Complete nucleotide sequence, genomic organization and phylogenetic analysis of Citrus leprosis virus cytoplasmic type

The complete nucleotide sequence of the genomic RNA 1 (8745 nt) and RNA 2 (4986 nt) of Citrus leprosis virus cytoplasmic type (CiLV-C) was determined using cloned cDNA. RNA 1 contains two open reading frames (ORFs), which correspond to 286 and 29 kDa proteins. The 286 kDa protein is a polyprotein putatively involved in virus replication, which contains four conserved domains: methyltransferase, protease, helicase and polymerase. RNA 2 contains four ORFs corresponding to 15, 61, 32 and 24 kDa proteins, respectively. The 32 kDa protein is apparently involved in cell-to-cell movement of the virus, but none of the other putative proteins exhibit any conserved domain. The 5' regions of the two genomic RNAs contain a 'cap' structure and poly(A) tails were identified in the 3'-terminals. Sequence analyses and searches for structural and non-structural protein similarities revealed conserved domains with members of the genera Furovirus, Bromovirus, Tobravirus and Tobamovirus, although phylogenetic analyses strongly suggest that CiLV-C is a member of a distinct, novel virus genus and family, and definitely demonstrate that it does not belong to the family Rhabdoviridae, as previously proposed. Based on these results it was proposed that Citrus leprosis virus be considered as the type member of a new genus of viruses, Cilevirus.

Stress-induced ordering due heavy interstitial atoms in Nb-0.3 wt.% Ti alloys

The mechanical properties of metals with bee structure, such as niobium and their alloys, are changed of a significant way by the introduction of heavy interstitial elements. These interstitial elements (oxygen, for example) present in the metallic matrix occupy octahedral sites and constitute an elastic dipole of tetragonal symmetry and might produce anelastic relaxation. Polycrystalline samples of Nb-0.3 wt.% Ti (Nb-Ti) alloy with oxygen in solid solution were analysed. The anelastic spectroscopy measurements had been made in a torsion pendulum, with frequencies in the Hz range, in a temperature range between 300 and 700 K. The results showed thermally activated relaxation structures were identified four relaxation process attributed to stress-induced ordering of single oxygen, nitrogen and carbon atoms around niobium and stress-induced ordering of single oxygen atoms around titanium atoms. (c) 2005 Elsevier B.V. All rights reserved.

Microfacies and sequence stratigraphy of the Amapa Formation, Late Paleocene to Early Eocene, Foz do Amazonas Basin, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Phase II clinical study of an association for the treatment of interstitial cystitis (Cystex (R))

Painful bladder syndrome associated with interstitial cystitis (PBS/IC) is a clinical condition characterized pelvic pain, urinary urgency, and urinary frequency. In this study, 22 patients were assigned to make two visits over a three weeks period. The patients were randomly, double-blinded assigned in two groups. The first group received Cystex (R) capsules. The second group received placebo capsules. Two capsules were taken three times a day away from meals. The change from baseline in the O'Leary-Sant IC symptom and problem index was the primary outcome parameter. Changes in functional bladder capacity and intensity of pain and urgency have been chosen as secondary outcome parameters. Mood as well as physical and sexual activity were rated by 10 questions on a scale 0 to 6. The ratings were analyzed and the average for each patient in both groups Cystex (R) and placebo was determined as the quality of life index. For the primary outcome there was a statistically significant difference between the groups. Mean symptom score-sum decreased from 28.4 to 20.5 in the Cystex (R) group compared with 29.5 to 26.8 in the placebo group (p<0.05). For the secondary end points, pain and urgency intensity improved statistically significantly in the Cystex (R) group compared with the placebo group (p<0.05). The frequency and functional bladder capacity improved to greater degree in the Cystex (R) group. The differences were statistically significant for comparison of frequency (p<0.05) and not for functional bladder capacity (p>0.05). In our study, Cystex (R) enhanced quality of life over the placebo showing a statistically significant. This trial have shown that the efficacy and safety of therapy with Cystex (R) in the treatment of interstitial cystitis and is an alternative for patients suffering from this pathology. Therefore, it can be concluded that the composition of Cystex (R), increased the quality of life in treated patients.

Contrasting intra versus interspecies DNA sequence variation for representatives of the Batrachospermales (Rhodophyta): Insights from a DNA barcoding approach

Sixty-five accessions of the species-rich freshwater red algal order Batrachospermales were characterized through DNA sequencing of two regions: the mitochondrial cox1 gene (664 bp), which is proposed as the DNA barcode for red algae, and the UPA (universal plastid amplicon) marker (370 bp), which has been recently identified as a universally amplifying region of the plastid genome. upgma phenograms of both markers were consistent in their species-level relationships, although levels of sequence divergence were very different. Intraspecific variation of morphologically identified accessions for the cox1 gene ranged from 0 to 67 bp (divergences were highest for the two taxa with the greatest number of accessions; Batrachospermum helminthosum and Batrachospermum macrosporum); while in contrast, the more conserved universal plastid amplicon exhibited much lower intraspecific variation (generally 0-3 bp). Comparisons to previously published mitochondrial cox2-3 spacer sequences for B. helminthosum indicated that the cox1 gene and cox2-3 spacer were characterized by similar levels of sequence divergence, and phylogeographic patterns based on these two markers were consistent. The two taxa represented by the largest numbers of specimens (B. helminthosum and B. macrosporum) have cox1 intraspecific divergence values that are substantially higher than previously reported, but no morphological differences can be discerned at this time among the intraspecific groups revealed in the analyses. DNA barcode data, which are based on a short fragment of an organellar genome, need to be interpreted in conjunction with other taxonomic characters, and additional batrachospermalean taxa need to be analyzed in detail to be able to draw generalities regarding intraspecific variation in this order. Nevertheless, these analyses reveal a number of batrachospermalean taxa worthy of more detailed DNA barcode study, and it is predicted that such research will have a substantial effect on the taxonomy of species within the Batrachospermales in the future.

Spermatogenesis and nucleolar behavior in males of aquatic Heteroptera

Aspects of spermatogenesis and nucleolar behavior were analyzed in Brachymetra albinerva, Cylindrostethus palmaris, Halobatopsis platensis, Limnogonus aduncus (Gerridae), Martarega sp (Notonectidae), Rhagovelia whitei, and Rhagovelia sp (Veliidae). The testicles are rounded (Veliidae), elongated (Gerridae) or spiral (Notonectidae) and have a transparent membrane covering them. The complement chromosome was 2n = 23 (22A + X0, L. aduncus and Rhagovelia sp), 25 (24A + X0, B. albinerva and H. platensis), 26 (22A + 2m + XY, Martarega sp), 29 (28A + X0, C. palmaris), or 39 (38A + X0, R. whitei) chromosomes, and the only species with a different sex chromosome system was Martarega sp, which showed an XY system and m-chromosomes. The meiotic behavior of all species was similar: holocentric chromosomes and heteropyknotic material at prophase, interstitial and/or terminal chiasmata, and first reductional division for the autosomes and the reverse for the sex chromosomes. The only difference observed was related to the very large size of Martarega sp cells in all stages of spermatogenesis. With regard to nucleolar behavior, the species did not show differences, except for Martarega sp with larger nucleoli than the other species. The only species in which it was clearly possible to identify the nucleolar organizer region was L. aduncus, in the region of a terminal autosome. It was also confirmed that the telomeric associations do not occur at random. In the other species, specific staining was very discrete, and the nucleolar organizer region location was not at all evident.

Expressed sequence tags from Atta laevigata and identification of candidate genes for the control of pest leaf-cutting ants.

Leafcutters are the highest evolved within Neotropical ants in the tribe Attini and model systems for studying caste formation, labor division and symbiosis with microorganisms. Some species of leafcutters are agricultural pests controlled by chemicals which affect other animals and accumulate in the environment. Aiming to provide genetic basis for the study of leafcutters and for the development of more specific and environmentally friendly methods for the control of pest leafcutters, we generated expressed sequence tag data from Atta laevigata, one of the pest ants with broad geographic distribution in South America. Results: The analysis of the expressed sequence tags allowed us to characterize 2,006 unique sequences in Atta laevigata. Sixteen of these genes had a high number of transcripts and are likely positively selected for high level of gene expression, being responsible for three basic biological functions: energy conservation through redox reactions in mitochondria; cytoskeleton and muscle structuring; regulation of gene expression and metabolism. Based on leafcutters lifestyle and reports of genes involved in key processes of other social insects, we identified 146 sequences potential targets for controlling pest leafcutters. The targets are responsible for antixenobiosis, development and longevity, immunity, resistance to pathogens, pheromone function, cell signaling, behavior, polysaccharide metabolism and arginine kynase activity. Conclusion: The generation and analysis of expressed sequence tags from Atta laevigata have provided important genetic basis for future studies on the biology of leaf-cutting ants and may contribute to the development of a more specific and environmentally friendly method for the control of agricultural pest leafcutters.

Interstitial long-arm deletion of chromosome 7 and ectrodactyly

An interstitial deletion of 7q21 was found in a boy with mental retardation, microcephaly, convergent strabismus, micrognathia, genital anomalies, and other findings, including ectrodactyly.

Renal interstitial foam cells are macrophages

Immunohistochemical studies on renal biopsies from eight patients with various types of glomerulonephritis showed that the interstitial foam cells belonged to the monocyte-macrophage lineage. There was a strong association between hypercholesterolaemia and the presence of renal interstitial foam cells.

Thermally activated dynamics of the tilts of the CuO6 octahedra, hopping of interstitial O, and possible instability towards the LTT phase in La2CuO4+δ

The anelastic spectrum (dynamic Young's modulus and elastic energy absorption) of La2CuO4+δ has been measured between 1 and 700 K with 0<δ<0.02. The spectrum of stoichiometric La2CuO4 in the low-temperature orthorhombic (LTO) phase is dominated by two intense relaxation processes which cause softenings of 16% around 150 K and 9% below 30 K at f∼1 kHz. The relaxation at 150 K is attributed to the presence of a fraction of the CuO6 octahedra which are able to change their tilted configuration by thermal activation between orientations which are nearly energetically equivalent, possibly within the twin boundaries. The relaxation below 30 K is governed by tunneling, and involves a considerable fraction of the lattice atoms. It is proposed that the double-well potentials for the low-temperature relaxation are created by the tendency of the LTO phase to form low-temperature tetragonal (LTT) domains, which however are not stabilized like when La is partially substituted with Ba. On doping with excess O, the relaxation rates of these processes are initially enhanced by hole doping, while their intensities are depressed by lattice disorder; an explanation of this behavior is provided. Excess O also causes two additional relaxation processes. The one appearing at lower values of δ is attributed to the hopping of single interstitial O2- ions, with a hopping rate equal to τ-1=2×10-14exp(-5600/T) s. The second process is slower and can be due to O pairs or other complexes containing excess O.

Alteration of soil properties through a weathering sequence as evaluated by spectral reflectance

In the study of physical, chemical, and mineralogical data related to the weathering of soils and the quantification of their properties, remote sensing constitutes an important technique that, in addition to conventional analyses, can contribute to soil survey. The objectives of this research were to characterize and differentiate soils developed from basaltic rocks that occur in the Parana state, Brazil and to quantify soil properties based on their spectral reflectance. These observations were used to verify the relationship between the soils and reflectance with regard to weathering, organic matter (OM), and forms of Fe. From the least to the most weathered soil, we used a Typic Argiudoll (Reddish Brunizem), Rhodudalf (Terra Roxa Estruturada), and Rhodic Hapludox (Very Dark Red Latosol). The spectral reflectances between 400 and 2500 nm were obtained in the laboratory from soil samples collected at two depth increments, 0- to 20- and 40- to 60-cm, using an Infra Red Intelligent Spectroradiometer (IRIS). Correlation, regression, and discriminant estimates were used in analyzing the soil and spectral data. Results of this study indicated that soils could be separated at the soil-type level based on reflectance intensity in various absorption bands. Soil collected in the 40- to 60-cm depth appeared to have higher reflectance intensities than those from the 0- to 20-cm depth. Removal of OM from soil samples promoted higher reflectance intensity in the entire spectrum. Amorphous and crystalline Fe influenced reflectance differently. Weathering of basaltic soils was correlated with alterations in the reflectance intensities and absorption features of the spectral curves. Multivariate analysis demonstrated that this technique was efficient in the estimation of clay, silt, kaolinite, crystalline Fe, amorphous Fe, and Mg through the use of reflected energy of the soils.

Nucleotide sequence of 5S rDNA and localization of the ribosomal RNA genes to metaphase chromosomes of the Tilapiine cichlid fish, Oreochromis niloticus

In this study, we report the cloning and nucleotide sequence of PCR-generated 5S rDNA from the Tilapiine cichlid fish, Oreochromis niloticus. Two types of 5S rDNA were detected that differed by insertions and/or deletions and base substitutions within the non-transcribed spacer (NTS). Two 5S rDNA loci were observed by fluorescent in situ hybridization (FISH) in metaphase spreads of tilapia chromosomes. FISH using an 18S rDNA probe and silver nitrate sequential staining of 5S-FISH slides showed three 18S rDNA loci that are not syntenic to the 5S rDNA loci.

Affinities of the Saw-billed Hermit (Ramphodon naevius) determined by cytochrome-b sequence data

We sequenced 912 bp of the cytochrome-b gene to examine phylogenetic relationships of the enigmatic Saw-billed Hermit (Ramphodon naevius), a large and distinctive hummingbird endemic to tropical forests of southeastern Brazil. Bootstrapped maximum parsimony and maximum likelihood analyses of sequence data from 11 hummingbirds and several outgroups (two swifts, one goatsucker) support: (a) monophyly of the traditional hermit (Phaethornithinae) and nonhermit (Trochilinae) subfamilies, (b) placement of Ramphodon among hermits, and (c) a sister relationship between Ramphodon and an exemplar of the widespread polytypic hermit genus Glaucis. The association of Ramphodon with derived hermit lineages is concordant with subfamilial patterns of wing anatomy and nest architecture. However, the unusual plumages (striped underparts) and male bills (long, serrated, hooked) shared by Ramphodon and the Tooth-billed Hummingbird (Androdon aequatorialis) appear to have evolved within separate hermit and nonhermit tooth-billed clades. Distal placement of the Ramphodon-Glaucis clade within hermits implies that even distinctive Brazilian endemics such as Ramphodon are derived forms that evolved relatively recently.

The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) ≈500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) wide-spread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications.