Changes in diatom assemblages in the profundal sediments of two large oligohumic lakes in eastern Finland

Sedimentary diatom assemblages in two large oligotrophic clear-water lakes were analysed, to assess their present ecological state and possible eutrophication due to diffuse nutrient loading. The lakes Pyhäjärvi and Puruvesi (Finnish lake district) are proportionally large for their catchment areas which accounts for their long retention times (ca 7 and 11 yr) and oligohumic character. Pyhäjärvi was studied by pairwise comparison of surface sediment diatom assemblages collected in 1985 and 1990 at 12 sites from different parts of the lake. In Puruvesi, the stratigraphy of diatoms was analysed in two short cores from 8 m and 32 m depths.The diatom assemblages of the two lakes are rather similar, and quite distinct from the assemblages of the mesohumic large lakes of the area. Cyclotella kuetzingiana is the most common planktonic dia- tom, but Aulacoseira ambigua abounds in Pyhäjärvi at sites with local sources of eutrophication. A diverse assemblage of benthic forms, especially Fragilaria and Achnanthes spp. characterizes the shallow bottoms in both lakes.There was little change within the short-core diatom profiles of Puruvesi, but the floral composition of the 8-m and 32-m sites differed markedly. The 8-m site, with 60–70% of benthic forms, represents illuminated bottom, on which much of the buried algae have lived in situ, while the deeper site is true profundal, dominated by sedimented planktonic algae.In Pyhäjärvi there was a slight increase in the benthic diatoms from 1985 to 1990, coinciding with increased phosphorus and chlorophyll concentrations as well as Secchi depth lowering. We interprete this observation as a very early step of eutrophication, of which first the sessile algal communities of the illuminated bottom areas have benefited.     

Molecular basis of chromosome banding

Silver and mercury ions are known to react with the bases of nucleic acids in solution. At low cation/base ratios Ag+ has an affinity for GC pairs in DNA, whereas Hg++ is preferentially bound to AT-rich nucleic acids. We have used fluorometry to measure the effect of these cations on the fluorescence intensity of preformed complexes of acranil and DNA in solution. The results are: 1) Ag+ enhances the fluorescence intensity presumably by affecting the dye intercalated in the vicinity of GC-pairs. 2) The addition of Hg++ leads to a quenching of the fluorescence intensity of the complex at low ion/base ratios, suggesting an effect on the dye molecules bound to AT pairs. At high GC-content of the nucleic acid, slight enhancement of the fluorescence intensity occurs with Hg++. 3) With both metals there is a correlation between base content of DNA and effect on the intensity of fluorescence indicating base specificity of the dye-polymer interaction.     

Lignification related enzymes in Picea abies suspension cultures

Activity of a number of enzymes related to lignin formation was measured in a Picea abies (L) Karsten suspension culture that is able to produce native-like lignin into the nutrient medium. This cell culture is an attractive model for studying lignin formation, as the process takes place independently of the complex macromolecular matrix of the native apoplast. Suspension culture proteins were fractionated into soluble cellular proteins, ionically and covalently bound cell wall proteins and nutrient medium proteins. The nutrient medium contained up to 5.3% of total coniferyl alcohol peroxidase (EC 1.11.1.7) activity and a significant NADH oxidase activity that is suggested to be responsible for hydrogen peroxide (H2O2) production. There also existed some malate dehydrogenase (EC 1.1.1.37) activity in the apoplast of suspension culture cells (in ionically and covalently bound cell wall protein fractions), possibly for the regeneration of NADH that is needed for peroxidase-catalysed H2O2 production. However, there is no proof of the existence of NADH in the apoplast. Nutrient medium peroxidases could be classified into acidic, slightly basic and highly basic isoenzyme groups by isoelectric focusing. Only acidic peroxidases were found in the covalently bound cell wall protein fraction. Several peroxidase isoenzymes across the whole pI range were detected in the protein fraction ionically bound to cell walls and in the soluble cellular protein fraction. One laccase-like isoenzyme with pI of approximately 8.5 was found in the nutrient medium that was able to form dehydrogenation polymer from coniferyl alcohol in the absence of H2O2. The total activity of this oxidase towards coniferyl alcohol was, however, several orders of magnitude smaller than that of peroxidases in vitro. According to 2D 1H-13C correlation NMR spectra, most of the abundant structural units of native lignin and released suspension culture lignin are present in the oxidase produced dehydrogenation polymer but in somewhat different amounts compared to peroxidase derived synthetic lignin preparations. A coniferin beta-glucosidase (EC 3.2.1.21) was observed to be secreted into the culture medium.     

Dual target strategy: combining distinct non‐dopaminergic treatments reduces neuronal cell loss and synergistically modulates l‐DOPA‐induced rotational behavior in a rodent model of Parkinson's disease

The glutamate metabotropic receptor 5 (mGluR5) and the adenosine A_2A receptor (A_2AR) represent major non‐dopaminergic therapeutic targets in Parkinson's disease (PD) to improve motor symptoms and slow down/revert disease progression. The 6‐hydroxydopamine rat model of PD was used to determine/compare the neuroprotective and behavioral impacts of single and combined administration of one mGluR5 antagonist, 2‐methyl‐6‐(phenylethynyl)pyridine (MPEP), and two A_2AR antagonists, (E)‐phosphoric acid mono‐[3‐[8‐[2‐(3‐methoxyphenyl)vinyl]‐7‐methyl‐2,6‐dioxo‐1‐prop‐2‐ynyl‐1,2,6,7‐tetrahydropurin‐3‐yl]propyl] (MSX‐3) and 8‐ethoxy‐9‐ethyladenine (ANR 94). Chronic treatment with MPEP or MSX‐3 alone, but not with ANR 94, reduced the toxin‐induced loss of dopaminergic neurons in the substantia nigra pars compacta. Combining MSX‐3 and MPEP further improved the neuroprotective effect of either antagonists. At the behavioral level, ANR 94 and MSX‐3 given alone significantly potentiated l ‐DOPA‐induced turning behavior. Combination of either A_2AR antagonists with MPEP synergistically increased L‐DOPA‐induced turning. This effect was dose‐dependent and required subthreshold drug concentration, which per se had no motor stimulating effect. Our findings suggest that co‐treatment with A_2AR and mGluR5 antagonists provides better therapeutic benefits than those produced by either drug alone. Our study sheds some light on the efficacy and advantages of combined non‐dopaminergic PD treatment using low drug concentration and establishes the basis for in‐depth studies to identify optimal doses at which these drugs reach highest efficacy.

     

Sniper: improved SNP discovery by multiply mapping deep sequenced reads

SNP (single nucleotide polymorphism) discovery using next-generation sequencing data remains difficult primarily because of redundant genomic regions, such as interspersed repetitive elements and paralogous genes, present in all eukaryotic genomes. To address this problem, we developed Sniper, a novel multi-locus Bayesian probabilistic model and a computationally efficient algorithm that explicitly incorporates sequence reads that map to multiple genomic loci. Our model fully accounts for sequencing error, template bias, and multi-locus SNP combinations, maintaining high sensitivity and specificity under a broad range of conditions. An implementation of Sniper is freely available at .     

Diploidization in megagametophyte-derived cultures of the gymnosperm Larix decidua

Tested haploid embryogenic lines (n=12) of Larix dedicua Mill, initiated from megagametophyte tissue were maintained on half-strength LM medium without growth regulators. The cultures were analyzed for ploidy level after 1–9 years. All lines tested were found to have doubled (2n=24) their chromosome number at the end of the experiment, though there were a few lines that still gave occasional haploid counts. Flow cytometric data of embryogenic tissue confirmed these results. Protoplasts were stained in ethidium bromide, and cultured human leucocytes and chicken erythrocytes were used as internal standards. Haploid megagametophytes from immature seeds of L. decidua and known diploid culture lines of a related hybrid (L. x eurolepis) were also analyzed by flow cytometry. Haploid reference material had 12.3–13.6 pg DNA per cell, whereas formerly haploid callus lines had an average of 25.0 pg DNA per cell. The one exception was a known, genetically unstable line of L. decidua (34.8 pg DNA per cell). The diploid cell line of L. x eurolepis had 27.6 pg DNA per cell. The results show that spontaneous diploidization of megagametophyte lines is relatively rapid and that both haploid and dihaploid lines are embryogenic in larch.     

Molecular basis of chromosome banding

The effects of mouse satellite, main band and total DNA on the fluorescence intensity of quinacrine and of the bibenzimidazole derivative Hoechst 33258 were tested in solution. No significant differences were noticed between the double-stranded DNAs in spite of the 5% difference in AT-content between satellite and main band DNA. Single-stranded DNAs enhanced the fluorescence intensity of Hoechst 33258 far less than double-stranded DNAs. Having been denaturated and then reassociated the DNA fractions were intermediate in their enhancing effects on the fluorescence intensity of Hoechst 33258, the differences presumably being due to different degrees of reassociation. The effect of denatured and subsequently reassociated satellite DNA on the fluorescence intensity of quinacrine was similar to that of the native DNAs. Main band and total DNA quenched the fluorescence intensity of quinacrine more after denaturation-reassociation than it did when native. In the discussion the results are related to known cytological data.     

Paleolimnological reflections of fiber-plant retting in the sediment of a small clear-water lake

Likolampi is a small groundwater kettle-hole lake in Ilomantsi, Eastern Finland. At 11 m water depth the uppermost 51 cm of sediment contains about 390 varves. A thin layer of chrysophyte statospores is the main structural unit in these; in some varves it is followed by a layer of cf. Drepanocladus fluitans moss spores. Below the laminated sequence, two layers of moss detritus (110–87 cm, 81–51 cm) alternate with greyish brown fine detritus. Pollen analysis reveals that the start of the deposition of varved sediment coincides with the beginning of intensive fiber plant retting with large quantities of Cannabis/Humulus -type pollen and even regular occurrence of the insect-pollinated Linum usitatissimum. The cf. Drepanocladus spores are almost absent during the retting period (c. 1590–1900 by the varves), but very common before and after it. Drepanocladus fluitans is capable of assimilating dissolved CO₂ in water, so it thrives at low pH and is typical for oligotrophic clear-water lakes. We conclude that the stratigraphy of Drepanocladus fragments and spores is a true negative indicator of cultural influence in Likolampi.     

Recent stratigraphy and accumulation of sediment in the deep,oligotrophic Lake Pääjärvi in South Finland

Laminated sediment is deposited in the deep areas (> 30 m) of Lake Pääjärvi. In the diatom microstratigraphy a regular alteration of planktonic and littoral floras, which goes in pace with the visual structure, reflects the yearly cycle of sedimentation. Considerable variation in sedimentation was found to have occurred during the past two decades. A sequence, dated to the early 1960's, in which the organic content was exceptionally high, could be identified in the sediment at 6–14 cm depth even in shallower areas where laminations are not formed. This level was used as a marker horizon when determining the recent distribution of sediment by means of 19 cores taken from different parts of the lake. The average annual sediment accumulation in the profundal zone of the lake is 340 g m^?2a^?1 dry weight, of which 25 g m^?2 a^?1 (1100 kJ m^?2 a^?1) is organic carbon.     

On the mechanism of apoplastic H<Subscript>2</Subscript>O<Subscript>2</Subscript> production during lignin formation and elicitation in cultured spruce cells—peroxidases after elicitation

A cell culture of Picea abies (L.) Karst. was used for studies of H₂O₂ generation during constitutive extracellular lignin formation and after elicitation by cell wall fragments of a pathogenic fungus, Heterobasidium parviporum. Stable, micromolar levels of H₂O₂ were present in the culture medium during lignin formation. Elicitation induced a burst of H₂O₂, peaking at ca. 90 min after elicitation. Of exogenous reducing substrates that may be responsible for the synthesis of H₂O₂ from O₂, NADH stimulated H₂O₂ production irrespective of elicitation. Cysteine (Cys) and glutathione (GSH) partially scavenged the constitutive H₂O₂, but usually increased or prolonged elicitor-induced H₂O₂ formation. Culture medium peroxidases were not able to generate H₂O₂ in vitro with Cys or GSH as reductants. These thiols, however, generated H₂O₂ non-enzymically at pH 4.5. [³⁵S]Sulphate feeding to spruce cells showed that endogenous sulphur-containing compounds (including GSH, GSSG and cysteic acid) existed in the culture medium. The apoplastic levels of these were, however, undetectable by the monobromobimane method suggesting that their contribution to apoplastic H₂O₂ formation is probably minor. Azide, an inhibitor of haem-containing enzymes, slightly inhibited constitutive H₂O₂ generation but strongly delayed the elicitor-induced H₂O₂ accumulation. Diphenylene iodonium, an inhibitor of flavin-containing enzymes, efficiently inhibited H₂O₂ production irrespective of elicitation. Elicitation led to downregulation of the expression of several peroxidase genes, and peroxidase activity in the culture medium was slightly reduced. Expression of three other peroxidase genes and a respiratory burst oxidase homologue (rboh) gene were upregulated. These data suggest that both peroxidases and rboh may contribute to H₂O₂ generation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.