
(författare)
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Efficacy and moderators of short-term psychodynamic psychotherapy for depression : A systematic review and meta-analysis of individual participant data
- 2023
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Ingår i: Clinical Psychology Review. - : Elsevier. - 0272-7358 .- 1873-7811. ; 101
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Forskningsöversikt (refereegranskat)abstract
- Background: Short-term psychodynamic psychotherapy (STPP) is frequently used to treat depression, but it is unclear which patients might benefit specifically. Individual participant data (IPD) meta-analyses can provide more precise effect estimates than conventional meta-analyses and identify patient-level moderators. This IPD meta-analysis examined the efficacy and moderators of STPP for depression compared to control conditions.Methods: PubMed, PsycInfo, Embase, and Cochrane Library were searched September 1st, 2022, to identify randomized trials comparing STPP to control conditions for adults with depression. IPD were requested and analyzed using mixed-effects models.Results: IPD were obtained from 11 of the 13 (84.6%) studies identified (n = 771/837, 92.1%; mean age = 40.8, SD = 13.3; 79.3% female). STPP resulted in significantly lower depressive symptom levels than control conditions at post-treatment (d = −0.62, 95%CI [−0.76, −0.47], p < .001). At post-treatment, STPP was more efficacious for participants with longer rather than shorter current depressive episode durations.Conclusions: These results support the evidence base of STPP for depression and indicate episode duration as an effect modifier. This moderator finding, however, is observational and requires prospective validation in future large-scale trials.
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