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The structure and function of regulators and anti-terminators is under discussion in gram-positive bacteria. The regulators of lichen and levan operons (LiR and LevR) as well as the implementation of both gram-positive and negative regulations of operons by them are in the focus of attention. Po-independent termination is regarded by the example of the regulatory activity for the utilization systems of glucose (GlcT) beta-glucosides (LicT), sucrose (low-efficiency system SacY-SacX) and of glycerin (GlcP). Changes in the functional activity of the above systems, which are dependent on a condition of anti-terminators (phosphorylated or dephosphorylated forms and an ability to demirelize etc.) are regarded from the viewpoint of a possibility of occurrence of catabolic repression.
Mol Gen Mikrobiol Virusol 2003
PMID:[The pleiotropic function of the phosphoenolpyruvate-dependent phosphotransferase system in bacteria. Communication II]. 1296 19

Molecular methods are widely used for species identification of mammals. In particular, the mitochondrial cytochrome b gene sequence has proven helpful for this purpose. Microarray technology can now open up new perspectives for biodiversity monitoring. With microarrays, many thousands of genetically based characteristics can be tested on one microscopic glass slide called a 'chip'. A 'Mammalia-Chip', for example, could include redundant diagnostic markers to unambiguously identify all European mammal species. Of broader use, and therefore economically more relevant, could be a 'Biodiversity-Chip', containing diagnostic features to distinguish key species in the taxa of bacteria, lichen, molluscs, insects, fungi, mammals, etc. An important prerequisite for any mixed-phyla chip is a standardization of methods. One of the most promising genes as a universal marker for all eukaryotes is cytochrome oxidase I. We show that cytochrome oxidase I is adequate for the discrimination of different species of voles and shrews with cluster analysis. Based on these results we present a diagnostic microarray-chip using cytochrome oxidase I sequences for the identification of three species of Sorex (Soricidae, Insectivora) and four species of Microtus (Arvicolinae, Rodentia). We conclude that cytochrome oxidase I can be used as an alternative marker to cytochrome b in a mixed-phyla chip, or both genes can be used in combination to enhance redundance and thus robustness of a specific chip including small mammals.
Mol Ecol 2004 May
PMID:Development of microarray-based diagnostics of voles and shrews for use in biodiversity monitoring studies, and evaluation of mitochondrial cytochrome oxidase I vs. cytochrome b as genetic markers. 1507 63

Seven highly-coloured lichen species belonging to the genera Caloplaca, Candelariella, Aspicilia and Xanthoria from ecclesiastical buildings in northern Spain have been analysed non-destructively by FT-Raman spectroscopy. The vibrational band assignments in the spectra of the specimens, which were still attached to their limestone or sandstone substrata, were accomplished with the assistance of the chemical compositions obtained from wet chemical extraction methods. beta-Carotene was found in all specimens as the major pigment, and the characteristic spectral signatures of calcium oxalate monohydrate (whewellite) and dihydrate (weddelite) could be identified; chemical signatures were found for these materials even in lichen thalli growing the non-calcareous substrata, indicating, probably, that the calcium was provided here from wind-or-rain-borne sources. The Raman spectral biomarkers found in the lichens broadly agreed with the chemical extraction profiles as expected, but the present study indicates that some form of non-destructive taxonomic identification based on Raman spectroscopy was possible.
Spectrochim Acta A Mol Biomol Spectrosc 2004 Apr
PMID:Lichen biodeterioration of ecclesiastical monuments in northern Spain. 1508 42

Phylogenetic relationships of lichen-forming discomycetes and their relatives in the class Lecanoromycetes were examined by using nuclear large subunit and mitochondrial small subunit ribosomal DNA sequences. Ninety-eight partial sequences of 53 ascomycetes were generated and aligned with the corresponding sequences retrieved from GenBank resulting in an alignment of 100 taxa that was analyzed using a Bayesian approach with Markov chain Monte Carlo (B/MCMC) methods. The analysis revealed the monophyly of the Lecanoromycetes with two major clades: one clade including the monophyletic orders Graphidales and Ostropales and the paraphyletic Gyalectales, the other clade including the monophyletic Lecanorales (incl. Caliciales, Peltigerales, and Teloschistales) and a clade containing the polyphyletic Agyriales, a yet undescribed order Umbilicariales (including Elixiaceae and Umbilicariaceae), and Pertusariales. The monophyly of the Pertusariales was not resolved. Testing of alternative hypotheses revealed that a placement of Chaetothyriomycetes and Eurotiomycetes within Lecanoromycetes and the monophyly of Agyriales s. lat. (incl. Elixiaceae and Schaereriaceae) and Ostropales s. lat. (incl. Graphidales) can be rejected, while monophyly of Gyalectales and the Pertusariales and placement of Umbilicariales on the Lecanorales branch cannot be rejected with the current data set.
Mol Phylogenet Evol 2004 Jun
PMID:Supraordinal phylogenetic relationships of Lecanoromycetes based on a Bayesian analysis of combined nuclear and mitochondrial sequences. 1512 Mar 81

The lichen-forming genus Porpidia (Porpidiaceae, Ascomycota) provides excellent opportunities for evolutionary, reproductive, and ecological studies of crustose epilithic lichen symbioses. However, despite the fact that the genus itself seemed to be clearly delimited, the group was thought to be a hopeless case with regard to intrageneric relationships and species delimitations due to apparently rampant homoplasy throughout most character systems. Contrary to the situation for non-molecular data, a robust and generally well-resolved phylogeny was recovered based on DNA-sequence data. Separate and combined analyses of nuclear ribosomal RNA large subunit and nuclear beta-tubulin gene fragments were performed using maximum parsimony, maximum likelihood, and Bayesian approaches. Branch support was estimated using non-parametic bootstrapping and posterior probabilities, while monophyly of a priori defined groups was tested using posterior probabilities. The results reveal a highly supported "Porpidia sensu lato," however, Porpidia itself is not monophyletic. Several smaller genera of the Porpidiaceae and probably the large genus Lecidea (Lecideaceae) are nested within the group. Most taxa analyzed fall into one of four major subgroups within Porpidia s.l., though the basal relationships among these subgroups could not be supported. This phylogeny will make it possible to re-evaluate morphological and chemical characters in the group, and to conduct detailed studies of species delimitations within the monophyletic subgroups.
Mol Phylogenet Evol 2004 Jul
PMID:Resolving evolutionary relationships in the lichen-forming genus Porpidia and related allies (Porpidiaceae, Ascomycota). 1518 98

The role of Antarctic epilithic lichens in the primary colonization of rocks and in the formation of soils is receiving attention because of the production of the stress-protective biochemicals needed to combat radiation, desiccation and extremes of temperature. Raman microscopy has been used here to study the encrustations produced at the interface between the rock substratum and Buellia spp. lichen thalli; in addition to whewellite, calcium oxalate monohydrate, the presence of weddellite, the metastable dihydrate form, was confirmed in the encrustations. An unusual pigmentation of the rock surface found on detachment of the lichen growths is identified as beta-carotene from its characteristic Raman bands at 1525, 1191, 1157 and 1003 cm(-1); normally, beta-carotene, which has been identified as a UV-radiation protectant, is found at the exposed upper surface of the biological organism. The interface between the detached lichen thalli and the rock also contains whewellite as the sole biomineralization product--which suggests a possible strategy for the formulation of weddelite in the growing Buellia spp. colony as an anti-desiccant.
Spectrochim Acta A Mol Biomol Spectrosc 2004 Jul
PMID:Stratified response to environmental stress in a polar lichen characterized with FT-Raman microscopic analysis. 1524 82

Despite the recent progress in molecular phylogenetics, many of the deepest relationships among the main lineages of the largest fungal phylum, Ascomycota, remain unresolved. To increase both resolution and support on a large-scale phylogeny of lichenized and non-lichenized ascomycetes, we combined the protein coding-gene RPB2 with the traditionally used nuclear ribosomal genes SSU and LSU. Our analyses resulted in the naming of the new subclasses Acarosporomycetidae and Ostropomycetidae, and the new class Lichinomycetes, as well as the establishment of the phylogenetic placement and novel circumscription of the lichen-forming fungi family Acarosporaceae. The delimitation of this family has been problematic over the past century, because its main diagnostic feature, true polyspory (numerous spores issued from multiple post-meiosis mitoses) with over 100 spores per ascus, is probably not restricted to the Acarosporaceae. This observation was confirmed by our reconstruction of the origin and evolution of this form of true polyspory using maximum likelihood as the optimality criterion. The various phylogenetic analyses carried out on our data sets allowed us to conclude that: (1) the inclusion of phylogenetic signal from ambiguously aligned regions into the maximum parsimony analyses proved advantageous in reconstructing phylogeny; however, when more data become available, Bayesian analysis using different models of evolution is likely to be more efficient; (2) neighbor-joining bootstrap proportions seem to be more appropriate in detecting topological conflict between data partitions of large-scale phylogenies than posterior probabilities; and (3) Bayesian bootstrap proportion provides a compromise between posterior probability outcomes (i.e., higher accuracy, but with a higher number of significantly supported wrong internodes) vs. maximum likelihood bootstrap proportion outcomes (i.e., lower accuracy, with a lower number of significantly supported wrong internodes).
Mol Phylogenet Evol 2004 Sep
PMID:Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. 1528 74

The Pertusariaceae is a diverse, cosmopolitan group of crustose lichen-forming fungi. It is particularly rich in secondary metabolites, containing a variety of compounds from different substance classes, such as xanthones, depsides, depsidones, and depsones. Morphology and chemistry-based studies have provided conflicting views of relationships among taxa, and phylogenetic relationships among genera in the Pertusariaceae are still unsettled. To evaluate these relationships, we generated a phylogeny based on nucleotide sequences of the nuclear large subunit (nu LSU) and the mitochondrial small subunit (mt SSU) rRNA genes. For a subset of taxa, we additionally sequenced the mitochondrial large subunit (mt LSU) rDNA. We studied a total of 49 taxa from the family Pertusariaceae and the enigmatic genus Loxosporopsis including four Agyrialean taxa used as outgroups. The alignments were analyzed using a Bayesian approach with Markov Chain Monte Carlo tree sampling (B/MCMC), and maximum parsimony methods. In the resulting phylogenetic estimates the genus Pertusaria in its current circumscription is polyphyletic comprising three major clades: the Pertusaria s.str.-group, the Variolaria-group and the Varicellaria-group. Loxosporopsis is closely related to Pertusaria s.str. We re-analyzed morphological, anatomical, and chemical features in the light of the molecular study and found novel character combinations to describe monophyletic entities. The taxonomic significance of particular secondary chemical constituents in the Pertusariaceae is corroborated.
Mol Phylogenet Evol 2004 Oct
PMID:Molecular phylogeny of the Pertusariaceae supports secondary chemistry as an important systematic character set in lichen-forming ascomycetes. 1532 38

Termites are among the most important cellulose-digesting animals on earth, and are well-known for the symbiotic relationship they have with cellulolytic trichomonad and oxymonad flagellates (unicellular eukaryotes). Perhaps less well-known is the fact that approximately 75% of the approximately 2600 described termite species -- those belonging to the family Termitidae -- do not harbour such flagellates. Unlike most termites from other families, the majority of termitids do not consume wood, feeding instead on soil, leaf litter, fungi, grass, or lichen. Recent years have seen the characterization of the endogenous cellulase enzymes that help termites digest cellulose, from one flagellate-harbouring species (Reticulitermes speratus), as well as one termitid (Nasutitermes takasagoensis). The genes encoding the enzymes in these two termites are similar. However, their site of expression differs markedly -- the salivary glands in R. speratus and the midgut in N. takasagoensis. To investigate this difference further, we performed a comparative study of cellulase expression in various termitid and flagellate-harbouring species, using enzyme assays and reverse transcription polymerase chain reactions. Taxa from phylogenetically basal lineages were consistently found to express endogenous genes specifically in the salivary glands, whilst those from a relatively apical lineage containing termitids expressed cellulases solely in the midgut. Relatively low levels of cellulase activity were found in nonwood-feeding species, while the wood-feeding Coptotermes formosanus -- arguably the most destructive pest species world-wide -- was found to have high levels of activity in all parts of the gut when compared to all other termites. In the light of these results, as well as recently accumulated phylogenetic data, we discuss scenarios for the evolution of cellulose digestion in termites.
Mol Ecol 2004 Oct
PMID:Major alteration of the expression site of endogenous cellulases in members of an apical termite lineage. 1536 34

Symbiosis is a major theme in the history of life and can be an important force driving evolution. However, across symbioses, it is difficult to tease apart the mechanisms that structure the interactions among potential partners. We used genetic similarity and frequency-based methods to qualitatively and quantitatively examine the patterns of association among several co-occurring Cladonia lichen fungi and their algal photobionts in six disjunct Florida scrub sites. The patterns of association were described by the degree of specificity, i.e. the phylogenetic range of associated partners, and of selectivity, i.e. the frequency of association among partners. Six fungal species associated with only one algal internal transcribed spacer clade, with the remaining two fungi being associated with two algal clades. In all cases, the fungi associated in unequal frequencies with the observed algal photobiont genotypes within those clades--suggesting that both specificity and selectivity were higher than expected. Fungal species can be grouped into three significantly different specificity classes: photobiont specialists, intermediates and generalists. In contrast to the pronounced specificity for photobionts among fungal species, the different Florida scrub sites do not harbour distinct photobiont pools, and differential photobiont availability cannot explain the patterning of lichen associations at this spatial scale. Therefore, we conclude that fungal specificity and selectivity for algal photobionts are major factors in determining the local composition of symbiotic partnerships.
Mol Ecol 2004 Nov
PMID:Strong fungal specificity and selectivity for algal symbionts in Florida scrub Cladonia lichens. 1548 96


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