Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus

We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility ( het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer ( HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated ""gene dumps'' and, perhaps, simultaneously, as "" gene factories''.

A New Genus of Microteiid Lizard from the Caparao Mountains, Southeastern Brazil, with a Discussion of Relationships among Gymnophthalminae (Squamata)

A new genus and species of microteiid lizard is described based on a series of specimens obtained at Parque Nacional do Caparao (20 degrees 28'S, 41 degrees 49'W), southeastern Brazil, along the division line between the States of Minas Gerais and Espirito Santo. The new lizard occurs in isolated high-altitude, open, rocky habitats above the altitudinal lit-nits of the Atlantic forest. It is characterized by the presence of prefrontals, frontoparietals, parietals, interparietal, and occipital scales; ear opening and eyelid distinct; three pairs of genials; absence of collar; lanceolate and mucronate dorsal scales; six regular transverse and longitudinal series of smooth ventrals that are longer than wide, with the lateral ones narrower. Maximum parsimony (MP) and partitioned Bayesian (PBA) phylogenetic analyses based on morphological and molecular characters with all known genera of Gymnophthalminae (except for Scriptosaura) Plus Rhachisaurus recovered this new lizard in a clade having Colobodactylus and Heterodactylus as its closest relatives. Both analyses recovered the monophyly of Gymnophthalminae and Gymnophthalmini. The monophyly of the Heterodactylini received moderate support in MP analyses but was not recovered in PBA. To eliminate classification controversy between these results, the present concept of Heterodactylini is restricted to accommodate the new genus, Colobodactylus and Heterodactylus, and a new tribe Iphisiini is proposed to allocate Alexandresaurus, Iphisa, Colobosaura, Acratosaura, and Stenolepis. Current phylogenetic knowledge of Gymnophthalminae suggests that fossoriality and increase of body elongation arose as adaptive responses to avoid extreme surface temperatures, either cold or hot, depending on circumstances.

Luminescent Mycena: new and noteworthy species

Seven species or Mycena are reported as luminescent, representing specimens collected in Belize, Brazil, Dominican Republic, Jamaica, japan (Bonin Islands), Malaysia (Borneo) and Puerto Rico. Four of them represent new species (Mycena luxaeterna, M. luxarboricola, M. luxperpetua, M. silvaelucens) and three represent new reports of luminescence in previously described species (M. aff. abieticola, M. aspratilis, M. margarita). Mycena subepipterygia is synonymized with M. margarita, and M. chlorinosma is proposed as a possible synonym. Comprehensive descriptions, illustrations, photographs and comparisons with phenetically similar species are provided. A redescription of M. chlorophos, based on analyses of type specimens and recently collected topotypical material, is provided. The addition of these seven new or new, reported luminescent species of Mycena brings the total to 71 known bioluminescent species of fungi.

Anacroneuria (Plecoptera, Perlidae) from the Mantiqueira Mountains, Sao Paulo State, Brazil

Seven species of Anacroneuria Klapalek are considered; of these 4 were known, A. debilis (Pictet, 1841), A. flintorum Froehlich, 2002, A. toriba Froehlich, 2002 (the female is described herein), and A. vanini Froehlich, 2004. Three are new: A. mantiqueirae, A. simulans, and A. tabatae.

Kempnyia (Plecoptera) from the Mantiqueira Mountains of Brazil

Eight species of Kempnyia Klapalek were collected in the Mantiqueira Mountains at Campos do Jordao, of which six were known: K. colossica (Navas, 1934), K. flava Klapalek, 1916, K. neotropica (Jacobson and Bianchi, 1905), K. obtusa Klapalek, 1916, K. reichardti Froehlich, 1984 and K. tamoya Froehlich, 1984; two are new, K. pirata and K. tupinamba. One new synonymy is proposed. Comments are provided for all species from the area and a key to these species is presented.

Palisada flagellifera (Ceramiales, Rhodophyta) from the Canary Islands, Spain: a new record for the eastern Atlantic Ocean based on morphological and molecular evidence

Palisada flagellifera (Ceramiales, Rhodophyta) is recorded for the first time in the eastern Atlantic Ocean off Tenerife, La Gomera, La Palma and Fuerteventura, Canary Islands, Spain. The specimens were collected in 2006-2009 growing from the lower intertidal to subtidal zones to 2 m depth at sites exposed to wave action. The species possesses a palisade-like arrangement of cortical cells in cross section, lacks secondary pit connections between them, and has tetrasporangia produced by three fertile pericentral cells (the third and the fourth additional and the second that becomes fertile), and a right-angled arrangement of tetrasporangia. Gametangia were not observed. The phylogenetic relationships were inferred by analyses of the chloroplast-encoded rbcL gene sequences from 46 taxa. The Canarian and Brazilian P. flagellifera specimens formed a highly supported clade with a low level of genetic variation in the rbcL sequences (0.02-0.04%), confirming that they are the same taxonomic entity. This study expands the geographical distribution of P. flagellifera to the eastern Atlantic Ocean.

The spider genus Chrysometa (Araneae, Tetragnathidae) from the Pico da Neblina and Serra do Tapirapeco mountains (Amazonas, Brazil): new species, new records, diversity and distribution along two altitudinal gradients

Eight new species of the spider genus Chrysometa Simon, 1894 (Araneae, Tetragnathidae) are described and illustrated. Chrysometa nubigena n. sp., C. waikoxi n. sp., C. petrasierwaldae n. sp., C. santosi n. sp., C. yanomami n. sp., C. candianii n. sp., C. lomanhungae n. sp., and C. saci n. sp. Those species were collected in a study on the diversity of spider communities along altitudinal gradients in Brazilian Amazonia. C. saci was captured at the Serra do Tapirapeco (Barcelos), while all the other species are from the Pico da Neblina (Sao Gabriel da Cachoeira), the highest mountain in Brazil. We provide new records for C. boraceia, C. flava, C. guttata, C. minuta and C. opulenta, and we describe the male of C. minuta for the first time. We also present the first results on the diversity and altitudinal distribution of the species of Chrysometa at the Pico da Neblina and Serra do Tapirapeco. We sampled the first locality at six different elevations, and obtained 336 specimens distributed in 12 species. Richness and abundance, as well as relative importance peaked at the highest sites sampled (2,000 and 2,400 m). The three most abundant species showed a segregated distribution, being dominant or exclusively distributed in different altitudes. At the Serra do Tapirapeco, sampling at four different elevations up to 1200 m, we only obtained 40 individuals divided in four species, and there was no clear relation to altitude. Most of the new species were found at mid and high altitude sites, while species from lower altitude sites represented widespread species. The comparison with other neotropical spiders inventories highlights the high diversity recorded at Pico da Neblina, which could be assigned to the large environmental variation covered in this work and to the sampling of high-altitude environments. Inventories in the Andean region and other information in the literature also seem to support the association of Chrysometa with high altitude environments.

Laterally transferred genomic islands in Xanthomonadales related to pathogenicity and primary metabolism

Lateral gene transfer (LGT) is considered as one of the drivers in bacterial genome evolution, usually associated with increased fitness and/or changes in behavior, especially if one considers pathogenic vs. non-pathogenic bacterial groups. The genomes of two phytopathogens, Xanthomonas campestris pv. campestris and Xanthomonas axonopodis pv. citri, were previously inspected for genome islands originating from LGT events, and, in this work, potentially early and late LGT events were identified according to their altered nucleotide composition. The biological role of the islands was also assessed, and pathogenicity, virulence and secondary metabolism pathways were functions highly represented, especially in islands that were found to be recently transferred. However, old islands are composed of a high proportion of genes related to cell primary metabolic functions. These old islands, normally undetected by traditional atypical composition analysis, but confirmed as product of LGT by atypical phylogenetic reconstruction, reveal the role of LGT events by replacing core metabolic genes normally inherited by vertical processes.

Growth of EuTe islands on SnTe by molecular beam epitaxy

Semiconductor magnetic quantum dots are very promising structures, with novel properties that find multiple applications in spintronic devices. EuTe is a wide gap semiconductor with NaCl structure, and strong magnetic moments S=7/2 at the half filled 4f(7) electronic levels. On the other hand, SnTe is a narrow gap semiconductor with the same crystal structure and 4% lattice mismatch with EuTe. In this work, we investigate the molecular beam epitaxial growth of EuTe on SnTe after the critical thickness for island formation is surpassed, as a previous step to the growth of organized magnetic quantum dots. The topology and strain state of EuTe islands were studied as a function of growth temperature and EuTe nominal layer thickness. Reflection high energy electron diffraction (RHEED) was used in-situ to monitor surface morphology and strain state. RHEED results were complemented and enriched with atomic force microscopy and grazing incidence X-ray diffraction measurements made at the XRD2 beamline of the Brazilian Synchrotron. EuTe islands of increasing height and diameter are obtained when the EuTe nominal thickness increases, with higher aspect ratio for the islands grown at lower temperatures. As the islands grow, a relaxation toward the EuTe bulk lattice parameter was observed. The relaxation process was partially reverted by the growth of the SnTe cap layer, vital to protect the EuTe islands from oxidation. A simple model is outlined to describe the distortions caused by the EuTe islands on the SnTe buffer and cap layers. The SnTe cap layers formed interesting plateau structures with easily controlled wall height, that could find applications as a template for future nanostructures growth. (C) 2010 Elsevier B.V. All rights reserved.

Velocity-dependent KAM islands

We revisit the non-dissipative time-dependent annular billiard and we consider the chaotic dynamics in two planes of conjugate variables in order to describe the behavior of the growth, or saturation, of the mean velocity of an ensemble of particles. We observed that the changes in the 4-d phase space occur without changing any parameter. They occur depending on where the initial conditions start. The emerging KAM islands interfere in the behavior of the particle dynamics especially in the Fermi acceleration mechanism. We show that Fermi acceleration can be suppressed, without dissipation, even considering the non-dissipative energy context. (C) 2011 Published by Elsevier Ltd.

TEM, XRD and AFM study of poly(o-ethoxyaniline) films: new evidence for the formation of conducting islands

The existence of conducting islands in polyaniline films has long been proposed in the literature, which would be consistent with conducting mechanisms based on hopping. Obtaining direct evidence of conducting islands, however, is not straightforward. In this paper, conducting islands were visualized in poly(o-ethoxyaniline) (POEA) films prepared at low pH, using Transmission Electron Microscopy (TEM) and atomic force spectroscopy (AFS). The size of the islands varied between 67 and 470 angstrom for a pH=3.0, with a larger average being obtained with AFS, probably due to the finite size effect of the atomic force microscopy tip. In AFS, the conducting islands were denoted by regions with repulsive forces due to the double-layer forces. On the basis of X-ray diffraction (XRD) patterns for POEA in the powder form, we infer that the conducting islands are crystalline, and therefore a POEA film is believed to consist of conducting islands dispersed in an insulating, amorphous matrix. From conductivity measurements we inferred the charge transport to be governed by a typical quasi-one dimensional variable range hopping (VRH) mechanism.

Sr and Nd isotope composition of the metamorphic, sedimentary and ultramafic xenoliths of Lanzarote (Canary Islands): Implications for magma sources

The lavas produced by the Timanfaya eruption of 1730-1736 (Lanzarote, Canary Islands) contain a great many sedimentary and metamorphic (metasedimentary), and mafic and ultramafic plutonic xenoliths. Among the metamorphosed carbonate rocks (calc-silicate rocks [CSRs]) are monomineral rocks with forsterite or wollastonite, as well as rocks containing olivine +/- orthopyroxene +/- clinopyroxene +/- plagioclase: their mineralogical compositions are identical to those of the mafic (gabbros) and ultramafic (dunite, wherlite and lherzolite) xenoliths. The (87)Sr/(16)Sr (around 0.703) and (143)Nd/(144)Nd (around 0.512) isotope ratios of the ultramafic and metasedimentary xenoliths are similar, while the (147)Sm/(144)Nd ratios show crustal values (0.13-0.16) in the ultramafic xenoliths and mantle values (0.18-0.25) in some CSRs. The apparent isotopic anomaly of the metamorphic xenoliths can be explained in terms of the heat source (basaltic intrusion) inducing strong isotopic exchange ((87)Sr/(86)Sr and (143)Nd/(144)Nd) between metasedimentary and basaltic rocks. Petrofabric analysis also showed a possible relationship between the ultramafic and metamorphic xenoliths. (C) 2009 Elsevier B.V. All rights reserved.