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PubMed1995

A mutation hotspot in the chloroplast genome of a conifer (Douglas-fir: Pseudotsuga) is caused by variability in the number of direct repeats derived from a partially duplicated tRNA gene.

We determined the DNA sequence of a 2.7-kb cpDNA XbaI fragment from douglas-fir [Pseudotsuga menziesii (Mirb.) Franco]. RFLPs revealed by the 2.7-kb XbaI clone were observed to vary up to 1 kb among species within the genus Pseudotsuga and up to 200 bp among trees of P. menziesii. The polymerase chain reaction (PCR) allowed the locus of polymorphism to be identified, and the variable region was then sequenced in a second Douglas-fir tree, a single tree of a related species, Japanese Douglas-fir (P. japonica), and in a species lacking a mutation hotspot in the region, Pinus radiata (Monterey pine). The locus of polymorphism is characterized by hundreds of base pairs of imperfect, tandem direct repeats flanked by a partially duplicated and an intact trn Y-GUA gene. The duplication is direct in orientation and consists of 43 bp of the 3' end of trnY and 25 bp of its 3' flanking sequence. Tandem repeats show high sequence similarity to a 27-bp region of the trnY gene that overlaps one end of the duplication. The two trees of Douglas-fir sequenced differed by a single tandem repeat unit, whereas these trees differed from the Japanese Douglas-fir sequenced by approximately 34 repeat units. Repetitive DNA in the Pseudotsuga cpDNA hotspot was most likely generated at the time of the partial trnY gene duplication and these sequences expanded by slipped-strand mispairing and unequal crossing-over.

Base Sequence↗

PubMed1992

Genetic transformation of the symbiotic basidiomycete fungus Hebeloma cylindrosporum.

The pAN7.1 plasmid containing the E. coli hygromycin B phosphotransferase gene was used to transform protoplasts of the ectomycorrhizal fungus Hebeloma cylindrosporum. Hygromycin-resistant transformants were selected at a frequency of one to five per micrograms of transforming DNA. Southern blot analyses revealed multiple copy integration of the transforming plasmid into the genome. The selection system was used to introduce other genes of interest by co-transformation. Two plasmids, one containing tryptophan biosynthesis genes and the other the NADP-glutamate dehydrogenase gene from the saprophytic basidiomycete Coprinus cinereus, were successfully introduced into the H. cylindrosporum genome with up to 70% efficiency of co-transformation. The hygromycin resistance phenotype was stably maintained during growth of transformants on hygromycin-free medium. All transformants retained their ability to form mycorrhizae with the habitual host plant Pinus pinaster, making them suitable for future physiological studies.

Basidiomycota↗

PubMed1976

S-formylgluthathione: the substrate for formate dehydrogenase in methanol-utilizing yeasts.

Formaldehyde dehydrogenase and formate dehydrogenase were purified 45- and 16-fold, respectively, from Hansenula polymorpha grown on methanol. Formaldehyde dehydrogenase was strictly dependent on NAD and glutathione for activity. The Km values of the enzyme were found to be 0.18 mM for glutathione, 0.21 mM for formaldehyde and 0.15 mM for NAD. The enzyme catalyzed the glutathione-dependent oxidation of formaldehyde to S-formylglutathione. The reaction was shown to be reversible: at pH 8.0 a Km of 1 mM for S-formylglutathione was estimated for the reduction of the thiol ester with NADH. The enzyme did not catalyze the reduction of formate with NADH. The NAD-dependent formate dehydrogenase of H. polymorpha showed a low affinity for formate (Km of 40 mM) but a relatively high affinity for S-formylglutathione (Km of 1.1 mM). The Km values of formate dehydrogenase in cell-free extracts of methanol-grown Candida biodinii and Pichia pinus for S-formylglutathione were also an order of magnitude lower than those for formate. It is concluded that S-formylglutathione rather than free formate is an intermediate in the oxidation of methanol by yeasts.

Aldehyde Oxidoreductases↗

PubMed1994

Aluminum contents of the edible portions of the winged bean, Psophocarpus tetragonolobus (L.) DC. (Fabaceae): field study and caveat.

The winged bean, Psophocarpus tetragonolobus (L.) DC has been widely recognised as a potentially useful source of protein for tropical regions of the world. A neglected aspect of the plants nutritional quality has been the reporting of the accumulation of aluminum (Al) in the edible parts of the plant; the leaves, pods, seeds and tubers. The accumulation of Al in the plant on acidic tropical soils and the implication of Al to human health problems further justified the inclusion of Al in nutritional analysis. Field experiments on two varieties of the winged bean, the USDA-release Hi-Flyer and an unnamed variety from the Phillipines, showed that all edible portions of the plant accumulate Al from high to very high levels when compared to an average of usually less than 300 ppm in other crop plants. Aluminum accumulation is generally highest in the youngest tissues particularly in the young roots with levels recorded as high as 25,000 ppm and these contents are as high as levels for recognised 'Al accumulators' such as the leaves of Pinus and tea. Future improvement breeding programs for the winged bean will necessarily require identifying and taking advantage of possible variation in Al accumulation between varieties.

Aluminum↗

PubMed1993

Production of tremorgenic mycotoxins by isolates of Aspergillus fumigatus from sawmills in Sweden.

One hundred and six strains of A. fumigatus were isolated from 21 sawmills in Sweden, and 73 of these strains were examined for production of fumitremorgen B and verruculogen (tremorgenic mycotoxins) on YES-medium using thin layer chromatography (TLC). Twenty-three strains (32%) were tremorgen producers and 50 strains (68%) were non-producers. Tremorgenic mycotoxins were detected in conidia of seven A. fumigatus strains. The amount of toxin varied between 0.6-8.0 microgram/10(8) conidia (mean value 2.3 micrograms/10(8) conidia, equivalent with 0.18%). No production of the mycotoxin gliotoxin was detected in 6 strains of A. fumigatus. No tremorgens were detected during mould growth on wood substrates, in spite of the use of different wood species (Scots pine, Pinus sylvestris: Norway spruce, Picea abies and birch, Betula spp.), dried versus non-dried wood, bark (pine), leached wood, and wood after various sterilization methods.

Air Pollutants↗

PubMed1990

Non-morphogenic metabolism during shoot induction in radiata pine cotyledon explants.

The effects of excision, light and cytokinin (N6-benzyladenine) on 14C-acetate metabolism in cotyledons of Pinus radiata (D. Don) were determined. 14CO2 was released and the distribution of radioactivity into lipids, sugars, organic acids and amino acids was determined. While light and cytokinin generally caused some increase in metabolism, the effect of excision, i.e., wounding, was most pronounced. Specific metabolites examined (citrate, malate, succinate, alanine, aspartate, glutamate and glutamine) were at least 50% greater in 14C-labeling in excised cotyledons as compared to intact seedlings. This enhancement of wound metabolism would mask possible morphogenically-related changes occurring at that time.

Acetates↗

PubMed1996

Development of a generalized phenomenological model describing the kinetics of the enzymatic hydrolysis of NaOH-treated pine wood.

Pinus pinaster wood samples were treated during 3 h with alkaline solutions (containing 1, 5.5, or 10 weight percent NaOH) at 100, 115, or 130 degrees C using liquor/wood ratios of 6, 8, or 10 g/g. The solid residues obtained in treatments were used as substrates for enzymatic hydrolysis. In the hydrolysis assays, the reaction time (in the range 0-48 h) was considered as an operational variable. The cellulose conversion achieved at the end of assays were highest for samples pretreated at high temperature and high alkali concentration using low liquor/wood ratios. The experimental results obtained in each hydrolysis trial were fitted to an empirical model based on the assumption that the cellulose contained in substrates was composed by two fractions having different susceptibility to hydrolysis. The kinetic parameters obtained for the various experiments performed were correlated with the operational variables by means of empirical, statistically significant equations, which provided a generalized interpretation of the process.

Enzymes↗

PubMed1981

Effect of fire on soil microorganisms in a Meghalaya pine forest.

The effect of man-made fire on soil microbial population in a natural subtropical pine forest eco-system, was studies. a nearly fifty years old pine (Pinus kesiya Royle) forest was cut and burnt in March 1977. Another half of this pine forest was left uncut and unburnt. Microbial population was destroyed completely just after the burning and recolonization occurred after some days. Bacteria and actinomycetes were found to be the first colonizers followed by fungi. Burning initiated better growth and higher population of bacteria after two or three showers. Bacterial population was highest in July in burnt and in May in unburnt forest. Maximum fungal population in burnt site was recorded in July while it was highest in april and May in unburnt site. Penicillium spp., Cladosporium sp. and Trichoderma sp. were found to be first colonizing fungi just after the burning. In unburnt forest eco-system Absidia sp., Trichoderma sp., Fusarium sp. and Penicillium spp. were found to be dominant.

Bacteria↗

PubMed1998

Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages.

In the plant chloroplast genome the codon usage of the highly expressed psbA gene is unique and is adapted to the tRNA population, probably due to selection for translation efficiency. In this study the role of selection on codon usage in each of the fully sequenced chloroplast genomes, in addition to Chlamydomonas reinhardtii, is investigated by measuring adaptation to this pattern of codon usage. A method is developed which tests selection on each gene individually by constructing sequences with the same amino acid composition as the gene and randomly assigning codons based on the nucleotide composition of noncoding regions of that genome. The codon bias of the actual gene is then compared to a distribution of random sequences. The data indicate that within the algae selection is strong in Cyanophora paradoxa, affecting a majority of genes, of intermediate intensity in Odontella sinensis, and weaker in Porphyra purpurea and Euglena gracilis. In the plants, selection is found to be quite weak in Pinus thunbergii and the angiosperms but there is evidence that an intermediate level of selection exists in the liverwort Marchantia polymorpha. The role of selection is then further investigated in two comparative studies. It is shown that average relative codon bias is correlated with expression level and that, despite saturation levels of substitution, there is a strong correlation among the algae genomes in the degree of codon bias of homologous genes. All of these data indicate that selection for translation efficiency plays a significant role in determining the codon bias of chloroplast genes but that it acts with different intensities in different lineages. In general it is stronger in the algae than the higher plants, but within the algae Euglena is found to have several unusual features which are noted. The factors that might be responsible for this variation in intensity among the various genomes are discussed.

Chloroplasts↗

PubMed1999

New Plant Growth Regulators Protect Photosynthesis and Enhance Growth Under Drought of Jack Pine Seedlings.

To determine whether natural plant growth regulators (PGRs) can enhance drought tolerance and the competitive ability of transplanted seedlings, 1.5-year-old jack pine (Pinus banksana Lamb.) seedlings were treated with homobrassinolide, salicylic acid, and two polyamines, spermine and spermidine, triacontanol, abscisic acid (ABA), and the synthetic antioxidant, Ambiol. PGRs were fed into the xylem for 7 days and plants were droughted by withholding water for 12 days. ABA, Ambiol, spermidine, and spermine at a concentration of 10 µg L(-1) stimulated elongation growth under drought, whereas ABA, Ambiol, and spermidine maintained higher photosynthetic rates, higher water use efficiency, and lower Ci/Ca ratio under drought compared with control plants. The damaging effects of drought on membrane leakage was reversed by Ambiol, ABA, triacontanol, spermidine, and spermine. Because ABA, Ambiol, and both polyamines enhanced elongation growth and also reduced membrane damage in jack pine under drought, they show promise as treatments to harden seedlings against environmental stress. The protective action of these compounds on membrane integrity was associated with an inhibition of ethylene evolution, with a reduction in transpiration rate and an enhancement of photosynthesis, which together increased water use efficiency under drought. Although most of the tested compounds acted as antitranspirants, the inhibition in membrane leakage in ABA-, Ambiol-, and polyamine-treated plants appeared more closely related to the antiethylene action.

Journal Article↗

PubMed1998

Pycnogenol enhances immune and haemopoietic functions in senescence-accelerated mice.

Pycnogenol (procyanidin extracted from Pinus maritima) has been shown to be a potent free radical scavenger and an antioxidant phytochemical. The effects of pycnogenol on immune and haemopoietic dysfunction in senescence-accelerated mice (SAM), as a murine model of accelerated ageing, were determined. SAMP8, a strain of senile-prone mice, exhibit learning and memory deficits, immunodeficiency and dysfunction of the haemopoietic system. Oral feeding with pycnogenol for 2 months significantly improved their T- and B-cell function. Pycnogenol also augmented the proliferative capacity of haemopoietic progenitors of bone marrow in SAMP8. These data suggest that pycnogenol may be useful for either retardation or restoration of parameters associated with ageing.

Aging↗

PubMed2000

Strategies of a bark beetle, Pityogenes bidentatus, in an olfactory landscape.

Volatiles from leaves or bark of nonhost birch (Betula pendula) and Norway spruce (Picea abies) dramatically reduced the attraction of the bark beetle, Pityogenes bidentatus (Coleoptera: Scolytidae), to their aggregation pheromone components (cis-verbenol and grandisol) in the field. In addition, odors from both the needles and bark of the host Scots pine (Pinus sylvestris) similarly inhibited attraction. Monoterpenes of pine and spruce (alpha-pinene, beta-pinene, terpinolene, and 3-carene) as well as ethanol, chalcogran and some nonhost green leaf alcohols [(Z)-3-hexen-1-ol, (E)-2-hexen-1-ol, and 1-hexanol], also reduced catches. Collections of volatiles from the field-tested plant tissues indicated they released monoterpenes in amounts similar to the synthetics that inhibited responses. The various plant and insect sources of these inhibitory compounds indicate that P. bidentatus bark beetles have evolved several strategies to increase their fitness by avoiding nonhost and unsuitable host trees in a complex olfactory landscape.

Animals↗

PubMed2002

Mapping quantitative trait loci controlling early growth in a (longleaf pine x slash pine) x slash pine BC(1) family.

Random amplified polymorphic DNA (RAPD) markers were employed to map the genome and quantitative trait loci controlling the early growth of a pine hybrid F(1) tree ( Pinus palustris Mill. x P. elliottii Engl.) and a recurrent slash pine tree ( P. elliottii Engl.) in a (longleaf pine x slash pine) x slash pine BC(1) family consisting of 258 progeny. Of the 150 hybrid F(1) parent-specific RAPD markers, 133 were mapped into 17 linkage groups covering a genetic distance of 1,338.2 cM. Of the 116 slash pine parent-specific RAPD markers, 83 were mapped into 19 linkage groups covering a genetic distance of 994.6 cM. A total of 11 different marker intervals were found to be significantly associated with 13 of the 20 traits on height and diameter growth using MAPMAKER/QTL. Nine of the eleven marker intervals were unique to the hybrid parent 488 genome, and two were unique to the recurrent parent 18-27 genome. The amount of phenotypic variance explained by the putative QTLs ranged from 3.6% to 11.0%. Different QTLs were detected at different ages. Two marker intervals from the hybrid parent 488 were found to have QTL by environment interactions.

Journal Article↗

PubMed2004

A full saturated linkage map of Picea abies including AFLP, SSR, ESTP, 5S rDNA and morphological markers.

Based on an F(1) progeny of 73 individuals, two parental maps were constructed according to the double pseudo-test cross strategy. The paternal map contained 16 linkage groups for a total genetic length of 1,792 cM. The maternal map covered 1,920 cM, and consisted of 12 linkage groups. These parental maps were then integrated using 66 intercross markers. The resulting consensus map covered 2,035 cM and included 755 markers (661 AFLPs, 74 SSRs, 18 ESTPs, the 5S rDNA and the early cone formation trait) on 12 linkage groups, reflecting the haploid number of chromosomes of Picea abies. The average spacing between two adjacent markers was 2.6 cM. The presence of 39 of the SSR and/or ESTP markers from this consensus map on other published maps of different Picea and Pinus species allowed us to establish partial linkage group homologies across three P. abies maps (up to five common markers per linkage group). This first saturated linkage map of P. abies could be therefore used as a support for developing comparative genome mapping in conifers.

Chromosome Mapping↗

PubMed2005

Two classes of 5S rDNA unit arrays of the silver fir, Abies alba Mill.: structure, localization and evolution.

The structure and organization of the 5S ribosomal DNA units of the silver fir, Abies alba Mill., as well as their position in the chromosome complement were investigated. PCR amplification of the gene and nontranscribed spacer region, sequence analysis and Southern hybridization, using a homologous probe, detected DNA sequences of approximately 550 bp and 700 bp. Sequence analysis of the spacers revealed that the difference in length between the sequences occurred in the middle spacer region as a result of the amplification of a 75-bp sequence of the short unit class, which is organized in four 54- to 68-bp tandem repeats in the long spacer unit. The 5S rDNA transcribed region is 120 bp long and shows high sequence similarity with other gymnosperm species. The comparative analysis of 5' and 3' flanking sequences of 5S rRNA genes of silver fir and other gymnosperms indicates that A. alba spacer units have the same rate of evolution and are more closely related to Larix and Pseudotsuga than to Pinus and Picea. Southern hybridization and fluorescence in situ hybridization of metaphase chromosomes of A. alba suggest that the short and long spacer units are organized as separate tandem arrays at two chromosomal loci on chromosomes V and XI.

Abies↗

PubMed2006

Comparative genome mapping among Picea glauca, P. mariana x P. rubens and P. abies, and correspondence with other Pinaceae.

A composite linkage map was constructed from four individual maps for the conifer Picea glauca (Moench) Voss, from anonymous and gene-specific markfers (714 AFLPs, 38 SSRs, and 53 ESTPs). A total of 12 linkage groups were delineated with an average marker density of 2.7 cM. Macro-synteny and macro-colinearity comparisons with two other composite linkage maps developed for the species complex P. mariana (Mill.) B.S.P. x P. rubens Sarg., and for P. abies (L.) Karst. revealed an identical number of linkage groups and a remarkable conservation of the gene content and gene order of linkage groups over the million years since the split between these taxa. Identical gene order among taxa was observed for 10 of the 12 assembled composite linkage groups. The discovery of one breakdown in synteny between P. glauca and the other two taxa indicated the occurrence of an inter-chromosomal rearrangement involving an insertional translocation. Analysis of marker colinearity also revealed a putative segmental duplication. The combined information from these three Picea genomes validated and improved large-scale genome comparisons at the inter-generic level in the family Pinaceae by allowing for the identification of 11 homoeologous linkage groups between Picea and Pinus, and nine such groups between Picea and Pseudotsuga menziesii. Notably, the analysis of synteny among the three genera revealed a putative case of chromosomal fission and an inter-chromosomal rearrangement in the genome of P. menziesii. Both of these changes are inter-connected, indicating much instability in this part of the P. menziesii genome. Overall, the macro-structure of the Pinaceae genome was well conserved, which is notable given the Cretaceous origin of its main lineages.

Genome, Plant↗

PubMed2004

HPLC micro-fractionation coupled to a cell-based assay for automated on-line primary screening of calcium antagonistic components in plant extracts.

High performance liquid chromatography (HPLC) micro-fractionation was successfully coupled to an automated 45Ca2+ uptake assay using GH4C1 cells for the separation of natural product extracts and for the primary detection of their calcium antagonistic components. The reliability of the procedure was first established with a reference solution consisting of pure compounds with a known effect on the Ca2+ uptake. No loss of activity was observed to occur after HPLC micro-fractionation. Extracts of Peucedanum palustre and Pinus sylvestris, showing high and no inhibition of Ca2+ uptake as total extracts, respectively, were analysed and the inhibitory activity of the P. palustre extract could be traced to two components, identified as columbianadin and isoimperatorin. As expected, no significant inhibition was observed with the micro-fractionated P. sylvestris samples. In summary, the procedure was found to be applicable for primary detection of calcium antagonistic components in complex matrices and to significantly reduce the time previously needed for bioactivity-guided isolation.

Animals↗

PubMed1996

Decomposer animal communities in forest soil along heavy metal pollution gradient.

Responses of soil decomposer animals to heavy metal contamination and to concomitant changes in organic matter quality and quantity and in soil microbial biomasses have been studied along a pollution gradient from a Cu-Ni smelter. Samples have been taken separately for nematodes, enchytraeids and microarthropods 0.5, 2 and 8 km from the smelter. Special attention has been paid to the changes in the collembolan fauna. The sampling sites have been located in homogeneous Scots pine ( Pinus sylvestris) forests with podsolic soil profiles. In addition, an experiment has been carried out in which intact soil cores have been transferred in mesh baskets between the sites 2 and 8 km from the smelter (control samples have been transferred within the sites). Although most soil animals seemed to be quite resistant to direct and indirect effects of heavy metals, results indicate that certain soil animals like enchytraeids can be useful and easy to monitor when the effects of heavy metals on soil decomposition systems are assessed.

Journal Article↗