| 61. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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The ITS region as a target for characterization of fungal communities using emerging sequencing technologies
- 2009
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Ingår i: FEMS Microbiology Letters. - 0378-1097 .- 1574-6968. ; 296:1, s. 97-101
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Tidskriftsartikel (refereegranskat)abstract
- The advent of new high-throughput DNA-sequencing technologies promises to redefine the way in which fungi and fungal communities – as well as other groups of organisms – are studied in their natural environment. With read lengths of some few hundred base pairs, massively parallel sequencing (pyrosequencing) stands out among the new technologies as the most apt for large-scale species identification in environmental samples. Although parallel pyrosequencing can generate hundreds of thousands of sequences at an exceptional speed, the limited length of the reads may pose a problem to the species identification process. This study explores whether the discrepancy in read length between parallel pyrosequencing and traditional (Sanger) sequencing will have an impact on the perceived taxonomic affiliation of the underlying species. Based on all 39 200 publicly available fungal environmental DNA sequences representing the nuclear ribosomal internal transcribed spacer (ITS) region, the results show that the two approaches give rise to quite different views of the diversity of the underlying samples. Standardization of which subregion from the ITS region should be sequenced, as well as a recognition that the composition of fungal communities as depicted through different sequencing methods need not be directly comparable, appear crucial to the integration of the new sequencing technologies with current mycological praxis.
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| 62. |
- An, Junghwa, et al.
(författare)
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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.
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| 63. |
- Anderbrant, Olle, et al.
(författare)
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Release of sex pheromone and its precursors in the pine sawfly Diprion pini (Hym., Diprionidae)
- 2005
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Ingår i: Chemoecology. - : Springer Science and Business Media LLC. - 0937-7409 .- 1423-0445. ; 15:3, s. 147-151
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Tidskriftsartikel (refereegranskat)abstract
- The first identification of a sex pheromone of a pine sawfly (Hymenoptera, Diprionidae) dates back almost thirty years. Since then, female-produced pheromones of over twenty diprionid species have been investigated by solvent extraction followed by separation and identification. However, no study has shown what the females actually release. Collection of airborne compounds using absorbtion on charcoal filter as well as solid phase microextraction (SPME) followed by analysis employing gas chromatography combined with mass spectrometry (GC-MS), revealed an unusual system in Diprion pini, in which the pheromone precursor alcohol, 3,7-dimethyl-2-tridecanol, is released together with acetic, propionic, butyric and isobutyric acids. The corresponding acetate, propionate and butyrate esters of 3,7-dimethyl-2-tridecanol were also found in the samples. All esters were electrophysiologically active, and the propionate and isobutyrate were attractive in trapping experiments. Based on these and earlier reported results, it seems that at least in part of its range, the pheromone response of D. pini is not very specific with regard to the functional group, as long as this is an ester.
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| 64. |
- Ariöz, Candan, 1983-
(författare)
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Exploring the Interplay of Lipids and Membrane Proteins
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The interplay between lipids and membrane proteins is known to affect membrane protein topology and thus have significant effect (control) on their functions. In this PhD thesis, the influence of lipids on the membrane protein function was studied using three different membrane protein models.A monotopic membrane protein, monoglucosyldiacylglyecerol synthase (MGS) from Acholeplasma laidlawii is known to induce intracellular vesicles when expressed in Escherichia coli. The mechanism leading to this unusual phenomenon was investigated by various biochemical and biophysical techniques. The results indicated a doubling of lipid synthesis in the cell, which was triggered by the selective binding of MGS to anionic lipids. Multivariate data analysis revealed a good correlation with MGS production. Furthermore, preferential anionic lipid sequestering by MGS was shown to induce a different fatty acid modeling of E. coli membranes. The roles of specific lipid binding and the probable mechanism leading to intracellular vesicle formation were also investigated.As a second model, a MGS homolog from Synechocystis sp. PCC6803 was selected. MgdA is an integral membrane protein with multiple transmembrane helices and a unique membrane topology. The influence of different type of lipids on MgdA activity was tested with different membrane fractions of Synechocystis. Results indicated a very distinct profile compared to Acholeplasma laidlawii MGS. SQDG, an anionic lipid was found to be the species of the membrane that increased the MgdA activity 7-fold whereas two other lipids (PG and PE) had only minor effects on MgdA. Additionally, a working model of MgdA for the biosynthesis and flow of sugar lipids between Synechocystis membranes was proposed.The last model system was another integral membrane protein with a distinct structure but also a different function. The envelope stress sensor, CpxA and its interaction with E. coli membranes were studied. CpxA autophosphorylation activity was found to be positively regulated by phosphatidylethanolamine and negatively by anionic lipids. In contrast, phosphorylation of CpxR by CpxA revealed to be increased with PG but inhibited by CL. Non-bilayer lipids had a negative impact on CpxA phosphotransfer activity.Taken together, these studies provide a better understanding of the significance of the interplay of lipids and model membrane proteins discussed here.
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| 65. |
- Asker, Noomi, 1968, et al.
(författare)
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Biomarker responses in eelpouts from four coastal areas in Sweden, Denmark and Germany
- 2016
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Ingår i: Marine Environmental Research. - : Elsevier BV. - 0141-1136 .- 1879-0291. ; 120, s. 32-43
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Tidskriftsartikel (refereegranskat)abstract
- To increase our understanding of possible chemical impacts on coastal fish populations in the Baltic Sea, Kattegat and Skagerrak, the viviparous eelpout (Zoarces viviparus) was used as sentinel species in two major sampling campaigns (spring and autumn) in 16 different coastal sites. Condition factor (CF), liver somatic index (LSI), gonad somatic index (GSI) were measured and the activity of the hepatic enzymes ethoxyresorufin-O-deethylase (EROD), glutathione reductase GR), glutathione S-transferase (GST), catalase (CAT) and muscular activity of acetylcholinesterase (AChE) were assessed. PAH metabolites in bile were also analyzed. The most notable finding in the data set was the low EROD activity in eelpouts collected at the relatively polluted region in Germany compared to the other regions, which could be due to an inhibition of the CYP1A-system or to adaptation to chronic exposure of pollutants in this area. Additionally, low AChE activity was noted in the German region in the autumn campaign and low AChE activity detected in the Danish region in the spring campaign. These differences suggest possible season-specific differences in the use and release of AChE-inhibiting chemicals in the Danish and German regions. Clustering of biomarkers on site level indicated a relationship between CF and GSI and suggested that sites with a high CF contained eelpout that put a larger effort into their larvae development. Clustering of the oxidative stress markers GR, GST and CAT on the individual level reflected a possible coordinated regulation of these enzymes. Overall, the results support the importance of taking into account general regional differences and seasonal variation in biomarker activity when monitoring and assessing the effects of pollution. Despite the expected seasonal variation for most of the measured endpoint, several markers (GSI, EROD and CF) vary similarly between all selected sites in both spring and autumn. This suggests that the differences between sites for these endpoints are independent of season.
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| 66. |
- Astorga, Jeanette, 1976, et al.
(författare)
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Hedgehog induction of murine vasculogenesis is mediated by Foxf1 and Bmp4
- 2007
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Ingår i: Development. - : The Company of Biologists. - 0950-1991 .- 1477-9129. ; 134:20, s. 3753-61
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Tidskriftsartikel (refereegranskat)abstract
- The first vasculature of the developing vertebrate embryo forms by assembly of endothelial cells into simple tubes from clusters of mesodermal angioblasts. Maturation of this vasculature involves remodeling, pruning and investment with mural cells. Hedgehog proteins are part of the instructive endodermal signal that triggers the assembly of the first primitive vessels in the mesoderm. We used a combination of genetic and in vitro culture methods to investigate the role of hedgehogs and their targets in murine extraembryonic vasculogenesis. We show that Bmps, in particular Bmp4, are crucial for vascular tube formation, that Bmp4 expression in extraembryonic tissues requires the forkhead transcription factor Foxf1 and that the role of hedgehog proteins in this process is to activate Foxf1 expression in the mesoderm. We show in the allantois that genetic disruption of hedgehog signaling (Smo(-/-)) has no effect on Foxf1 expression, and neither Bmp4 expression nor vasculogenesis are disturbed. By contrast, targeted inactivation of Foxf1 leads to loss of allantoic Bmp4 and vasculature. In vitro, the avascular Foxf1(-/-) phenotype can be rescued by exogenous Bmp4, and vasculogenesis in wild-type tissue can be blocked by the Bmp antagonist noggin. Hedgehogs are required for activation of Foxf1, Bmp4 expression and vasculogenesis in the yolk sac. However, vasculogenesis in Smo(-/-) yolk sacs can be rescued by exogenous Bmp4, consistent with the notion that the role of hedgehog signaling in primary vascular tube formation is as an activator of Bmp4, via Foxf1.
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| 67. |
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| 68. |
- Backhaus, Thomas, 1967
(författare)
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Interactions and their impact on the applicability of Concentration Addition for environmentally realistic mixtures
- 2011
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Ingår i: Ecosystem Protection in a Sustainable World: A challange for Science and Regulation, Abstract Book.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Regulatory guidelines make heavy use of Concentration Addition (CA) as a tool for predicting and assessing the toxicity of chemical mixtures. CA assumes that the compounds in a mixture do not interact with each other, neither in their toxicokinetic nor in their toxicodynamic phase. However, several of those interactions are described in the scientific literature for almost all major groups of environmental chemicals. These result in essentially synergistic or antagonistic mixture toxicities, i.e. higher, respectively lower mixture toxicities than expected by CA. With a view on the regulatory risk assessment of chemical mixtures, it is hence important to quantify the range of expectable synergisms, respectively antagonisms. I discuss the quantitative consequences of interactions for the predictive power of CA using two published studies on the hazards and risks of environmentally realistic mixtures. One case study concerns the human health effects of a mixture of anti-androgens, the other the ecotoxicity of a pesticide mixture. Based on a series of simulation studies in which interactions were gradually assumed to occur in the mixtures, I outline the limiting cases (worst case situations) as well as the fundamental relationship between expectable deviations from CA and number of mixture components, mixture ratio and number of interacting substances in the mixture.
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| 69. |
- Caballero, Antonio, et al.
(författare)
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Absence of mitochondrial translation control proteins extends life span by activating sirtuin-dependent silencing.
- 2011
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Ingår i: Molecular cell. - : Elsevier BV. - 1097-4164 .- 1097-2765. ; 42:3, s. 390-400
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Tidskriftsartikel (refereegranskat)abstract
- Altered mitochondrial functionality can extend organism life span, but the underlying mechanisms are obscure. Here we report that inactivating SOV1, a member of the yeast mitochondrial translation control (MTC) module, causes a robust Sir2-dependent extension of replicative life span in the absence of respiration and without affecting oxidative damage. We found that SOV1 interacts genetically with the cAMP-PKA pathway and the chromatin remodeling apparatus. Consistently, Sov1p-deficient cells displayed reduced cAMP-PKA signaling and an elevated, Sir2p-dependent, genomic silencing. Both increased silencing and life span extension in sov1Δ cells require the PKA/Msn2/4p target Pnc1p, which scavenges nicotinamide, a Sir2p inhibitor. Inactivating other members of the MTC module also resulted in Sir2p-dependent life span extension. The data demonstrate that the nuclear silencing apparatus senses and responds to the absence of MTC proteins and that this response converges with a pathway for life span extension elicited by reducing TOR signaling.
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| 70. |
- Carlsbecker, Annelie, et al.
(författare)
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The MADS-box gene DAL1 is a potential mediator of the juvenile-to-adult transition in Norway spruce (Picea abies)
- 2004
-
Ingår i: The Plant Journal. ; 40:4, s. 546-557
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Tidskriftsartikel (refereegranskat)abstract
- Progression through the plant life cycle involves changes in many essential features, most notably in the capacity to reproduce. The transition from juvenile vegetative and non-reproductive to an adult reproductive phase is gradual and can take many years; in the conifer Norway spruce, Picea abiea, typically 20-25 years. We present a detailed analysis of the activities of three regulatory genes with potential roles in the transition in Norway spruce: DAL1, a MADS-box gene related to the AGL6 group of genes from angiosperms, and the two LEAFY-related genes PaLFY and PaNLY. DAL1 activity is initiated in the shoots of juvenile trees at an age of 3-5 years, and then increases with age, whereas both LFY genes are active throughout the juvenile phase. The activity of DAL1 further shows a spatial pattern along the stem of the tree that parallels a similar gradient in physiolpoical and morphological features associated with maturation to the adult phase. Constitutive expression of DAL1 in transgenic Arabidopsis plants caused a dramatic attenuation of both juvenile and adult growth phases;flowers forming immediately after the embryogenic phase of development in severely affected plants. Taken together, our resulsts support the notion that DAL1 may have a regulatory role in the juvenile-to-adult transition in Norway spruce.
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