Isolation and characterization of EST‐derived microsatellite loci from the fungal wheat pathogen Phaeosphaeria nodorum

Eleven polymorphic microsatellite loci and one minisatellite locus originating from expressed sequence tag (EST) libraries of Phaeosphaeria (syn. Stagonospora) nodorum were isolated and characterized. The satellite markers were used to genotype isolates from field populations collected in China, North America and South Africa. The number of alleles per locus ranged from two to 15. Genotype diversity ranged from 87.5 to 95.3 and gene diversity from 0.1 to 0.8. The variable levels of polymorphism within and among populations of P. nodorum renders these 12 satellite loci ideal markers for population genetic analysis of P. nodorum.     

Mating Types of Phaeosphaeria nodorum (anamorph Stagonospora nodorum) from Central Asia

The distribution was examined of the mating type idiomorphs (MAT‐1 and ‐2) of Phaeosphaeria (anamorph Stagonospora) nodorum using DNA from 49 isolates collected from commercial and experimental fields in 2003 and 2004 in Central Asia. MAT‐1 and ‐2 isolates were present in the Kazakh and Russian origins of P. nodorum, but no MAT‐2 isolates were found in Tajikistan. The possibility of a skewed Tajik population cannot be excluded, considering that the sampled region in Tajikistan was geographically isolated from Kazakhstan and Russia.     

Tubulin and actin protein patterns in Scots pine (Pinus sylvestris) roots and developing ectomycorrhiza with Suillus bovinus

The role of tubulin and actin in the development of Scots pine ( Pinus sylvestris ) roots and in the formation of the ectomycorrhiza with the basidiomycete Suillus bovinus was studied by immunoblotting of 2D-gels with anti-tubulin and anti-actin antibodies. In the short roots the α-tubulin pattern was different from that in the other root types due to the more acidic pI of the two α-tubulins. During the formation of the ectomycorrhiza, two new α-tubulins were detected in the acidic α-tubulin cluster. No such variation occurred in the plant β-tubulin patterns. The fungal tubulins dominated in the ectomycorrhiza, but no changes in tubulin polypeptide patterns from those in the S. bovinus mycelium were observed. Contrary to the tubulins, plant actin dominated in the mycorrhiza. The specific α-tubulin patterns of uninfected and infected short roots indicate that α-tubulin is involved in the morphogenesis of Pinus sylvestris short roots. The high level of plant actin at early stage of the mycorrhiza formation suggests a significant role of this protein in the interaction between plant cells and fungal hyphae.     

STRUCTURAL FEATURES OF NUCLEAR GENES IN THE CENTRIC DIATOM THALASSIOSIRA WEISSFLOGII (BACILLARIOPHYCEAE)

Thalassiosira weissflogii (Grun.) Fryxell et Hasle is one of the more commonly studied centric diatoms, and yet molecular studies of this organism are still in their infancy. The ability to identify open reading frames and thus distinguish between introns and exons, coding and noncoding sequence is essential to move from nuclear DNA sequences to predicted amino acid sequences. To facilitate the identification of open reading frames in T. weissflogii , two newly identified nuclear genes encoding β-tubulin and t  -complex polypeptide (TCP)-γ, along with six previously published nuclear DNA sequences, were examined for general structural features. The coding region of the nuclear open reading frames had a G + C content of about 49% and could readily be distinguished from noncoding sequence due to a significant difference in G + C content. The introns were uniformly small, about 100 base pairs in size. Furthermore, the 5' and 3' splice sites of introns displayed the canonical GT/AG sequence, further facilitating recognition of noncoding regions. Six of the nuclear open reading frames displayed relatively little bias in the use of synonymous codons, as exemplified by the cDNAs encoding β-tubulin and TCP-γ. Two open reading frames displayed strong bias in the use of particular codons (although the codons used were different), as exemplified by the cDNA encoding fucoxanthin chlorophyll a/c binding protein. Knowledge of codon bias should facilitate, for example, design of degenerate PCR primers and potential heterologous reporter gene constructs.     

Concordant evolution of mitochondrial and nuclear genomes in the wheat pathogen Phaeosphaeria nodorum

We compared patterns of mitochondrial restriction fragment length polymorphism (RFLP) diversity with patterns of nuclear RFLP diversity to investigate the effects of selection, gene flow, and sexual reproduction on the population genetic structure and evolutionary history of the wheat pathogen Phaeosphaeria nodorum. A total of 315 fungal isolates from Texas, Oregon, and Switzerland were analyzed using seven nuclear RFLP probes that hybridized to discrete loci and purified mitochondrial DNA that hybridized to the entire mtDNA genome. Forty-two different mitochondrial haplotypes and 298 different nuclear haplotypes were detected. The two most frequent mtDNA haplotypes were present in every population and represented 32% of all isolates. High levels of gene flow, low levels of population subdivision, no evidence for either host specificity or cyto-nuclear disequilibrium were inferred from the analysis of both genomes. The concordance in estimates of these population genetic parameters from both genomes suggests that the two genomes experienced similar degrees of migration, genetic drift and selection.     

Thiabendazole resistance and mutations in the β-tubulin gene of Penicillium expansum strains isolated from apples and pears with blue mold decay

Penicillium expansum is the causal agent of blue mold rot, a postharvest decay of stored fruits. This fungus also produces the mycotoxins patulin and citrinin. Control of P. expansum still relies mainly on the use of fungicides such as thiabendazole. Since its introduction, resistant strains have been reported. The aim of this work was to investigate the thiabendazole resistance and mutations in the β-tubulin gene of P. expansum strains isolated from apples and pears with blue mold decay from Spain. A total of 71 strains of P. expansum were scored for resistance to thiabendazole and the β-tubulin gene was sequenced. Out of 71 strains, 37 were sensitive and 34 were resistant to thiabendazole. Regarding the β-tubulin gene sequence, 10 different genetic types were determined, with a 99.7–100% similarity. When the amino acid sequence was deduced, five different amino acid sequences were found. All except one of the sensitive strains lacked mutations in the region sequenced. Of the 34 resistant strains, only eight had mutations that involved the residues 198 and 240. All the strains with mutations at position 198 always corresponded to resistant isolates. However, a high percentage of resistant strains had no mutations in the region of the β-tubulin gene sequenced, and so other mechanisms may be involved in thiabendazole resistance.     

Identity and conservation of mating type genes in geographically diverse isolates of Phaeosphaeria nodorum

Mating type idiomorphs (MAT1-1 and MAT1-2) were identified from the heterothallic loculoascomycete Phaeosphaeria nodorum (wheat biotype) using DNA from a pair of isolates from Poland and Georgia, USA that are known to mate. MAT predicted proteins of P. nodorum are similar in sequence and in phylogenetic relationship to those described for other loculoascomycetes such as Cochliobolus spp., Alternaria alternata, and Didymella zeae-maydis. The organization of the MAT locus of the P. nodorum differs from these species in that its idiomorph begins within an adjacent upstream conserved ORF of unknown function. MAT-specific primers were used to identify isolates of both mating types in field populations, demonstrating that an absence of either mating type is not the reason that the teleomorph has not been found in New York. Portions of MAT1-1 and MAT1-2 were sequenced from geographically diverse isolates, including those from regions where the teleomorph has been reported. MAT was highly conserved and no significant differences in sequence were found.     

Species level identification of conifer associated Ceratocystis sapstain fungi by PCR-RFLP on a beta-tubulin gene fragment

The genus Ceratocystis includes several morphologically similar species commonly found as agents of sapstain in coniferous trees. In this paper we describe a simple and reliable polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique that aids in the identification and differentiation of these fungi. PCR was used to amplify a 1.3-kb fragment of the beta-tubulin gene from C. coerulescens, C. pinicola, C. douglassi, C. resinifera, C. rufipenni, C. polonica and C. adiposa. The PCR amplicon from representative isolates was sequenced. This information was utilized to select restriction enzymes that generated species-specific RFLP patterns. This approach was tested on our collection of over 200 Ceratocystis isolates and identified the fungi with a high level of confidence, reducing the time needed to identify these species by classical methods.     

Long-term relationships between environment and abundance in wheat of Phaeosphaeria nodorum and Mycosphaerella graminicola

Relationships between weather, agronomic factors and wheat disease abundance were examined to determine possible causes of variability on century time scales. In archived samples of wheat grain and leaves obtained from the Rothamsted Broadbalk experiment archive (1844-2003), amounts of wheat, Phaeosphaeria nodorum and Mycosphaerella graminicola DNA were determined by quantitative polymerase chain reaction (PCR). Relationships between amounts of pathogens and environmental and agronomic factors were examined by multiple regression. Wheat DNA decayed at approx. 1% yr(-1) in stored grain. No M. graminicola DNA was detected in grain samples. Fluctuations in amounts of P. nodorum in grain were related to changes in spring rainfall, summer temperature and national SO(2) emission. Differences in amounts of P. nodorum between grain and leaf were related to summer temperature and spring rainfall. In leaves, annual variation in spring rainfall affected both pathogens similarly, but SO(2) had opposite effects. Previous summer temperature had a highly significant effect on M. graminicola. Cultivar effects were significant only at P = 0.1. Long-term variation in P. nodorum and M. graminicola DNA in leaf and grain over the period 1844-2003 was dominated by factors related to national SO(2) emissions. Annual variability was dominated by weather factors occurring over a period longer than the growing season.     

Phylogenetic relationships between Tuber pseudoexcavatum, a Chinese truffle, and other Tuber species based on parsimony and distance analysis of four different gene sequences

Phylogenetic relationships between Tuber pseudoexcavatum and other Tuber species were investigated by studying the sequences of four genes: 5.8S-ITS2, beta-tubulin, protein kinase C and elongation factor 1alpha. The four phylogenetic trees allowed to differentiate the black truffle clade, composed of two subclades, one comprising the Asian black truffles (T. indicum, T. sinense, T. himalayense) and the Perigord black truffle (T. melanosporum), the second comprising T. pseudoexcavatum and T. brumale. These two subclades diverged relatively early. We propose a common ancestor, located between Europe and China, to all the black truffles. The T. brumale/pseudoexcavatum subclade would have started to diverge and migrate first, T. brumale towards Europe through a northern route and T. pseudoexcavatum towards China. Later the T. melanosporum subclade would have started to migrate through the same route, T. melanosporum towards Europe and T. indicum towards China, leading to vicariant species.     

Nucleotide sequence of the thermostable direct hemolysin gene (tdh gene) of Vibrio mimicus and its evolutionary relationship with the tdh genes of Vibrio parahaemolyticus

During an outbreak of infection with ampicillin-resistant, TEM-1 beta-lactamase-producing Escherichia coli serotype O15, some strains were noted to differ from the majority in that they showed reduced susceptibility to amoxycillin/clavulanic acid (Augmentin), ureidopenicillins and first generation cephalosporins and produced increased amounts of beta-lactamase. The plasmid from one such isolate was compared with that from an isolate that produced normal amounts of beta-lactamase. Restriction analysis with EcoRI revealed extra fragments in the plasmid from the beta-lactamase hyperproducer and use of DNA-DNA hybridisation with a biotinylated TEM-1 probe showed genetic rearrangement in the beta-lactamase hyperproducer so that the TEM gene appeared to be present in larger amounts and was located on a smaller fragment than for the plasmid from the strain that produced normal amounts of beta-lactamase.     

Axogenesis in the stomatopod crustacean Gonodactylaceus falcatus (Malacostraca)

Abstract. The formation of the central nervous system of the stomatopod crustacean Gonodactylaceus falcatus is described by means of antibody stainings against synapsin and α-tubulin. It is shown that the longitudinal fiber tracts of the ventral nervous system are formed by two centers of origin comprising a number of pioneer neurons, one at the posterior part of the forming brain, the other in the area of the telson anlage at the posteriormost region of the embryo. In addition to the lateral anlagen of the connectives, a median longitudinal nerve is formed beginning in the mandibular segment neuromere. In contrast to those of other segments, the mandibular ganglia are connected by a single commissure. The brain forms a circumoral ring. There is evidence that the deutocerebrum possesses praestomodeal and poststomodeal commissural fibers. The anlage of the nauplius eye reveals a specific pattern of pigment and sensory cells with the two pigment cells expressing synapsin. Clear differences between the expression patterns of synapsin and α-tubulin recommend the combination of a variety of antibodies to gain a complete picture of embryonic neuroanatomy. Our results show overall similarities to other malacostracan and non-malacostracan crustaceans. The comparisons with other crustaceans and arthropods indicate homology of crustacean nauplius eyes, a circumoral deutocerebrum, and a more widespread occurrence of posterior pioneer neurons forming the axon scaffold of the ventral central nervous system than previously thought.     

Diversity of the trifunctional histidine biosynthesis gene (his) in cereal Phaeosphaeria species.

Phaeosphaeria species are important causal agents of Stagonospora leaf blotch diseases in cereals. In this study, the nucleotide sequence and deduced polypeptide of the trifunctional histidine biosynthesis gene (his) are used to investigate the phylogenetic relationships and provide molecular identification among cereal Phaeosphaeria species. The full-length sequences of the his gene were obtained by PCR amplification and compared among cereal Phaeosphaeria species. The coding sequence of the his gene in wheat-biotype P. nodorum (PN-w) was 2697 bp. The his genes in barley-biotype P. nodorum (PN-b), two P. avenaria f. sp. triticea isolates (homothallic Pat1 and Pat3), and Phaeosphaeria species from Polish rye and dallis grass were 2694 bp. The his gene in heterothallic isolate Pat2, however, was 2693 bp because the intron had one fewer base. In P. avenaria f. sp. avenaria (Paa), the his gene was only 2670 bp long. The differences in the size of the his gene contributed to the variation in amino acid sequences in the gap region located between the phosphoribosyl-ATP pyrophosphohydrolase and histidinol dehydrogenase sub-domains. Based on nucleotide and deduced amino acid sequences of the his gene, Pat1 was not closely related to either PN-w or the Paa clade. It appears that rates of evolution of the his gene were fast in cereal Phaeosphaeria species. The possible involvement of meiotic recombination in genetic diversity of the his gene in P. nodorum is discussed.     

Characterization of a Cytosolic Protein (P36) Isolated from Pig Brain by Benzodiazepine-Affinity Chromatography

Benzodiazepine-affinity chromatography, on a column of 1012S-Sepharose, resulted in the detection and purification of a binding protein (P36) from the cytosolic fraction of pig cerebral cortex. Purified P36 was enriched over 3,500-fold in a single step and was recovered with an efficiency of 50-60%. Analysis of the purified preparation by sodium dodecyl sulphate-polyacrylamide gel electrophoresis demonstrated a single polypeptide of Mr 36,000. The Stokes radius (3.44 nm) and sedimentation coefficient (4.43S) indicated that purified P36 is a dimeric protein. Analysis of the amino acid composition of P36 revealed a relatively high content of the hydrophobic amino acids, valine and leucine. Immunoblotting of several pig tissue preparations with an antiserum raised against purified P36 demonstrated approximately equal enrichment of P36 in cerebral cortex, cerebellum, and adrenal glands. Lesser enrichment was observed in kidney and liver, whereas a number of other tissues displayed no immunoreactivity. The gamma-aminobutyrate/benzodiazepine receptor complex and P36 showed no immunological cross-reactivity. High-affinity binding activity for [3H]Ro 15-4513, [3H]flunitrazepam, or [3H]PK11195 was not detected in preparations of purified P36. However, the ability of the gamma-aminobutyrate/benzodiazepine receptor inverse agonists, methyl- and ethyl-beta-carboline-3-carboxylate, to inhibit the binding of P36 to 1012S-Sepharose at relatively low concentrations indicates that P36 exhibits a degree of binding specificity.     

Purification and characterization of the (1-->3)-beta-glucanases from Acremonium sp. IMI 383068

Three extracellular (1-->3)-beta-glucanases were purified from the fungus Acremonium sp. IMI 383068. Higher activities were unexpectedly obtained with pustulan, a (1-->6)-beta-glucan as carbon source, than when grown with laminarin, a (1-->3)-beta-glucan. Preliminary evidence suggests that these enzymes are not constitutive, but are inducible, and that their synthesis is repressed by glucose. All three had the same molecular masses, similar pH and temperature optima and none were glycosylated. They all appeared to have an exo-hydrolytic mode of substrate attack. N-terminal amino acid sequence data indicate that substantial post-translational modification of these had occurred, and that while two may be encoded by the same gene, the third may be genetically different.     

Plasmid-mediated extended-spectrum beta-lactamase (CTX-M-3 like) from India and gene association with insertion sequence ISEcp1

Six non-clonally related enterobacterial isolates producing a same extended-spectrum beta-lactamase CTX-M-15 were isolated in 1999 from patients hospitalized in a New Delhi hospital. CTX-M-15 differed from CTX-M-3 by an asparagine to glycine substitution in position ABL238. Its gene was located on large plasmids varying in size. In each case, a same insertion sequence ISEcp1 was identified upstream of the 5' end of bla(CTX-M-15). Typical -35 and -10 promoter sequences of Enterobacteriaceae were identified in the 3' end of ISEcp1. The location of ISEcp1 upstream of plasmid-mediated CTX-M-type beta-lactamase genes may contribute to their spread or/and their expression.     

Species divergence and the measurement of microbial diversity

Diversity measurement is important for understanding community structure and dynamics, but has been particularly challenging for microorganisms. Microbial community characterization using small subunit rRNA (SSU rRNA) gene sequences has revealed an extensive, previously unsuspected diversity that we are only now beginning to understand, especially now that advanced sequencing technologies are producing datasets containing hundreds of thousands of sequences from hundreds of samples. Efforts to quantify microbial diversity often use taxon-based methods that ignore the fact that not all species are equally related, which can therefore obscure important patterns in the data. For example, alpha-diversity (diversity within communities) is often estimated as the number of species in a community (species richness), and beta-diversity (partitioning of diversity among communities) is often based on the number of shared species. Methods for measuring alpha- and beta-diversity that account for different levels of divergence between individuals have recently been more widely applied. These methods are more powerful than taxon-based methods because microorganisms in a community differ dramatically in sequence similarity, which also often correlates with phenotypic similarity in key features such as metabolic capabilities. Consequently, divergence-based methods are providing new insights into microbial community structure and function.     

A novel gene mutation that confers abnormal patterns of beta-carotene accumulation in cauliflower (Brassica oleracea var. botrytis)

The Or gene of cauliflower (Brassica oleracea var. botrytis) causes many tissues of the plant to accumulate carotenoids and turn orange, which is suggestive of a perturbation of the normal regulation of carotenogenesis. A series of experiments to explore the cellular basis of the carotenoid accumulation induced by the Or gene was completed. The Or gene causes obvious carotenoid accumulation in weakly or unpigmented tissues such as the curd, pith, leaf bases and shoot meristems, and cryptically in some cells of other organs, including the roots and developing fruits. The dominant carotenoid accumulated is beta-carotene, which can reach levels that are several hundred-fold higher than those in comparable wild-type tissues. The beta-carotene accumulates in plastids mainly as a component of massive, highly ordered sheets. The Or gene does not affect carotenoid composition of leaves, nor does it alter color and chromoplast appearance in flower petals. Interestingly, mRNA from carotenogenic and other isoprenoid biosynthetic genes upstream of the carotenoid pathway was detected both in orange tissues of the mutant, and in comparable unpigmented wild-type tissues. Thus the unpigmented wild-type tissues are likely to be competent to synthesize carotenoids, but this process is suppressed by an unidentified mechanism. Our results suggest that the Or gene may induce carotenoid accumulation by initiating the synthesis of a carotenoid deposition sink in the form of the large carotenoid-sequestering sheets.