Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (similar to 2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.

The Infection of Soybean Leaves by Phakopsora pachyrhizi during Conditions of Discontinuous Wetness

The ability of Phakopsora pachyrhizi to cause infection under conditions of discontinuous wetness was investigated. In in vitro experiments, droplets of a uredospore suspension were deposited onto the surface of polystyrene. After an initial wetting period of either 1, 2 or 4 h, the drops were dried for different time intervals and then the wetness was restored for 11, 10 or 8 h. Germination and appressorium formation were evaluated. In in vivo experiments, soybean plants were inoculated with a uredospore suspension. Leaf wetness was interrupted for 1, 3 or 6 h after initial wetting periods of 1, 2 or 4 h. Then, the wetting was re-established for 11, 10 or 8 h, respectively. Rust severity was evaluated 14 days after inoculation. The germination of the spores and the formation of the appressoria on the soybean leaves after different periods of wetness were also quantified in vivo by scanning electron microscopy. P. pachyrhizi showed a high infective capacity during short periods of time. An interruption of wetness after 1 h caused average reductions in germination from 56 to 75% and in appressorium formation from 84 to 96%. Rust severity was lower in all of the in vivo treatments with discontinuous wetness when compared to the control plants. Rust severity was zero when the interruption of wetness occurred 4 h after the initial wetting. Wetting interruptions after 1 and 2 h reduced the average rust severity by 83 and 77%, respectively. The germination of the uredospores on the soybean leaves occurred after 2 h of wetness, with a maximum germination appearing after 4 h of wetness. Wetness interruption affected mainly the spores that had initiated the germination.

Spatial pattern of black spot incidence within citrus trees related to disease severity and pathogen dispersal

Guignardia citricarpa, the causal agent of citrus black spot, forms airborne ascospores on decomposing citrus leaves and water-spread conidia on fruits, leaves and twigs. The spatial pattern of diseased fruit in citrus tree canopies was used to assess the importance of ascospores and conidia in citrus black spot epidemics in Sao Paulo State, Brazil. The aggregation of diseased fruit in the citrus tree canopy was quantified by the binomial dispersion index (D) and the binary form of Taylor`s Power Law for 303 trees in six groves. D was significantly greater than 1 in 251 trees. The intercept of the regression line of Taylor`s Power Law was significantly greater than 0 and the slope was not different from 1, implying that diseased fruit was aggregated in the canopy independent of disease incidence. Disease incidence (p) and severity (S) were assessed in 2875 citrus trees. The incidence-severity relationship was described (R-2 = 88.7%) by the model ln(S) = ln(a) + bCLL(p) where CLL = complementary log-log transformation. The high severity at low incidence observed in many cases is also indicative of low distance spread of G. citricarpa spores. For the same level of disease incidence, some trees had most of the diseased fruit with many lesions and high disease severity, whereas other trees had most of the fruit with few lesions and low disease severity. Aggregation of diseased fruit in the trees suggests that splash-dispersed conidia have an important role in increasing the disease in citrus trees in Brazil.

Dosage-dependent shift in the spore community of arbuscular mycorrhizal fungi following application of tannery sludge

The controlled disposal of tannery sludge in agricultural soils is a viable alternative for recycling such waste; however, the impact of this practice on the arbuscular mycorrhizal fungi (AMF) communities is not well understood. We studied the effects of low-chromium tannery sludge amendment in soils on AMF spore density, species richness and diversity, and root colonization levels. Sludge was applied at four doses to an agricultural field in Rolandia, Parana state, Brazil. The sludge was left undisturbed on the soil surface and then the area was harrowed and planted with corn. The soil was sampled at four intervals and corn roots once within a year (2007/2008). AMF spore density was low (1 to 49 spores per 50 cm(3) of soil) and decreased as doses of tannery sludge increased. AMF root colonization was high (64%) and unaffected by tannery sludge. Eighteen AMF species belonging to six genera (Acaulospora, Glomus, Gigaspora, Scutellospora, Paraglomus, and Ambispora) were recorded. At the sludge doses of 9.0 and 22.6 Mg ha(-1), we observed a decrease in AMF species richness and diversity, and changes in their relative frequencies. Hierarchical grouping analysis showed that adding tannery waste to the soil altered AMF spore community in relation to the control, modifying the mycorrhizal status of soil and selectively favoring the sporulation of certain species.

Preservation of Phakopsora pachyrhizi uredospores

This study compared different temperatures and dormancy-reversion procedures for preservation of Phakopsora pachyrhizi uredospores. The storage temperatures tested were room temperature, 5 degrees C, -20 degrees C and -80 degrees C. Dehydrated and non-dehydrated uredospores were used, and evaluations for germination (%) and infectivity (no. of lesions/cm(2)) were made with fresh harvested spores and after 15, 29 76, 154 and 231 days of storage. The dormancy-reversion procedures evaluated were thermal shock (40 degrees C/5 min) followed or not by hydration (moist chamber,24 h). Uredospores stored at room temperature were viable only up to a month of storage, regardless of their hydration condition. Survival of uredospores increased with storage at lower temperatures. Dehydration of uredospores prior to storage increased their viability, mainly for uredospores stored at 5 degrees C, -20 degrees C and -80 degrees C. At 5 degrees C and -20 degrees C, dehydrated uredospores showed increases in viability of at least 47 and 127 days, respectively, compared to non-dehydrated spores. Uredospore germination and infectivity after storage for 231 days (7.7 months), could only be observed at -80 degrees C, for both hydration conditions. At this storage temperature, dehydrated and non-dehydrated uredospores exhibited 56 and 28% of germination at the end of the experiment, respectively. Storage at -80 degrees C also maintained uredospore infectivity, based upon levels of Infection frequency, for both hydration conditions. Among the dormancy-reversion treatments applied to spores stored at -80 degrees C, those involving hydration allowed recoveries of 85 to 92% of the initial germination.

Sterilization by pure oxygen plasma and by oxygen-hydrogen peroxide plasma: An efficacy study

Plasma is an innovative sterilization method characterized by a low toxicity to operators and patients, and also by its operation at temperatures close to room temperatures. The use of different parameters for this method of sterilization and the corresponding results were analyzed in this study. A low-pressure inductive discharge was used to study the plasma sterilization processes. Oxygen and a mixture of oxygen and hydrogen peroxide were used as plasma source gases. The efficacy of the processes using different combinations of parameters such as plasma-generation method, type of gas, pressure, gas flow rate, temperature, power, and exposure time was evaluated. Two phases were developed for the processes, one using pure oxygen and the other a mixture of gases. Bacillus subtilis var. niger ATCC 9372 (Bacillus atrophaeus) spores inoculated on glass coverslips were used as biological indicators to evaluate the efficacy of the processes. All cycles were carried out in triplicate for different sublethal exposure times to calculate the D value by the enumeration method. The pour-plate technique was used to quantify the spores. D values of between 8 and 3 min were obtained. Best results were achieved at high power levels (350 and 40oW) using pure oxygen, showing that plasma sterilization is a promising alternative to other sterilization methods. (c) 2007 Elsevier B.V. All rights reserved.

Liquid-liquid extraction of commercial and biosynthesized nisin by aqueous two-phase micellar systems

Nisin is a natural additive for conservation of food, and can also be used as a therapeutic agent. Nisin inhibits the outgrowth of spores, the growth of a variety of Gram-positive and Grain-negative bacteria. In this paper we present a potentially scalable and cost-effective way to purify commercial and biosynthesized in bioreactor nisin, including simultaneously removal of impurities and contaminants, increasing nisin activity. Aqueous two-phase micellar systems (ATPMS) are considered promising for bioseparation and purification purposes. Triton X-114 was chosen as the as phase-forming surfactant because it is relatively mild to proteins and it also forms two coexisting phases within a convenient temperature range. Nisin activity was determined by the agar diffusion assay utilizing Lactobacillus sake as a sensitive indicator microorganism. Results indicated that nisin partitions preferentially to the micelle rich-phase, despite the surfactant concentration tested, and its antimicrobial activity increases. The successful implementation of this peptide partitioning, from a suspension containing other compounds, represents an important step towards developing a separation method for nisin, and more generally, for other biomolecules of interest. (C) 2007 Elsevier Inc. All rights reserved.

Novel nano-organisms from Australian sandstones

We report the detection of living colonies of nano-organisms (nanobes) on Triassic and Jurassic sandstones and other substrates. Nanobes have cellular structures that are strikingly similar in morphology to Actinomycetes and fungi (spores, filaments, and fruiting bodies) with the exception that they are up to 10 times smaller in diameter (20 nm to 1.0 mu m). Nanobes are noncrystalline structures that are composed of C, O, and N. Ultra thin sections of nanobes show the existence of an outer layer or membrane that may represent a cell wall. This outer layer surrounds an electron dense region interpreted to be the cytoplasm and a less electron dense central region that may represent a nuclear area. Nanobes show a positive reaction to three DNA stains, [4',6-diamidino-2 phenylindole (DAPI), Acridine Orange, and Feulgen], which strongly suggests that nanobes contain DNA. Nanobes are communicable and grow in aerobic conditions at atmospheric pressure and ambient temperatures. While morphologically distinct, nanobes are in the same size range as the controversial fossil nannobacteria described by others in various rock types and in the Martian meteorite ALH84001.

Streptomyces sp ASBV-1 reduces aflatoxin accumulation by Aspergillus parasiticus in peanut grains

To evaluate the ability of Streptomyces sp. (strain ASBV-1) to restrict aflatoxin accumulation in peanut grains. In the control of many phytopathogenic fungi the Streptomyces sp. ASBV-1 strain showed promise. An inhibitory test using this strain and A. parasiticus was conducted in peanut grains to evaluate the effects of this interaction on spore viability and aflatoxin accumulation. In some treatments the Streptomyces sp ASBV-1 strain reduced the viability of A. parasiticus spores by c. 85%, and inhibited aflatoxin accumulation in peanut grains. The values of these reductions ranged from 63 to 98% and from 67% to 96% for aflatoxins B(1) and G(1), respectively. It was demonstrated that Streptomyces sp. ASBV-1 is able to colonize peanut grains and thus inhibit the spore viability of A. parasiticus, as well as reducing aflatoxin production. The positive finding for aflatoxin accumulation reduction in peanut grains seems promising and suggests a wider use of this actinobacteria in biological control programmes.

Correlation of fungi and endotoxin with PM2.5 and meteorological parameters in atmosphere of Sao Paulo, Brazil

Particulate matter, especially PM2.5, is associated with increased morbidity and mortality from respiratory diseases. Studies that focus on the chemical composition of the material are frequent in the literature, but those that characterize the biological fraction are rare. The objectives of this study were to characterize samples collected in Sao Paulo, Brazil on the quantity of fungi and endotoxins associated with PM2.5, correlating with the mass of particulate matter, chemical composition and meteorological parameters. We did that by Principal Component Analysis (PCA) and multiple linear regressions. The results have shown that fungi and endotoxins represent significant portion of PM2.5, reaching average concentrations of 772.23 spores mu g(-1) of PM2.5 (SD: 400.37) and 5.52 EU mg(-1) of PM2.5 (SD: 4.51 EU mg(-1)), respectively. Hyaline basidiospores, Cladosporium and total spore counts were correlated to factor Ba/Ca/Fe/Zn/K/Si of PM2.5 (p < 0.05). Genera Pen/Asp were correlated to the total mass of PM2.5 (p < 0.05) and colorless ascospores were correlated to humidity (p < 0.05). Endotoxin was positively correlated with the atmospheric temperature (p < 0.05). This study has shown that bioaerosol is present in considerable amounts in PM2.5 in the atmosphere of Sao Paulo, Brazil. Some fungi were correlated with soil particle resuspension and mass of particulate matter. Therefore, the relative contribution of bioaerosol in PM2.5 should be considered in future studies aimed at evaluating the clinical impact of exposure to air pollution. (C) 2010 Elsevier Ltd. All rights reserved.

Ultrastructure and small-subunit ribosomal DNA sequence of Henneguya lesteri n. sp (Myxosporea), a parasite of sand whiting Sillago analis (Sillaginidae) from the coast of Queensland, Australia

Henneguya lesteri n. sp, (Myxosporea) is described from sand whiting, Sillago analis, from the southern Queensland coast of Australia. H. lesteri displays a preference for the pseudobranchs and is typically positioned along the afferent blood vessels, displacing the adjoining lamellae and disrupting their normal array, The plasmodia appeared as whitish-hyaline, elliptical cysts (mean dimensions 230 x 410 mum) attached to the oral mucosa lining of the hyoid arch on the inner surface of the operculum. Infections of the gills were also found, in which the plasmodia were spherical, averaged 240 x 240 mum in size and were located on the inner hemibranch margin. The parasites lodged in the gill filament crypts and generated a mild hyperplastic response of the branchial epithelium, In histological sections, the plasmodium wall and adjoining ectoplasm appeared as a finely granulated, weakly eosinophilic layer, Ultrastructurally, this section of the host-parasite interface contained an intricate complex of pinocytotic channels. H. lesteri is polysporic, disporoblastic and pansporoblast forming. Sporogenesis is asynchronous, with the earliest developmental stages aligned predominantly along the plasmodium periphery, and maturing sporoblasts and spores toward the center. Ultrastructural details of sporoblast and spore development are in agreement with previously described myxosporeans. The mature spore is drop-shaped, length (mean) 9.1 mum, width 4.7 mum, thickness 2.5 mum, and comprises 2 polar capsules positioned closely together, a binucleated sporoplasm and a caudal process of 12.6 mum. The polar capsules are elongated, 3.2 x 1.6 mum, with 4 turns of the polar filament. Mean length of the everted filament is 23.2 mum, Few studies have analyzed the 18S gene-of marine Myxosporea. In fact, H. lesteri is the first marine species of Henneguya to be characterized at the molecular level: we determined 1966 bp of the small-subunit (18S) rDNA, The results indicated that differences between this and the hitherto studied freshwater Henneguya species are greater than differences among the freshwater Henneguya species.

Antagonism of the two-needle pine stem rust fungi Cronartium flaccidum and Peridermium pini by Cladosporium tenuissimum in vitro and in planta

Selected isolates of Cladosporium tenuissimum were tested for their ability to inhibit in vitro aeciospore germination of the two-needle pine stem rusts Cronartium flaccidum and Peridermium pini and to suppress disease development in planta. The antagonistic fungus displayed a number of disease-suppressive mechanisms. Aeciospore germination on water agar slides was reduced at 12, 18, and 24 h when a conidial suspension (1.5 x 10(7) conidia per ml) of the Cladosporium tenuissimum isolates was added. When the aeciospores were incubated in same-strength conidial suspensions for 1, 11, 21, and 31 days, viability was reduced at 20 and 4 degreesC. Light and scanning electron microscopy showed that rust spores were directly parasitized by Cladosporium tenuissimum and that the antagonist had evolved several strategies to breach the spore wail and gain access to the underlying tissues. Penetration occurred with or without appressoria. The hyperparasite exerted a mechanical force to destroy the spore structures (spinules, cell wall) by direct contact, penetrated the aeciospores and subsequently proliferated within them. However, an enzymatic action could also be involved. This was shown by the dissolution of the host tell wall that comes in contact with the mycelium of the mycoparasite, by the lack of indentation in the host wall at the contact site, and by the minimal swelling at the infecting hyphal tip. Culture filtrates of the hyperparasite inhibited germination of rust propagules. A compound purified from the filtrates was characterized by chemical and spectroscopic analysis as cladosporol, a known beta -1,3-glucan biosynthesis inhibitor. Conidia of Cladosporium tenuissimum reduced rust development on new infected pine seedlings over 2 years under greenhouse conditions. Because the fungus is an aggressive mycoparasite, produces fungicidal metabolites, and can survive and multiply in forest ecosystems without rusts, it seems a promising agent for the biological control of pine stem rusts in Europe.

Testicular myxosporidiasis in anurans, with a description of Myxobolus fallax n. sp.

During studies of amphibian sperm cryopreservation, a new species of myxosporidean parasite (Myxozoa, Myxosporae) was observed in the testes of the Australian dwarf green tree frog Litoria fallax (Peters). Myxosporidiasis was found to have no affect on L. fallax body condition or sperm numbers. Myxobolus spores from L. fallax are morphologically distinct from Myxobolus hylae spores (infecting the sympatric Litoria aurea Lesson) and the three previously named (exotic to Australia) Myxobolus species found in anurans. Myxobolus fallax n. sp. is characterised by: pseudocyst white, spherical to ovoid, 141 x74 to 438 x337 mum in diameter (mature); plasmodium with spores loosely arranged within interior. Spores ovoid 13.4 +/- 0.5 (12.6-14.6) mum length, 9.5 +/- 0.4 (8.3-10.6) mum width, 6.8 +/- 0.4 (6.5-7.6) mum depth, 1.4 +/- 0.1 (1.3-1.6) length/width; polar capsules broadly pyriform and equal in size 4.2 +/- 0.3 (3.3-4.7) mum length, 2.4 +/- 0.2 (2.1-2.8) mum width; filament coils 7-8, wound tightly and perpendicular to the longitudinal axis of the capsule; polar filament 34 +/- 7.0 (18-50) mum length; intercapsular appendix and sutural ridge folds absent; and iodinophilous vacuole and mucous envelope lacking. In addition to this new species, data from archival samples of M. hylae are provided which show two morphologically distinct spore types. Both appeared rarely in the same pseudocysts and we cautiously retain the single species.

Stratigraphic and palaeoenvironmental significance of a Pennsylvanian (Upper Carboniferous) palynoflora from the PiauFormation, Parnaba Basin, northeastern Brazil

A well-preserved palynoflora is reported from within a cored interval of a coal-exploratory borehole (1-UN-23-PI of the Geological Survey of Brazil) in the southern part of the Parnaiba Basin, northeastern Brazil. The sample studied is from the lower portion of the Piaui Formation. Its palynoflora is characterized by particular abundance of the trilete cavate/pseudosaccate miospores Spelaeotriletes triangulus Neves and Owens, 1966 and S. arenaceus Neves and Owens, 1966, together with cingulizonate forms mainly attributable to Vallatisporites Hacquebard, 1957 and Cristatisporites R. Potonie and Kremp emend. Butterworth et al., 1964. Radially and bilaterally symmetrical monosaccate pollen grains are also well-represented, chiefly by Plicatipollenites Lele, 1964 and Potonieisporites Bhardwaj, 1954, respectively. Taeniate grains (i.e., monosaccates and bisaccates) are relatively minor constituents of the palynoflora; no marine microplankton were encountered. Several species are described in detail : the trilete apiculate spores Brevitriletes levis (Balme and Hennelly) Bharadwaj and Srivastava, 1969 and Horriditriletes uruguaiensis (Marques-Toigo) Archangelsky and Gamerro, 1979; and the taeniate pollen grains Meristocorpus ostentus sp. nov. and Lahirites segmentatus sp. nov. A Pennsylvanian (Late Carboniferous : late Westphalian) age is adduced for the palynoflora via its correlation with part of the Tapajos Group (specifically, the upper Itaituba Formation) of the Amazonas Basin in northern Brazil. The entirely land-derived palynomorphs, associated with abundant plant debris, corroborate previous suggestions that the lower part of the Piaui Formation accumulated in a nonmarine setting under conditions of aridity.

Permian Palynofloral Assemblages of the Chaco-Paraná Basin (Argentina): Systematics and Stratigraphic Significance

Core samples from an upper Palaeozoic, partly glaciogene borehole section (Ordóñez: YPF Cd O es-1) in the southern Chaco-Paraná Basin (Córdoba Province, northeastern Argentina) have produced variable palynological results. Samples from the lower part of the section (i.e., from the diamictite-bearing upper Ordóñez Formation) proved non-palyniferous. Those from the overlying, essentially post-glacial Victoriano Rodríguez Formation yielded spore-pollen assemblages in varying concentrations and in good to excellent states of preservation, thus providing the material basis for the present account. The palynomorph taxa represented in the assemblages comprise 20 species of spores (distributed among 14 genera) and 25 species of pollen grains (14 genera). The majority of the species are described in systematic detail. One trilete spore species -Convolutispora archangelskyi- is newly proposed. Several other, possibly new species (three of trilete spores, one of monosaccate pollen) are represented insufficiently for other than informal naming. The following new combinations, also of trilete spore species, are instituted: Converrucosisporites confluens (Archangelsky & Gamerro, 1979), C. micronodosus (Balme & Hennelly, 1956), and Anapiculatisporites tereteangulatus (Balme & Hennelly, 1956). Sculptural intergradation (granulate through verrucate) among three species -Granulatisporites austroamericanus Archangelsky & Gamerro, 1979, C. confluens, and C. micronodosus- prompts their informal grouping, proposed herein, as the Converrucosisporites confluens Morphon, which is also recognizable elsewhere in the Gondwanan Permian. The possibility, if not the likelihood, that G. austroamericanus is conspecific with Microbaculispora tentula Tiwari, 1965 is canvassed. The palynologically productive borehole section of the Victoriano Rodríguez Formation studied here is assignable to the middle to upper Cristatisporites Zone and to the succeeding Striatites Zone, thus signifying an Early Permian age for this section and facilitating correlation with strata of the Paraná and Paganzo Basins. From this and prior work, the Ordóñez well sequence embracing the Ordóñez and Victoriano Rodríguez Formations includes, in addition to the latter two zones, the preceding (late Pennsylvanian) Potonieisporites-Lundbladispora Zone which is known from the lower to mid-upper part of the Ordóñez Formation. Thus, the Carboniferous-Permian boundary can be inferred to lie within the upper part of the latter formation