Mitochondrial Genome of Phlebia radiata Is the Second Largest (156 kbp) among Fungi and Features Signs of Genome Flexibility and Recent Recombination Events

Mitochondria are eukaryotic organelles supporting individual life-style via generation of proton motive force and cellular energy, and indispensable metabolic pathways. As part of genome sequencing of the white rot Basidiomycota species Phlebia radiata, we first assembled its mitochondrial genome (mtDNA). So far, the 156 348 bp mtDNA is the second largest described for fungi, and of considerable size among eukaryotes. The P. radiata mtDNA assembled as single circular dsDNA molecule containing genes for the large and small ribosomal RNAs, 28 transfer RNAs, and over 100 open reading frames encoding the 14 fungal conserved protein subunits of the mitochondrial complexes I, III, IV, and V. Two genes (atp6 and tRNA-Ile^GAU) were duplicated within 6.1 kbp inverted region, which is a unique feature of the genome. The large mtDNA size, however, is explained by the dominance of intronic and intergenic regions (sum 80% of mtDNA sequence). The intergenic DNA stretches harness short (≤200 nt) repetitive, dispersed and overlapping sequence elements in abundance. Long self-splicing introns of types I and II interrupt eleven of the conserved genes (cox1,2,3; cob; nad1,2,4,4L,5; rnl; rns). The introns embrace a total of 57 homing endonucleases with LAGLIDADGD and GYI-YIG core motifs, which makes P. radiata mtDNA to one of the largest known reservoirs of intron-homing endonucleases. The inverted duplication, intergenic stretches, and intronic features are indications of dynamics and genetic flexibility of the mtDNA, not fully recognized to this extent in fungal mitochondrial genomes previously, thus giving new insights for the evolution of organelle genomes in eukaryotes.     

High cholesterol diet induces tau hyperphosphorylation in apolipoprotein E deficient mice

We analysed the effects of high cholesterol (HC) intake and reduced apolipoprotein E (apoE) activity on tau phosphorylation and on the activities of the major tau kinases and phosphatases in brains from wild-type and apoE-knockout (apoEKO) mice. We show that HC diet potently induced intraneuronal accumulation of hyperphosphorylated tau in apoEKO mice, as well as upregulation of several tau kinases, without affecting tau phosphatases. Our results suggest an interaction between dietary and genetic factors in the development of tauopathies, which can be relevant in humans, where the apoE4 isoform could have a lack of function as compared to other isoforms.     

Temporal Trends in Metal Pollution: Using Bird Excrement as Indicator

Past mining and smelting activities have resulted in metal polluted environments all over the world, but long-term monitoring data is often scarce, especially in higher trophic levels. In this study we used bird (Parus major and Ficedula hypoleuca) excrement to monitor metal pollution in the terrestrial environment following 16 years of continuously reduced emissions from a copper/nickel smelter in Finland. In the early 1990s, lead and cadmium concentrations dropped significantly in excrement, but the reduction did not directly reflect the changes in atmospheric emission from the smelter. This is likely due to a continuous contribution of metals also from the soil pool. We conclude that bird excrement can be used to assess changes in the environment as a whole but not specifically changes in atmospheric emission. Inter-annual variation in excrement concentration of especially copper and nickel demonstrates the importance of long-term monitoring to discern significant trends.     

Identification and mapping of resistance gene analogs and a white rust resistance locus in<Emphasis Type="Italic"> Brassica rapa</Emphasis> ssp.<Emphasis Type="Italic"> oleifera</Emphasis>

The objective of this investigation was to tag a locus for white rust resistance in a Brassica rapa ssp. oleifera F₂ population segregating for this trait, using bulked segregant analysis with random amplified polymorphic DNA (RAPD) markers, linkage mapping and a candidate gene approach based on resistance gene analogs (RGAs). The resistance source was the Finnish line Bor4109. The reaction against white rust races 7a and 7v was scored in 20 seedlings from each self-pollinated F₂ individual. The proportion of resistant plants among these F₃ families varied from 0 to 67%. Bulked segregant analysis did not reveal any markers linked with resistance and, therefore, a linkage map with 81 markers was created. A locus that accounted for 18.4% of the variation in resistance to white rust was mapped to linkage group (LG) 2 near the RAPD marker Z19a. During the study, a bacterial resistance gene homologous to Arabidopsis RPS2 and six different RGAs were sequenced. RPS2 and five of the RGAs were mapped to linkage groups LG1, LG4 and LG9. Unfortunately, none of the RGAs could be shown to be associated with white rust resistance.Communicated by H.C. BeckerThe nucleotide sequence data reported has been deposited in the Genbank under the accession numbers AF315081–AF315087.     

Background Speech Effects on Sentence Processing during Reading: An Eye Movement Study

Effects of background speech on reading were examined by playing aloud different types of background speech, while participants read long, syntactically complex and less complex sentences embedded in text. Readers’ eye movement patterns were used to study online sentence comprehension. Effects of background speech were primarily seen in rereading time. In Experiment 1, foreign-language background speech did not disrupt sentence processing. Experiment 2 demonstrated robust disruption in reading as a result of semantically and syntactically anomalous scrambled background speech preserving normal sentence-like intonation. Scrambled speech that was constructed from the text to-be read did not disrupt reading more than scrambled speech constructed from a different, semantically unrelated text. Experiment 3 showed that scrambled speech exacerbated the syntactic complexity effect more than coherent background speech, which also interfered with reading. Experiment 4 demonstrated that both semantically and syntactically anomalous speech produced no more disruption in reading than semantically anomalous but syntactically correct background speech. The pattern of results is best explained by a semantic account that stresses the importance of similarity in semantic processing, but not similarity in semantic content, between the reading task and background speech.     

Performance of a spring-feeding moth in relation to time of oviposition and bud-burst phenology of different host species

Abstract. 1. As a spring-feeding moth committed to immature foliage, the autumnal moth Epirrita autumnata (Lepidoptera, Geometridae) must have egg hatch synchronised with the bud-burst of its host plants. Due to large individual variation in the length of the pupal period, however, E. autumnata populations exhibit a prolonged period of flight and oviposition. Because the timing of oviposition in autumn is associated with the timing of egg hatch in the following spring, the time window for egg hatch expands and more potential hosts may become attainable. This suggestion was evaluated under field conditions by rearing E. autumnata eggs and larvae on four different hosts.
2. The performance of E. autumnata was measured by using estimates for fecundity (pupal mass) as well as survivorship of eggs and larvae. Based on the availability of foliage and phenological synchrony between larval and leaf development, early-laid eggs and the larvae originating from them were predicted to perform better on the hosts that have early-flushing leaves. On the late-flushing hosts, the larvae that hatched later were predicted to perform better than the larvae that hatched earlier. Half of the trials were exposed to predators and parasitoids, while the rest were conducted inside mesh-bags preventing larval dispersal and mortality due to natural enemies.
3. The results of the experiment did not support the simple predictions. In particular, host-plant quality and natural enemies appeared to operate discordantly between early- and late-laid eggs. Larvae from the late-laid eggs had rapid development during the larval stages and pupated at the same time and with the same pupal mass as the larvae hatched from the early-laid eggs.
4. The results indicate an occurrence of several, unknown selective forces in E. autumnata populations maintaining variation in the length of the pupal period, timing of oviposition, and timing of egg hatch.     

Involvement of TRPC3 channels in calcium oscillations mediated by OX1 orexin receptors

Oscillations of intracellular Ca²⁺ provide a novel mechanism for sustained activation of cellular processes. Receptor-activated oscillations are mainly thought to occur through rhythmic IP₃-dependent store discharge. However, as shown here in HEK293 cells 1 nM orexin-A (Ox-A) acting at OX₁ receptors (OX₁R) triggered oscillatory Ca²⁺ responses, requiring external Ca²⁺. These responses were attenuated by interference with TRPC3 channel (but not TRPC1/4) function using dominant negative constructs, elevated Mg²⁺ (a blocker of many TRP channels) or inhibition of phospholipase A₂. These treatments did not affect Ca²⁺ oscillations elicited by high concentrations of Ox-A (100 nM) in the absence of external Ca²⁺. OX₁R are thus able to activate TRPC(3)-channel-dependent oscillatory responses independently of store discharge.     

Novel Vascular Endothelial Growth Factor D Variants with Increased Biological Activity

Members of the vascular endothelial growth factor (VEGF) family play a pivotal role in angiogenesis and lymphangiogenesis. They are potential therapeutics to induce blood vessel formation in myocardium and skeletal muscle, when normal blood flow is compromised. Most members of the VEGF/platelet derived growth factor protein superfamily exist as covalently bound antiparallel dimers. However, the mature form of VEGF-D (VEGF-D^ΔNΔC) is predominantly a non-covalent dimer even though the cysteine residues (Cys-44 and Cys-53) forming the intersubunit disulfide bridges in the other members of the VEGF family are also conserved in VEGF-D. Moreover, VEGF-D bears an additional cysteine residue (Cys-25) at the subunit interface. Guided by our model of VEGF-D^ΔNΔC, the cysteines at the subunit interface were mutated to study the effect of these residues on the structural and functional properties of VEGF-D^ΔNΔC. The conserved cysteines Cys-44 and Cys-53 were found to be essential for the function of VEGF-D^ΔNΔC. More importantly, the substitution of the Cys-25 at the dimer interface by various amino acids improved the activity of the recombinant VEGF-D^ΔNΔC and increased the dimer to monomer ratio. Specifically, substitutions to hydrophobic amino acids Ile, Leu, and Val, equivalent to those found in other VEGFs, most favorably affected the activity of the recombinant VEGF-D^ΔNΔC. The increased activity of these mutants was mainly due to stabilization of the protein. This study enables us to better understand the structural determinants controlling the biological activity of VEGF-D. The novel variants of VEGF-D^ΔNΔC described here are potential agents for therapeutic applications, where induction of vascular formation is required.Vascular endothelial growth factors (VEGFs)3 are considered as key growth factors inducing angiogenesis and lymphangiogenesis during embryogenesis as well as maintaining vasculature during adulthood. Their abnormal expression is found in pathological conditions such as cancer and retinopathies (1). Five mammalian VEGFs, VEGF-A, -B, -C, -D and placenta growth factor (PlGF), are known (2) as well as Orf virus-derived VEGF-E proteins (3) and multiple homologues from snake venoms (VEGF-Fs) (4). Several members of the VEGF family exist as different isoforms, either as a result of the alternative splicing of their mRNAs or due to proteolytic processing. These forms vary in their specificities and affinities to three main VEGF receptors, co-receptors such as neuropilins and heparan sulfate proteoglycans and other components of the extracellular matrix, translating into different biological effects (5).VEGFR-2 is an important receptor regulating vasculogenesis and angiogenesis. It is mainly expressed on endothelial cells, but expression is also found in several other cell types (6). Mammalian VEGFR-2 ligands include VEGF-A (7), VEGF-C (8), and VEGF-D (9). In addition to VEGFR-2, VEGF-C and VEGF-D are ligands for VEGFR-3, which mainly mediates lymphangiogenesis in adults but also participates in the formation of blood vessels during embryogenesis (2).Because of their importance in angiogenesis, VEGFs have been suggested as potential therapeutic agents in different pathological conditions to improve compromised blood flow. Studies aiming at inducing angiogenesis in vivo have been performed by introducing VEGFs to tissues either directly as recombinant proteins (10) or using gene therapy vectors (11). Findings from several laboratories have shown that VEGFs have strong angiogenic activity in vivo, and they could be used for the treatment of conditions like lower limb ischemia and ischemic coronary artery disease. The short in vivo half-life of these growth factors and the requirement for sustained angiogenic stimulus makes gene therapy a preferred option. Of the VEGFs, VEGF-A and the mature form of VEGF-D (VEGF-D^ΔNΔC, see below) are the strongest agents to induce vascular formation (12, 13).VEGFs share structural similarity with platelet-derived growth factors. Together they are classified as the VEGF/platelet-derived growth factor family, belonging to a larger family of cystine knot growth factors. The members of this family share a cystine knot motif, which is found in many extracellular proteins and is conserved among numerous species (14). Characteristic of the cystine knot proteins is that they contain a conserved structure of antiparallel β-sheets connected by three disulfide bonds. Typically cystine knot growth factors form dimers, which within the VEGF/platelet-derived growth factor family are often linked by intersubunit disulfide bonds. The crystal structures have been solved for VEGF-A (15), PlGF (16), VEGF-B (17), VEGF-E (18), and two snake venom VEGF-Fs, vammin and VR-1 (19).There are currently no published structures of VEGF-C or VEGF-D. They can be divided into their own subfamily based on sequence similarity and several characteristic features; 1) they are the only VEGFs that bind to VEGFR-3, 2) they are expressed as long precursor forms having poor receptor binding affinities, and 3) they require proteolytic processing at their N-terminal and C-terminal ends to become more active. In contrast to other members of the VEGF family, the mature, proteolytically processed ΔNΔC-forms of VEGF-C and VEGF-D exist predominantly as non-covalently bound dimers, even though they have the conserved cysteine residues that form the intersubunit disulfide bonds in other VEGFs (8, 20). However, both VEGF-C and VEGF-D also have an additional cysteine residue located at the dimer interface (8, 20). Mutation of this residue in VEGF-C only minimally altered the receptor binding affinity (21), but it stabilized the dimer structure (56).In the current study we investigated the importance of residues at the subunit interface for the function of VEGF-D^ΔNΔC. We built homology models of VEGF-D^ΔNΔC and used alanine scanning and site-specific mutagenesis as well as tested the biological activity of various mutated forms of VEGF-D^ΔNΔC. Our study revealed that the conserved cysteine residues (Cys-44 and Cys-53), which are known to form intersubunit disulfide bridges in other VEGFs, were essential for the activity of the recombinant VEGF-D^ΔNΔC. Furthermore, the monomer to dimer ratio of VEGF-D^ΔNΔC could be regulated by mutagenesis. In addition, it was found that replacement of the “extra” cysteine (Cys-25) by various amino acids, preferably Ile, Leu, or Val, actually enhanced the activity of VEGF-D^ΔNΔC. This was at least partially due to increased stability of the protein.     

Contamination routes of Clostridium botulinum in the honey production environment

Factors influencing Clostridium botulinum contamination in the honey production environment were evaluated in a 3-year survey. A number of 1,168 samples from 100 apiaries and related facilities were analysed for the presence of C. botulinum types A, B, E and F, using multiplex polymerase chain reaction targeted to botA, botB, botE and botF genes. Production methods and environmental factors were registered using a questionnaire and by personal observation. Clostridium botulinum was shown to be a common finding throughout the whole honey production chain, and the type most frequently detected was group I type B. In a pulsed-field gel electrophoresis (PFGE) analysis of 202 group I type B isolates, only six different PFGE profiles were observed, of which two clearly distinct profiles predominated. This may indicate the existence of at least two different genetic lineages. The high prevalence of C. botulinum in soil and in samples associated with beeswax suggests the accumulation of soil-derived botulinal spores in wax. Additionally, according to Spearman's rank order correlation and multivariate analysis, production hygiene-dependent factors have a significant influence on the contamination, and thus the number and frequency of C. botulinum spores in honey could possibly be diminished by increasing hygienic level in honey production.