Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and b-tubulin sequences,morphology, anatomy and secondary chemistry

Phylogenetic relationships within the family Parmeliaceae (lichenized ascomycetes) with emphasis on the heterogeneous group of cetrarioid lichens are reconstructed. The results are based on cladistic analyses of DNA-sequences, morphological and chemical data. Almost all currently recognized cetrarioid genera were included in the analyses together with parmelioid and alectorioid members of the presumably monophyletic family Parmeliaceae. We tried to sample taxonomic diversity of the family as widely as possible. The ITS1-5.8S-ITS2 region of the rDNA and a partial β-tubulin gene from 126 samples representing 82 species were analysed. Cetrarioid lichens were identified as a monophyletic group, supported by both ITS and β-tubulin characters. This group was reanalysed using 47 morphological, anatomical and secondary chemistry characters combined with the DNA data matrix. ITS and β-tubulin sequences provide congruent information, and a clear correlation between DNA-data and conidial shape is observed. The current taxonomy of the cetrarioid lichens is discussed and compared with the phylogenetic trees obtained here. A comprehensive study of the phylogeography of some bipolar or subcosmopolitic species with representatives from both hemispheres was performed. Cetraria aculeata is the only taxon where correlation between DNA-data and geographic origin is observed.     

Face cooling by cold wind in walking subjects

The effects of low to moderate wind speeds on face temperature, thermal and pain sensations while subjects walked on a treadmill during cold exposure were studied in eight healthy men. The purpose of the study was to evaluate further the risk of frostbite at different activity levels. The walking speed was 2.8 km h(-1) and two inclination levels were used, 0 degrees and 6 degrees. The subjects were exposed to -10 degrees C and 0, 1 or 5 m s(-1) wind for 60 min dressed in cold-protective clothing with only the face unprotected. Results from previous experiments with the same subjects standing for 30 min were included in the analysis of the data. Each individual was exposed to all combinations of air velocity and activity level. The exposure to -10 degrees C and the highest wind speed used would carry no risk of frostbite according to the wind chill index. Cold lowered the skin temperature of the face significantly and wind further increased skin cooling. The activity level did not affect forehead and cheek temperatures, but the average nose skin temperature was higher and pain sensations were reduced at a higher work rate. The predicted risk of frostbite in the nose, based on average responses, would thus be less at a higher work rate. However, the results indicate that exercise does not necessarily protect all individuals from frostbite at moderate air speeds, since the nose skin temperature of 25% of the subjects dropped to 0 degrees C at 5 m s(-1) during both standing and walking. Thus the potential individual risk of frostbite in the nose is similar during light exercise and standing. Moreover, the risk of frostbite seems to be underestimated by the wind chill index under the conditions tested in this study.     

Comparison of signature lipid methods to determine microbial community structure in compost

The microbial community structure changes substantially during the composting process and simple methods to follow these changes can potentially be used to estimate compost maturity. In this study, two such methods, the microbial identification (MIDI) method and the ester-linked (EL) procedure to determine the composition of long-chain fatty acids, were applied to compost samples of different age. The ability of the two methods to describe the microbial succession was evaluated by comparison with phospholipid fatty acid (PLFA) analysis on the same samples.Samples were taken from a 200-l laboratory compost reactor, treating source-separated organic household waste. During the initial stages of the process, the total concentration of fatty acids in compost samples treated with the EL and MIDI methods was many times higher than with the PLFA method. This was probably due to the presence of fatty acids from the organic material in the original waste. However, this substantial difference between PLFA and the other two methods was not found later in composting. Although the PLFA method gave the most detailed information about the growth and overall succession of the microbial community, the much simpler MIDI and EL methods also successfully described the shift from the initially dominating straight chain fatty acids to iso- and anteiso branched, 10 Me branched and cyclopropane fatty acids in the later stages of the process. Thus, the MIDI and EL extraction methods appear to be suitable for analysis of microbial FAME profiles in compost, particularly in the later stages of the process.     

EROD activity in gill filaments of anadromous and marine fish as a biomarker of dioxin-like pollutants

The applicability of a gill filament-based ethoxyresorufin O-deethylase (EROD) assay, originally developed in rainbow trout, was examined in Atlantic salmon (Salmo salar), Arctic charr (Salvelinus alpinus), Atlantic cod (Gadus morhua), saithe (Pollachius virens) and spotted wolffish (Anarhichas minor). All species but spotted wolffish showed strong EROD induction in tip pieces of gill filaments following 48 h of exposure to waterborne beta-naphthoflavone. Atlantic salmon parr, smolts held in freshwater and smolts transferred to seawater showed EROD induction of similar magnitude. Arctic charr, differing 11-fold in body weight, showed similar EROD activities as expressed per gill filament tip. Laboratory exposure of saithe to water and sediments collected at polluted sites, resulted in strong EROD induction. In conclusion, the gill filament assay seems useful for monitoring exposure to aryl hydrocarbon receptor agonists in various species. Furthermore, smoltification status, water salinity and body size proved to have minor influence on gill filament EROD activity. However, the results in spotted wolffish show that some species may be less suitable for monitoring using the gill assay. Assessment of gill filament EROD activity in fish exposed to polluted water and sediments in the laboratory proved to be an easy and cost-effective way to survey pollution with dioxin-like chemicals.     

A fast top-down method for constructing reliable radiation hybrid frameworks

MOTIVATION: Radiation Hybrid Mapping (RHM) is a technique used to order a set of markers on a genome and estimating physical distances between them. RHM provides information on marker placement independent from other methods such as sequencing, and can therefore be used for example in genome sequencing to help ordering contigs. A radiation hybrid framework can be constructed by choosing a set of markers so that the chromosome coverage is good and so that the markers can be ordered with high confidence. Automatically constructing RHM frameworks is a computationally challenging problem. RESULTS: We have developed a new method for constructing radiation hybrid frameworks. Given a relatively large set of markers for a chromosome, the algorithm aims to select an ordered subset that makes up a framework, and that contains as many markers as possible. The algorithm has a time complexity that is better than any of the existing methods that we are aware of. Furthermore, we propose a method for comparing if two frameworks are consistent, giving a visual presentation as well as quantitative measures of how well the two frameworks agree. Applying our method on marker sets from 22 human chromosomes and comparing the resulting frameworks with previously published frameworks, we demonstrate that our automatic method efficiently constructs frameworks with good coverage of each chromosome and with high degree of agreement on the marker ordering.     

A new circumscription of the lichen genus <Emphasis Type="Italic">Nephromopsis</Emphasis> (Parmeliaceae,lichenized Ascomycetes)

The phylogeny of the cetrarioid lichens with bifusiform spermatia and dorsiventral thalli which contain usnic acid is reanalysed using three parts of the genome, ITS rDNA, β-tubulin and GAPDH sequences. Molecular data from five cetrarioid species are presented for the first time, and 13 new sequences are combined with sequences from the gene bank to delimit the genus Nephromopsis. A monophyletic clade of Nephromopsis, Tuckneraria, ‘Cetraria’ leucostigma and ‘C.’ melaloma is identified and circumscribed as one genus, Nephromopsis, which now includes 19 species. Four new combinations are presented. A key to the species is provided.     

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)

Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.     

Monophyletic groups within the Parmeliaceae identified by ITS rDNA, β-tubulin and GAPDH sequences

Phylogenetic relationships within the Parmeliaceae are analysed cladistically on the basis of DNA characters from partial β-tubulin, partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ITS sequences. 100 taxa representing 73 of the 88 genera currently recognised are included in the analyses. Eight monophyletic groups including two or more genera were identified in the tree calculated from the combined data matrix. Three of the groups cover almost half of the species of the family. The largest and strongest supported group includes seven genera with their distribution centres in the Southern Hemisphere: Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Xanthomaculina and Xanthoparmelia. The second group is a clade of four essentially tropical genera: Concamerella, Flavoparmelia, Parmotrema and Rimelia. The third large group with strong support is the core of cetrarioid lichens, distributed primarily in cold areas of the Northern Hemisphere. The genus Parmelia sensu Hale is not closely related with most of its segregates. One new combination, Cetrariella commixta, is proposed. Coelopogon abraxas is reported from South America for the first time.     

Floristic, structural and seed bank diversity of a dry Afromontane forest at Mafai, central Tanzania

Flora, vegetation and seed bank were studied in a dry Afromontane forest in the Kondoa Irangi Hills, Tanzania with the objective to obtain information necessary for the promotion of conservation of this forest, which is rapidly degenerating due to human pressure. A preliminary checklist of 104 vascular plants occurring in the forest is provided. Based on 27 plots, each of 400m², the forest had the following ecological features: mean tree density 408 stems·ha^–1; basal area 66.56m²·ha^–1; Shannon and Wiener diversity 2.6406; evenness 0.7585 and species richness 31 tree species per 1.08ha. The seed bank was dominated by woody species, including mature forest tree species, and had several species in common with the standing vegetation. The forest contains species that are phytogeographically linked to Madagascan, Western and Southern African floras and also species disjunctly distributed in this forest and the Eastern Arc Mountains of Tanzania. Correspondence Analysis of tree species based on size classes showed that the timber species had declining populations, indicating the possibility of genetic erosion, while other species showed expanding or interrupted populations. Some DBH-size classes (e.g. 145.0–189.9cm) have disappeared from the forest, presumably due to their selective removal. We recommend detailed integrated floristic and faunistic studies of the forest, targeting the ecologically sensitive indicators of habitat change such as orchids, birds, reptiles and amphibians. Finally, a proposal to conserve the forest under a community-based forest conservation scheme is put forward.     

Kidney dysfunction and cadmium exposure--factors influencing dose-response relationships

Our early toxicological studies showed that metallothionein (MT) is a protein that carries cadmium (Cd) to the kidney, explaining why Cd exposures during long time periods may give rise to kidney dysfunction. This dysfunction is usually considered to be the critical effect, i.e. the adverse effect that occurs at the lowest exposure level. MT also provides intracellular protection against cadmium toxicity. In studies of population groups in cadmium contaminated areas in China, we investigated factors that affected the relationship between internal dose of Cd, as indicated by blood Cd (BCd) or urinary Cd (UCd), and the prevalence of kidney dysfunction. We found dose-response relationships between UCd and the prevalence of increased levels of biomarkers of renal tubular dysfunction (urinary beta-2-microglobulin, B2M, or N-acetyl-beta-d-glucosaminidase - NAG) or urinary albumin (UAlb), a biomarker of glomerular kidney dysfunction. Two years after Cd intake from contaminated rice was diminished, renal tubular dysfunction appeared unchanged or aggravated among those with higher UCd; Another 8 years later, i.e. 10 years after Cd intake was decreased, the prevalence of renal tubular dysfunction was still increased but UAlb had returned to normal. Factors that influenced the dose-response relationships were: (1) time after maximum exposure. (2) Concomitant exposure to other nephrotoxic agents such as inorganic arsenic. (3) Cd induced metallothionein mRNA levels in peripheral blood lymphocytes, used as a biomarker of the ability of each person, to synthesize MT. (4) The occurrence of increased levels in blood plasma of autoantibodies against MT. The two last points further support a role in humans of MT as a protective protein against tissue damage from cadmium and gives support to previous ideas developed partly in experimental systems.