Nucleotide polymorphism in the 5.8S nrDNA gene and internal transcribed spacers in Phakopsora pachyrhizi viewed from structural models

The assessment of nucleotide polymorphisms in environmental samples of obligate pathogens requires DNA amplification through the polymerase chain reaction (PCR) and bacterial cloning of PCR products prior to sequencing. The drawback of this strategy is that it can give rise to false polymorphisms owing to DNA polymerase misincorporation during PCR or bacterial cloning. We investigated patterns of nucleotide polymorphism in the internal transcribed spacer (ITS) region for Phakopsora pachyrhizi, an obligate biotrophic fungus that causes the Asian soybean rust. Field-collected samples of P. pachyrhizi were obtained from all major soybean production areas worldwide, including Brazil and the United States. Bacterially-cloned, PCR products were obtained using a high fidelity DNA polymerase. A total of 370 ITS sequences that were subjected to an array of complementary sequence analyses, which included analyses of secondary structure stability, the pattern of nucleotide polymorphisms, GC content, and the presence of conserved motifs. The sequences exhibited features of functional rRNAs. Overall, polymorphisms took place within less conserved motives, such as loops and bulges; alternatively, they gave rise to non-canonical G-U pairs within conserved regions of double stranded helices. We discuss the usefulness of structural analyses to filter out putative 'suspicious' bacterially cloned ITS sequences, thus keeping artificially-induced sequence variation to a minimum.

Trichomonads in pleural effusion: case report, literature review and utility of PCR for species identification

Trichomonas tenax is a flagellated protozoan commonly found in the human oral cavity but of unusual occurrence in pulmonary infections. We describe a case of a 67-year-old patient with glioblastoma who presented with severe pleurisy in the post-operative period while she was receiving high-dose corticotherapy. Several motile flagellated protozoa were identified in the pleural fluid. Trichomonas tenax was identified by molecular methods. Pulmonary infections with Trichomonads might be underestimated because of diagnostic difficulties. The utility of molecular biology for species identification is underlined and the pathogenicity of Trichomonad parasites in human lungs is discussed in light of previously reported cases.

Identification of Paramecium bursaria syngens through molecular markers--comparative analysis of three loci in the nuclear and mitochondrial DNA

This is the first attempt to resolve the phylogenetic relationship between different syngens of Paramecium bursaria and to investigate at a molecular level the intraspecific differentiation of strains originating from very distant geographical locations. Herein we introduce a new collection of five P. bursaria syngens maintained at St Petersburg State University, as the international collection of syngens was lost in the 1960s. To analyze the degree of speciation within Paramecium bursaria, we examined 26 strains belonging to five different syngens from distant and geographically isolated localities using rDNA (ITS1-5.8S-ITS2-5'LSU) fragments, mitochondrial cytochrome c oxidase subunit I (COI), and H4 gene fragments. It was shown that P. bursaria strains of the same syngens cluster together in all three inferred molecular phylogenies. The genetic diversity among the studied P. bursaria strains based on rDNA sequences was rather low. The COI divergence of Paramecium bursaria was also definitely lower than that observed in the Paramecium aurelia complex. The nucleotide sequences of the H4 gene analyzed in the present study indicate the extent of genetic differences between the syngens of Paramecium bursaria. Our study demonstrates the diagnostic value of molecular markers, which are important tools in the identification of Paramecium bursaria syngens.

Ribosomal RNA processing in Candida albicans

Ribosome assembly begins with conversion of a polycistronic precursor into 18S, 5.8S, and 25S rRNAs. In the ascomycete fungus Candida albicans, rRNA transcription starts 604 nt upstream of the 18S rRNA junction (site A1). One major internal processing site in the 5' external transcribed spacer (A0) occurs 108 nt from site A1. The A0-A1 fragment persists as a stable species during log phase growth and can be used to assess proliferation rates. Separation of the small and large subunit pre-rRNAs occurs at sites A2 and A3 in internal transcribed spacer-1 Saccharomyces cerevisiae pre-rRNA. However, the 5' end of the 5.8S rRNA is represented by only a 5.8S (S) form, and a 7S rRNA precursor of the 5.8S rRNA extends into internal transcribed spacer 1 to site A2, which differs from S. cerevisiae. External transcribed spacer 1 and internal transcribed spacers 1 and 2 show remarkable structural similarity with S. cerevisiae despite low sequence identity. Maturation of C. albicans rRNA resembles other eukaryotes in that processing can occur cotranscriptionally or post-transcriptionally. During rapid proliferation, U3 snoRNA-dependent processing occurs before large and small subunit rRNA separation, consistent with cotranscriptional processing. As cells pass the diauxic transition, the 18S pre-rRNA accumulates into stationary phase as a 23S species, possessing an intact 5' external transcribed spacer extending to site A3. Nutrient addition to starved cells results in the disappearance of the 23S rRNA, indicating a potential role in normal physiology. Therefore, C. albicans reveals new mechanisms that regulate post- versus cotranscriptional rRNA processing.

Diversity and killer activity of yeasts in Malaysian fermented food samples

The biodiversity and the killer activity of yeasts isolated from various types of fermented food in Malaysia were investigated in this study. Of 252 yeasts isolated from 48 fermented food samples in this study, 19 yeast species were identified based on sequence analysis of the ITS1-5.8S-ITS2 partial fragments of the yeasts. A total of 29 (11.5%) of the yeast isolates demonstrated killer activity to at least one Candida species tested in this study; including 22 isolates of Trichosporon asahii, 4 isolates of Pichia anomala, and one isolate each of Pichia norvegensis, Pichia fermentans and Issatchenkia orientalis, respectively. The presence of killer yeasts reflects antagonism that occurs during microbial interaction in the fermented food, whereby certain yeasts produce killer toxins and possibly other toxic substances in competition for limited nutrients and space. The anti-Candida activity demonstrated by killer yeasts in this study should be further explored for development of alternative therapy against candidiasis.

Aspergillus affinis sp. nov., a novel ochratoxin A-producing Aspergillus species (section Circumdati) isolated from decomposing leaves

Two ochratoxin A (OTA)-producing Aspergillus isolates, recently collected from submerged riparian decomposing leaves in Italy, were found to have a similar morphology to Aspergillus cretensis (subgenus Circumdati, section Circumdati). However, marked differences emerged between these two novel isolates and A. cretensis as the former displayed different colony features and had larger vesicles, metulae, phialides and conidia, as well as a distinct sclerotial form and size. In order to determine the taxonomic status and to infer the evolutionary relationships of these two morphologically identical isolates, a molecular phylogenetic analysis was performed on all the officially recognized lineages in the section Circumdati. The DNA sequences and the deduced amino acid residues from the nuclear loci were analysed. Both rRNA and protein coding genes were assessed, which are widely used to differentiate taxa belonging to genus Aspergillus at various evolutionary levels. The 5.8S rDNA gene and internal transcribed spacers (ITS), the D1/D2 domains of the 28S rDNA gene, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and then sequenced. The analysis of the rRNA regions and of the benA and cmd sequence data indicated that the two isogenic isolates belonged to a genetically distinct OTA-producing species of the genus Aspergillus. The isolates are proposed as representing a novel species, Aspergillus affinis sp. nov., with the type strain ATCC MYA-4773T=CBS 129190=417). Phylogenetically, A. affinis sp. nov. appeared to be very closely related to A. cretensis, from which it could be distinguished by means of a morphological trait analysis.

[Population characterization of Balantidium coli from pigs using ITS1-5.8S rRNA-ITS2 sequence]

OBJECTIVE

To determine the species and genotypes of Balantidium isolated from pigs in Henan province, China.

METHODS

Scatoscopy and the modified DMEM media were used to isolate trophozoites of Balantidium from pig feces. The ITS1-5.8S rRNA-ITS2-based molecular marker method, Acridine orange staining ( AO) and microscopic observation were used to determine the population characteristics among different isolates of B. coli from various pigs farms.

RESULTS

We isolated 15 isolates from the pigs at diagnosis in the Animal Hospital of Henan University of Science and Technology from the pig farms of the 8 counties or cities of the west of Henan province in total, and all of them belong to the same species B. coli. MJ-2 and SX-1 isolates were genotype A of B. coli, and the remaining 13 isolates were genotype B. Trophozoites of MJ-2 and SX-1 were bigger, moved more slowly and lower density in feces and in vitro culture than other 13 isolates, while structures of their nuclei were not different.

CONCLUSION

Both genotype A and B of B. coli are present in the pig farms of the west of Henan province, China, and genotype B is the determinant population in pigs farms. These findings could provide an important implication for the effective control of balantidiosis of human and other hosts.

Molecular characterization of Hysterothylacium aduncum (Nematoda: Raphidascaridae) from different fish caught off the Tunisian coast based on nuclear ribosomal DNA sequences

Larval forms of the genus Hysterothylacium have been previously reported in teleost fish from the North African coasts of central Mediterranean Sea by morphological analysis. In the present study, samples identified morphologically as Hysterothylacium aduncum (n = 62), from Merluccius merluccius, Trachurus mediterraneus and Pagellus erythrinus from different geographical locations of the Tunisian coasts, were genetically characterised by sequences of the first (ITS-1), the 5.8S and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA). Comparison of the sequences obtained with those available in public gene databases confirmed that all the samples from the Tunisian coasts belong to a single species, namely H. aduncum. All specimens from the Tunisian coasts showed one indel in position 787 in ITS-2 sequences not reported by any of the previously published sequences from the Atlantic and Pacific Oceans, Adriatic Sea (Mediterranean Sea) and the East Greenland Sea, suggesting the existence of a population-specific pattern exhibiting a low differentiation of this parasite in this area. This is the first molecular characterization of H. aduncum from the Tunisian coasts using ITS rDNA sequences which allows the definition of genetic markers for their unequivocal identification, and provides further biological data on these nematodes in marine fish off the Tunisian coasts, improving the picture of the occurrence of these taxa in the North African coasts of central Mediterranean Sea.

Postharvest dark skin spots in potato tubers are an oversuberization response to Rhizoctonia solani infection

Israeli farmers export 250,000 tons of potato tubers annually, ≈40,000 tons of which are harvested early, before skin set. In recent years, there has been an increase in the occurrence of dark skin spots on early-harvested potato tubers ('Nicola') packed in large bags containing peat to retain moisture. The irregular necrotic spots form during storage and overseas transport. Characterization of the conditions required for symptom development indicated that bag temperature after packing is 11 to 13°C and it reaches the target temperature (8°C) only 25 days postharvest. This slow decrease in temperature may promote the establishment of pathogen infection. Isolates from typical lesions were identified as Rhizoctonia spp., and Koch's postulates were completed with 25 isolates by artificial inoculation performed at 13 to 14°C. Phylogenetic analysis, using the internal transcribed spacer sequences (ITS1 and ITS2) of rDNA genes, assigned three isolates to anastomosis group 3 of Rhizoctonia solani. Inoculation of wounded tubers with mycelium of these R. solani isolates resulted in an oversuberization response in the infected area. With isolate Rh17 of R. solani, expression of the suberin biosynthesis-related genes StKCS6 and CYP86A33 increased 6.8- and 3.4-fold, respectively, 24 h postinoculation, followed by a 2.9-fold increase in POP_A, a gene associated with wound-induced suberization, expression 48 h postinoculation, compared with the noninoculated tubers. We suggest that postharvest dark spot disease is an oversuberization response to R. solani of AG-3 infection that occurs prior to tuber skin set.

Whole-exome re-sequencing in a family quartet identifies POP1 mutations as the cause of a novel skeletal dysplasia

Recent advances in DNA sequencing have enabled mapping of genes for monogenic traits in families with small pedigrees and even in unrelated cases. We report the identification of disease-causing mutations in a rare, severe, skeletal dysplasia, studying a family of two healthy unrelated parents and two affected children using whole-exome sequencing. The two affected daughters have clinical and radiographic features suggestive of anauxetic dysplasia (OMIM 607095), a rare form of dwarfism caused by mutations of RMRP. However, mutations of RMRP were excluded in this family by direct sequencing. Our studies identified two novel compound heterozygous loss-of-function mutations in POP1, which encodes a core component of the RNase mitochondrial RNA processing (RNase MRP) complex that directly interacts with the RMRP RNA domains that are affected in anauxetic dysplasia. We demonstrate that these mutations impair the integrity and activity of this complex and that they impair cell proliferation, providing likely molecular and cellular mechanisms by which POP1 mutations cause this severe skeletal dysplasia.

Skeletal dysplasias are a group of genetic disorders affecting skeletal development that cause deficiencies and deformities of the limbs and spine, dwarfism, or abnormal bone strength. Skeletal dysplasias are usually inherited as monogenic Mendelian traits or occur as a result of de novo mutations. We report identification of mutations in human POP1 gene as the cause of a severe novel skeletal dysplasia. Molecular analyses presented in our work provide an important link between the pathogenesis of the disease and basic cellular processes including RNA processing and the cell cycle. We posit that our work will also have an immediate impact on assessment and counselling of novel cases of severe short stature.

Quantitative PCR coupled with melt curve analysis for detection of selected pseudo-nitzschia spp. (Bacillariophyceae) from the Northwestern Mediterranean sea

The frequency and intensity of Pseudo-nitzschia spp. blooms along the coast of Catalonia have been increasing over the past 20 years. As species from this genus that are documented as toxigenic have been found in local waters, with both toxic and nontoxic species cooccurring in the same bloom, there is a need to develop management tools for discriminating the difference. Currently, differentiation of toxic and nontoxic species requires time-consuming electron microscopy to distinguish taxonomic features that would allow identification as to species, and cryptic species can still remain misidentified. In this study, cells of Pseudo-nitzschia from clonal cultures isolated from seawater were characterized to their species identity using scanning electron microscopy, and subsamples of each culture were used to create an internal transcribed spacer 1 (ITS-1), 5.8S, and ITS-2 ribosomal DNA database for development of species-specific quantitative PCR (qPCR) assays. Once developed, these qPCR assays were applied to field samples collected over a 2-year period in Alfaques Bay in the northwestern Mediterranean Sea to evaluate the possibility of a comprehensive surveillance for all Pseudo-nitzschia spp. using molecular methods to supplement optical microscopy, which can discern taxonomy only to the genus level within this taxon. Total Pseudo-nitzschia cell density was determined by optical microscopy from water samples collected weekly and compared to results obtained from the sum of eight Pseudo-nitzschia species-specific qPCR assays using duplicate samples. Species-specific qPCR followed by melt curve analysis allowed differentiation of amplicons and identification of false positives, and results correlated well with the total Pseudo-nitzschia cell counts from optical microscopy.

Two new chroman derivations from the endophytic Penicillium sp. DCS523

Strain DCS523 was isolated from the branch tissue of Daphniphyllum longeracemosum and determined to be a Penicillium sp. according to the ITS sequence analysis. The extracts from the PDA solid fermentation media of Penicillium sp. DCS523 were purified to give two new chroman derivatives as well as six known compounds. Based on their spectral data the new compounds were identified as (Z)-6-acetyl- 3-(1,2-dihydroxypropylidene)-5-hydroxy-8-methylchroman-2-one and 6-acetyl-2α,5- dihydroxy-2-(2-hydroxypropyl)- 3α,8-dimethylchroman, respectively.

A bioinformatics pipeline for sequence-based analyses of fungal biodiversity

The internal transcribed spacer (ITS) is the locus of choice with which to characterize fungal diversity in environmental samples. However, methods to analyze ITS datasets have lagged behind the capacity to generate large amounts of sequence information. Here, we describe our bioinformatics pipeline to process large fungal ITS sequence datasets, from raw chromatograms to a spreadsheet of operational taxonomic unit (OTU) abundances across samples. Steps include assembling of reads originating from one clone, identifying primer "barcodes" or "tags," trimming vectors and primers, marking low-quality base calls and removing low-quality sequences, orienting sequences, extracting the ITS region from longer amplicons, and grouping sequences into OTUs. We expect that the principles and tools presented here are relevant to datasets arising from ever-evolving new technologies.

1A6/DRIM, a novel t-UTP, activates RNA polymerase I transcription and promotes cell proliferation

BACKGROUND

Ribosome biogenesis is required for protein synthesis and cell proliferation. Ribosome subunits are assembled in the nucleolus following transcription of a 47S ribosome RNA precursor by RNA polymerase I and rRNA processing to produce mature 18S, 28S and 5.8S rRNAs. The 18S rRNA is incorporated into the ribosomal small subunit, whereas the 28S and 5.8S rRNAs are incorporated into the ribosomal large subunit. Pol I transcription and rRNA processing are coordinated processes and this coordination has been demonstrated to be mediated by a subset of U3 proteins known as t-UTPs. Up to date, five t-UTPs have been identified in humans but the mechanism(s) that function in the t-UTP(s) activation of Pol I remain unknown. In this study we have identified 1A6/DRIM, which was identified as UTP20 in our previous study, as a t-UTP. In the present study, we investigated the function and mechanism of 1A6/DRIM in Pol I transcription.

METHODOLOGY/PRINCIPAL FINDINGS

Knockdown of 1A6/DRIM by siRNA resulted in a decreased 47S pre-rRNA level as determined by Northern blotting. Ectopic expression of 1A6/DRIM activated and knockdown of 1A6/DRIM inhibited the human rDNA promoter as evaluated with luciferase reporter. Chromatin immunoprecipitation (ChIP) experiments showed that 1A6/DRIM bound UBF and the rDNA promoter. Re-ChIP assay showed that 1A6/DRIM interacts with UBF at the rDNA promoter. Immunoprecipitation confirmed the interaction between 1A6/DRIM and the nucleolar acetyl-transferase hALP. It is of note that knockdown of 1A6/DRIM dramatically inhibited UBF acetylation. A finding of significance was that 1A6/DRIM depletion, as a kind of nucleolar stress, caused an increase in p53 level and inhibited cell proliferation by arresting cells at G1.

CONCLUSIONS

We identify 1A6/DRIM as a novel t-UTP. Our results suggest that 1A6/DRIM activates Pol I transcription most likely by associating with both hALP and UBF and thereby affecting the acetylation of UBF.

[The origin of polyploid genomes of bluegrasses Poa L. and gene flow between Northern Pacific and sub-Antarctic islands]

The involvement of present-day diploid bluegrass species in the formation of polyploid genomes was investigated using comparison of sequences of internal transcribed spacers ITS1 and ITS2, and the 5.8S rDNA sequence. It was demonstrated that highly polyploid New Zealand bluegrasses, P. cita (2n = 84; ca. 96 to 100), P. chathamica (2n = 112), and P. litorosa (2n = 263 to 266) formed separate highly supported clade together with tetraploids (2n = 28) P. intrusa, P. anceps, and P. trioides (Austrofestuca littoralis). Among the diploid species (2n = 14), the closest relatives of these species, as well as of the polyploid species of section Poa, are the genomes of Eurasian species P. remota, P. chaixcii (sect. Homalopoa), P densa (Bolbophorum), and P. sibirica (sect. Macropoa). Nuclear genomes of polyploid Stenopoa, Tichopoa, Oreinos, and Secundae are definitely related to the genome of Arctic species P. pseudabbreviata (sect. Abbreviatae). On the contrary, judging by the genes for nuclear 45S rRNA, genomes of diploid P. trivialis (sect. Pandemos), P. annua, and P. supina (sect. Ochlopoa both) are only remotely related to the genomes of highly polyploid species (distances p between them and other bluegrass species from different sections of subgenus Poa constitute 6-10% and 11-15%, respectively). The conclusion on the relationships between highly polyploid and diploid bluegrass species was tested using analysis of synapomorphic mutations in the 5.8S rRNA gene. It was demonstrated that genomes of Poa eminens (2n = 42) and P. schischkinii (2n = 70) (sect. Arctopoa both) were noticeably different in ITS regions from the genomes of the members of the type subgenus Poa. A comparison of the Arctopoa ITS regions showed that the differences between them constituted only 0.2%. At the same time, p distances between the Arctopoa ITS and those from the species belonging to other sections of the genus Poa varied from 5 to 14%. South American species P chonotica (sect. Andinae) (=Ncoraepoa chonotica) (2n = 42) was found to be related to Arctagrostis, Festucella, and Hookerochloa, being at the same time quite distant from the other species of the genus Poa. Polymorphic in chromosome number highly polyploid species of Northern Hemisphere, P. arctica (2n = 42 to 106), P. turneri (2n = 42, 63 to 64), and P. smirnovii (2n = 42, 70) (sect. Malacanthae) are relative to a large group of tetraploid (2n = 28) endemic bluegrass species from New Zealand and sub-Antarctic islands (P. novae-zelandiae and allied species).

Candida galli strain PGO6: a novel isolated yeast strain capable of transformation of isoeugenol into vanillin and vanillic acid

Candida galli strain PGO6 isolated from oil-contaminated water is the first isolated yeast strain which is capable to form vanillin and vanillic acid during isoeugenol biotransformation. The products were confirmed by thin-layer chromatography (TLC), changes in the UV absorption pattern and high-performance liquid chromatography (HPLC). The phenotypic and physiochemical characteristics as well as molecular phylogenetic analysis based on amplification the ITS1-5.8S-ITS2 rDNA regions indicated the isolated strain PGO6 was identified as C. galli (GenBank accession number HM641231). Resting cells of C. galli PGO6 from the late-exponential of growth phase were used as biocatalysts for the biotransformation of isoeugenol. The optimal molar conversion of vanillin (48%) and vanillic acid (19%) was obtained after a 30 h incubation using 0.1% (v/v) of isoeugenol and 6 mg of dry weight of cells per ml without further optimization. Under these conditions, the total amount of vanillin and vanillic acid was 583 mg l(-1). Further biotransformation was carried out using 0.5% (v/v) of isoeugenol under the resting cells conditions, yielding a vanillin concentration of 1.12 g l(-1) (molar yield 25.7%) after 60 h incubation. This study brings the first evidence for biotransformation of isoeugenol to vanillin and vanillic acid by a yeast strain.

Phylogenetic relationships in genus Arachis based on ITS and 5.8S rDNA sequences

BACKGROUND

The genus Arachis comprises 80 species and it is subdivided into nine taxonomic sections (Arachis, Caulorrhizae, Erectoides, Extranervosae, Heteranthae, Procumbentes, Rhizomatosae, Trierectoides, and Triseminatae). This genus is naturally confined to South America and most of its species are native to Brazil. In order to provide a better understanding of the evolution of the genus, we reconstructed the phylogeny of 45 species using the variation observed on nucleotide sequences in internal transcribed spacer regions (ITS1 and ITS2) and 5.8 S of nuclear ribosomal DNA.

RESULTS

Intraspecific variation was detected, but in general it was not enough to place accessions of the same species in different clades. Our data support the view that Arachis is a monophyletic group and suggested Heteranthae as the most primitive section of genus Arachis. The results confirmed the circumscriptions of some sections (Caulorrhizae, Extranervosae), but raised questions about others. Sections Erectoides, Trierectoides and Procumbentes were not well defined, while sections Arachis and Rhizomatosae seem to include species that could be moved to different sections. The division of section Arachis into A and B genome species was also observed in the phylogenetic tree and these two groups of species may not have a monophyletic origin. The 2n = 2x = 18 species of section Arachis (A. praecox, A. palustris and A. decora) were all placed in the same clade, indicating they are closely related to each other, and their genomes are more related to B genome than to the A genome. Data also allowed insights on the origin of tetraploid A. glabrata, suggesting rhizome appeared twice within the genus and raising questions about the placement of that species in section Rhizomatosae.

CONCLUSION

The main clades established in this study in general agreed with many other studies that have used other types of evidences and sets of species, being some of them included in our study and some not. Thus, the relationships established can be a useful framework for future systematic reviews of genus Arachis and for the selection of species to pre-breeding programs.

Isolation and identification of Rhizoctonia-like fungi from roots of three orchid genera, Paphiopedilum, Dendrobium, and Cymbidium, collected in Chiang Rai and Chiang Mai provinces of Thailand

Three orchid genera, Paphiopedilum, Cymbidium, and Dendrobium, are among the most heavily traded ornamental plants in Thailand. In this study, 27 isolates of Rhizoctonia-like fungi were isolated from root sections of mature orchids in the three orchid genera, collected from diverse horticultural settings in Chiang Mai and Chiang Rai provinces of Thailand. Fungal identification was done by the morphological characterization, the comparison of the internal transcribed spacer and 5.8S ribosomal DNA sequences, and the phylogenetic analysis. Epulorhiza repens was found to be the most common species found in the roots of various species of all three orchid genera, whereas Epulorhiza calendulina-like isolates were strictly found in the roots of Paphiopedilum species. We have also isolated and described an anamorph of Tulasnella irregularis, four new anamorphic species in the genus Tulasnella, and a new anamorphic species in the family Tulasnellaceae. Our study provides information on diversity of root-associated fungi of the orchid genera and at the sampling sites that were rarely addressed in the previous studies.

Molecular evolution of Trichuris muris isolated from different Muridae hosts in Europe

A phylogeographic study was carried out of Trichuris muris, nematode parasitizing Murinae rodents from the Muridae family, isolated from four different hosts and from different geographical regions of Europe by amplification and sequencing of the ITS1-5.8S-ITS2 fragment of the ribosomal DNA. T. muris was found in the Apodemus sylvaticus, Apodemus flavicollis, Mus domesticus, and Rattus rattus rodents. The molecular results confirm the presence of DNA polymorphisms among T. muris isolates from Europe. The present study shows two clear-cut geographical and genetic lineages: one of them is widespread from northern Spain (Catalonia) to Denmark (Western European region), while the second is widespread in the Eastern European region (Croatia, Rumania, and Turkey). These two genotypes can be easily distinguished by a PCR-RFLP analysis of this sequence with the ApalI restriction enzyme. Moreover, networks and phylogenetic reconstructions also reveal that T. muris from various Murinae rodents did not differentiate according to the host species that they parasitize. Furthermore, T. muris isolated from The Canary Islands revealed a typical haplotype (H6) only present in The Canary Islands and not in continental Europe. It is suggested that one haplotype from La Gomera Island is the ancestor of T. muris in the Canary Islands.

Diverging diversity patterns in the Tulasnella (Basidiomycota, Tulasnellales) mycobionts of Aneura pinguis (Marchantiophyta, Metzgeriales) from Europe and Ecuador

Aneura pinguis (Aneuraceae) is a cosmopolitan thalloid liverwort that shows a specific mycorrhiza-like interaction with basidiomycetes. To date, tropical specimens have not been studied in great depth. Samples of A. pinguis were collected from 48 individuals in one plot in South Ecuador and 54 individuals in five European countries. Light and transmission electron microscopy and molecular analyses based on nuclear rDNA coding for the ribosomal large subunit (nucLSU) and from the 5.8s-ITS2 regions were carried out to identify the associated mycobionts and to study their phylogenetic relationships. Microscopic and ultrastructural investigations of the fungal colonisation showed a high congruence between the European and the Ecuadorian sites and confirmed previous results. Tulasnellales are the only mycobionts that could be detected from ultrastructural characters with certainty. Molecular phylogenetic analysis indicated the presence of tulasnelloid fungi from at least 13 distinct clades. The composition of the communities of tulasnelloid fungi in A. pinguis differs between Ecuador and Europe. The diversity of tulasnelloid fungal partners was much higher at the Ecuadorian site.

[Screening and identification of exopolysaccharide-producing yeasts]

OBJECTIVE

Most of microbial extracellular polysaccharide (EPS) has the favorable functionality and peculiarity, but little research has been done about EPS that were synthesized by yeasts. Screening of EPS-producing yeasts and studies on the optimal culture composition are the main purpose of this study.

METHODS

Yeasts were obtained by screening from natural samples using spread-plate method, Yield of EPS synthesized by yeasts was estimated by phenolsulfate acid method, Based on 5.8S rDNA sequence determination, three strains were identified and selected for the optimization of fermentative medium.

RESULTS

132 yeast strains were isolated from grapes, preserves and topsoil. Three yeast strains were proved to be as high exopolysaccharide-producing yeasts. The results of 5.8S rDNA sequence determination showed that similarities of two yeasts isolated from "Zuoyouhong" grape (Z14 and Z20) were over 99% compared with Issatchenkia orientalis, meanwhile another yeast L25 isolated from topsoil of Larix gmelini was identified as Cryptococcus humicolus, with the similarity of 98.8%. The optimal medium for strain Z20 for producing EPS was as followed: 8% glucose, 0.2% (NH4)SO4, 0.1% KH2PO4, 0.1% yeast extract powder and 0.01% CaCl2. Under the condition of initial pH 6.0, 28 degrees C and 160 r/min for 4 d, yield of EPS could reach to 2.046 g/L, which was 79.9% higher than the control (1.137 g/L).

CONCLUSION

Reports that yeasts belong to some genera possessed the abilities to synthesize EPS could be seen in some related references, according to the study, we could get the conclusion that yeasts belong to Issatchenkia can synthesize EPS and EPS yield of stain Z20 could be increased by changing culture composition.

The final step in 5.8S rRNA processing is cytoplasmic in Saccharomyces cerevisiae

The 18S rRNA component of yeast (Saccharomyces cerevisiae) 40S ribosomes undergoes cytoplasmic 3' cleavage following nuclear export, whereas exported pre-60S subunits were believed to contain only mature 5.8S and 25S rRNAs. However, in situ hybridization detected 3'-extended forms of 5.8S rRNA in the cytoplasm, which were lost when Crm1-dependent preribosome export was blocked by treatment with leptomycin B (LMB). LMB treatment rapidly blocked processing of 6S pre-rRNA to 5.8S rRNA, leading to TRAMP-dependent pre-rRNA degradation. The 6S pre-rRNA was coprecipitated with the 60S export adapter Nmd3 and cytoplasmic 60S synthesis factor Lsg1. The longer 5.8S+30 pre-rRNA (a form of 5.8S rRNA 3' extended by approximately 30 nucleotides) is processed to 6S by the nuclear exonuclease Rrp6, and nuclear pre-rRNA accumulated in the absence of Rrp6. In contrast, 6S to 5.8S processing requires the cytoplasmic exonuclease Ngl2, and cytoplasmic pre-rRNA accumulated in strains lacking Ngl2. We conclude that nuclear pre-60S particles containing the 6S pre-rRNA bind Nmd3 and Crm1 and are exported to the cytoplasm prior to final maturation by Ngl2.

Fusarium proliferatum soft tissue infection at the site of a puncture by a plant: recovery, isolation, and direct molecular identification

After allogeneic stem cell transplantation, a 49-year-old man developed fever and inflammation at the site of a plant puncture on a finger. A hyalohyphomycete was recovered by incubating the plant spine fragment following surgery. Amplification of the internal transcribed spacer region and 5.8S rRNA, beta-tubulin, and translation elongation factor coding genes identified Fusarium proliferatum, which was confirmed later by culture.

A comparison of Olpidium isolates from a range of host plants using internal transcribed spacer sequence analysis and host range studies

Olpidium brassicae is a ubiquitous obligate root-infecting fungal pathogen. It is an important vector of a wide range of plant viruses. Olpidium isolates that infected brassica plants did not infect lettuce plants and vice-versa. Host range tests, PCR amplification and sequencing of the internal transcribed spacer (ITS) and 5.8S regions of 25 Olpidium isolates from brassica, carrot, cucumber and lettuce originating from four continents revealed differences between isolates. Based on their ability to infect lettuce and brassicas and the differences between their ITS1, 5.8S and ITS2 regions they could be separated into a number of distinct groups. Comparisons with other published sequences revealed two distinct genetic groups of brassica-infecting isolates, two distinct groups of lettuce-infecting isolates, one of which contained a carrot-infecting isolate and a distinct group comprising a cucumber-infecting isolate and a melon-infecting isolate. The possibility of the isolates belonging to three distinct species is discussed.