Origins of the Xylella fastidiosa Prophage-Like Regions and Their Impact in Genome Differentiation

Xylella fastidiosa is a Gram negative plant pathogen causing many economically important diseases, and analyses of completely sequenced X. fastidiosa genome strains allowed the identification of many prophage-like elements and possibly phage remnants, accounting for up to 15% of the genome composition. To better evaluate the recent evolution of the X. fastidiosa chromosome backbone among distinct pathovars, the number and location of prophage-like regions on two finished genomes (9a5c and Temecula1), and in two candidate molecules (Ann1 and Dixon) were assessed. Based on comparative best bidirectional hit analyses, the majority (51%) of the predicted genes in the X. fastidiosa prophage-like regions are related to structural phage genes belonging to the Siphoviridae family. Electron micrograph reveals the existence of putative viral particles with similar morphology to lambda phages in the bacterial cell in planta. Moreover, analysis of microarray data indicates that 9a5c strain cultivated under stress conditions presents enhanced expression of phage anti-repressor genes, suggesting switches from lysogenic to lytic cycle of phages under stress-induced situations. Furthermore, virulence-associated proteins and toxins are found within these prophage-like elements, thus suggesting an important role in host adaptation. Finally, clustering analyses of phage integrase genes based on multiple alignment patterns reveal they group in five lineages, all possessing a tyrosine recombinase catalytic domain, and phylogenetically close to other integrases found in phages that are genetic mosaics and able to perform generalized and specialized transduction. Integration sites and tRNA association is also evidenced. In summary, we present comparative and experimental evidence supporting the association and contribution of phage activity on the differentiation of Xylella genomes.

1-[(Z)-1-Bromo-2-(butyldichloro-lambda(4)tellanyl)ethenyl]cyclohex-1-ene

The Te(IV) atom in the title compound, [Te(C(4)H(9))(C(8)H(10)Br)Cl(2)] or C(12)H(19)BrCl(2)Te, is in a distorted psi-trigonal-bipyramidal geometry, with the lone pair of electrons projected to occupy a position in the equatorial plane, and with the Cl atoms being mutually trans [172.48 (4)degrees]. Close intramolecular [Te center dot center dot center dot Br = 3.3444 (18) angstrom] and intermolecular [Te center dot center dot center dot Cl = 3.675 (3) angstrom] interactions are observed. The latter lead to centrosymmetric dimers which assemble into layers in the bc plane. The primary connections between layers are of the type C-H center dot center dot center dot Cl.

Patterns of distribution of the hermit crab Loxopagurus loxochelis (Moreira, 1901) (Decapoda, Diogenidae) in two coastal areas of southern Brazil

The present study determined the distribution pattern of the hermit crab Loxopagurus loxochelis by a comparison of catch, depth and environmental factors at two separate bays (Caraguatatuba and Ubatuba) of Sao Paulo State, Brazil. The influence of these parameters on the distribution of males, non- ovigerous females and ovigerous females was also evaluated. Crabs were collected monthly, over a period of one year (from July/2002 to June/2003), in seven depths, from 5 to 35 m. Abiotic factors were monitored as follows: superficial and bottom salinity (psu), superficial and bottom temperature (C), organic matter content (%) and sediment composition (%). In total, 366 hermit crabs were sampled in Caraguatatuba and 126 in Ubatuba. The highest frequency of occurrence was verified at 20 m during winter (July) in Caraguatatuba and 25 m during summer (January) in Ubatuba. The highest occurrences were recorded in the regions with bottom salinities ranging from 34 to 36 psu, bottom temperatures from 18 to 24 C and, low percentages of organic matter, gravel and mud; and large proportion of sand in the substrate. There was no significant correlation between the total frequency of organisms and the environmental factors analyzed in both regions. This evidence suggests that other variables as biotic interactions can influence the pattern of distribution of L. loxochelis in the analyzed region, which is considered the limit of the northern distribution of this species.

Data collapse, scaling functions, and analytical solutions of generalized growth models

We consider a nontrivial one-species population dynamics model with finite and infinite carrying capacities. Time-dependent intrinsic and extrinsic growth rates are considered in these models. Through the model per capita growth rate we obtain a heuristic general procedure to generate scaling functions to collapse data into a simple linear behavior even if an extrinsic growth rate is included. With this data collapse, all the models studied become independent from the parameters and initial condition. Analytical solutions are found when time-dependent coefficients are considered. These solutions allow us to perceive nontrivial transitions between species extinction and survival and to calculate the transition's critical exponents. Considering an extrinsic growth rate as a cancer treatment, we show that the relevant quantity depends not only on the intensity of the treatment, but also on when the cancerous cell growth is maximum.

Prevalence, Incidence Density, and Genotype Distribution of GB Virus C Infection in a Cohort of Recently HIV-1-Infected Subjects in Sao Paulo, Brazil

Background: The results of previous studies elsewhere have indicated that GB virus C (GBV-C) infection is frequent in patients infected with the human immunodeficiency virus type 1 (HIV-1) due to similar transmission routes of both viruses. The aim of this study was to determine the prevalence, incidence density and genotypic characteristics of GBV-C in this population. Methodology/Principal Findings: The study population included 233 patients from a cohort primarily comprised of homosexual men recently infected with HIV-1 in Sao Paulo, Brazil. The presence of GBV-C RNA was determined in plasma samples by reverse transcriptase-nested polymerase chain reaction and quantified by real-time PCR. GBV-C genotypes were determined by direct sequencing. HIV viral load, CD4+ T lymphocyte and CD8+ T lymphocyte count were also tested in all patients. The overall prevalence of GBV-C infection was 0.23 (95% CI: 0.18 to 0.29) in the study group. There was no significant difference between patients with and without GBV-C infection and Glycoprotein E2 antibody presence regarding age, sex, HIV-1 viral load, CD4+ and CD8+ T cell counts and treatment with antiretroviral drugs. An inverse correlation was observed between GBV-C and HIV-1 loads at enrollment and after one year. Also, a positive but not significant correlation was observed between GBV-C load and CD4+ T lymphocyte. Phylogenetic analysis of the GBV-C isolates revealed the presence of genotype 1 and genotype 2, these sub classified into subtype 2a and 2b. Conclusion/Significance: GBV-C infection is common in recently HIV -1 infected patients in Sao Paulo, Brazil and the predominant genotype is 2b. This study provides the first report of the GBV-C prevalence at the time of diagnosis of HIV-1 and the incidence density of GBV-C infection in one year.

Skewed Distribution of Circulating Activated Natural Killer T (NKT) Cells in Patients with Common Variable Immunodeficiency Disorders (CVID)

Common variable immunodeficiency disorder (CVID) is the commonest cause of primary antibody failure in adults and children, and characterized clinically by recurrent bacterial infections and autoimmune manifestations. Several innate immune defects have been described in CVID, but no study has yet investigated the frequency, phenotype or function of the key regulatory cell population, natural killer T (NKT) cells. We measured the frequencies and subsets of NKT cells in patients with CVID and compared these to healthy controls. Our results show a skewing of NKT cell subsets, with CD4+ NKT cells at higher frequencies, and CD8+ NKT cells at lower frequencies. However, these cells were highly activated and expression CD161. The NKT cells had a higher expression of CCR5 and concomitantly expression of CCR5+CD69+CXCR6 suggesting a compensation of the remaining population of NKT cells for rapid effector action.

Distribution of hepatitis c virus (hcv) genotypes in patients with chronic infection from Rondonia, Brazil

Background: Hepatitis C virus (HCV) is an important human pathogen affecting around 3% of the human population. In Brazil, it is estimated that there are approximately 2 to 3 million HCV chronic carriers. There are few reports of HCV prevalence in Rondonia State (RO), but it was estimated in 9.7% from 1999 to 2005. The aim of this study was to characterize HCV genotypes in 58 chronic HCV infected patients from Porto Velho, Rondonia (RO), Brazil. Methods: A fragment of 380 bp of NS5B region was amplified by nested PCR for genotyping analysis. Viral sequences were characterized by phylogenetic analysis using reference sequences obtained from the GenBank (n = 173). Sequences were aligned using Muscle software and edited in the SE-AL software. Phylogenetic analyses were conducted using Bayesian Markov chain Monte Carlo simulation (MCMC) to obtain the MCC tree using BEAST v. 1.5.3. Results: From 58 anti-HCV positive samples, 22 were positive to the NS5B fragment and successfully sequenced. Genotype 1b was the most prevalent in this population (50%), followed by 1a (27.2%), 2b (13.6%) and 3a (9.0%). Conclusions: This study is the first report of HCV genotypes from Rondonia State and subtype 1b was found to be the most prevalent. This subtype is mostly found among people who have a previous history of blood transfusion but more detailed studies with a larger number of patients are necessary to understand the HCV dynamics in the population of Rondonia State, Brazil.

Frequency and genotypic distribution of GB virus C (GBV-C) among Colombian population with Hepatitis B (HBV) or Hepatitis C (HCV) infection

Background: GB virus C (GBV-C) is an enveloped positive-sense ssRNA virus belonging to the Flaviviridae family. Studies on the genetic variability of the GBV-C reveals the existence of six genotypes: genotype 1 predominates in West Africa, genotype 2 in Europe and America, genotype 3 in Asia, genotype 4 in Southwest Asia, genotype 5 in South Africa and genotype 6 in Indonesia. The aim of this study was to determine the frequency and genotypic distribution of GBV-C in the Colombian population. Methods: Two groups were analyzed: i) 408 Colombian blood donors infected with HCV (n = 250) and HBV (n = 158) from Bogota and ii) 99 indigenous people with HBV infection from Leticia, Amazonas. A fragment of 344 bp from the 5' untranslated region (5' UTR) was amplified by nested RT PCR. Viral sequences were genotyped by phylogenetic analysis using reference sequences from each genotype obtained from GenBank (n = 160). Bayesian phylogenetic analyses were conducted using Markov chain Monte Carlo (MCMC) approach to obtain the MCC tree using BEAST v. 1.5.3. Results: Among blood donors, from 158 HBsAg positive samples, eight 5.06% (n = 8) were positive for GBV-C and from 250 anti-HCV positive samples, 3.2%(n = 8) were positive for GBV-C. Also, 7.7% (n = 7) GBV-C positive samples were found among indigenous people from Leticia. A phylogenetic analysis revealed the presence of the following GBV-C genotypes among blood donors: 2a (41.6%), 1 (33.3%), 3 (16.6%) and 2b (8.3%). All genotype 1 sequences were found in co-infection with HBV and 4/5 sequences genotype 2a were found in co-infection with HCV. All sequences from indigenous people from Leticia were classified as genotype 3. The presence of GBV-C infection was not correlated with the sex (p = 0.43), age (p = 0.38) or origin (p = 0.17). Conclusions: It was found a high frequency of GBV-C genotype 1 and 2 in blood donors. The presence of genotype 3 in indigenous population was previously reported from Santa Marta region in Colombia and in native people from Venezuela and Bolivia. This fact may be correlated to the ancient movements of Asian people to South America a long time ago.

Interethnic Differences in the Distribution of Matrix Metalloproteinases Genetic Polymorphisms Are Consistent with Interethnic Differences in Disease Prevalence

Interethnic differences exist in disease prevalence, especially with regard to cancer and cardiovascular diseases, which involve altered expression or activity of matrix metalloproteinases (MMPs). The hypothesis being tested in this study is that interethnic differences exist between blacks and whites with regard to the distribution of genetic variants of MMP polymorphisms and haplotypes. We examined the distribution of polymorphisms of MMP-2 and MMP-9 genes in 177 black and 140 white subjects. We studied the following polymorphisms: the C(-1306)T in the promoter of the MMP-2 gene, the C(-1562)T and a microsatellite -90(CA)(14-24) in the promoter, and the Q279R in exon 6 of the MMP-9 gene. We have also compared our results with those from Hapmap or Seattle SNPs Projects and estimated the haplotype frequency in these two ethnic groups. The ""C'' allele for the C(-1306)T polymorphism was more common in blacks (91.5%) than in whites (80.4%; p<0.0001). The ""T'' allele for the C(-1562)T polymorphism was more common in blacks (15.0%) than in whites (8.9%; p=0.0279), as well as the alleles with >21 repeats for the -90(CA)(14-24) were more common in blacks than in whites (61.9% in blacks and 49.3% in whites; p=0.0017). We found no interethnic differences for the Q279R polymorphism. Moreover, two haplotypes that combine ""detrimental'' alleles were found at higher frequencies in blacks than in whites (31% vs. 16.4%, respectively; p<0.05). The interethnic differences being reported here replicate those previously found with smaller number of subjects in the Hapmap or Seattle SNPs data and may help explain the higher prevalence of cancer and cardiovascular diseases in blacks compared with whites. Our findings suggest a proportional significance of these polymorphisms in each ethnic group.

Interethnic Differences in the Distribution of Clinically Relevant Vascular Endothelial Growth Factor Genetic Polymorphisms

Vascular endothelial growth factor (VEGF) is a homodimeric glycoprotein produced mostly in endothelial cells and its transcription is regulated by a variety of growth factors and cytokines. VEGF plays many relevant roles, and three functional polymorphisms in the promoter region of the VEGF gene (C-2578A, G-1154A, and G-634C) have been associated with disease conditions. Although some studies suggest that interethnic differences exist in the distribution of these variants, no previous study has examined this hypothesis in admixed populations. We examined the distribution of these three clinically relevant VEGF single-nucleotide polymorphisms in 175 white and 185 black subjects. We have also estimated the haplotype distribution and assessed associations between these variants. Although the A-2578 and A-1154 variants were more common in whites (39% and 29%, respectively) than in blacks (29% and 16%, respectively; both p < 0.05), no significant interethnic differences were found with regards to the G-634C polymorphism. While the haplotype including the C-2578, G-1154, and G-634 variants was the most common in both ethnic groups, it was more common in blacks than in whites (p < 0.05). The haplotype including the C-2578, A-1154, and G-634 alleles and the haplotype including the C-2578, A-1154, and C-634 alleles were more common in whites than in blacks (both p < 0.05). These results show marked interethnic differences in the distribution of genetic variants of VEGF that may explain, at least in part, interethnic disparities in the susceptibility to cardiovascular diseases.

Polarized Light (lambda 400-2000 nm) on Third-Degree Burns in Diabetic Rats: Immunohistochemical Study

Aim: The aim of this study was to evaluate with light microscopy the healing process of third-degree burns on diabetic rats treated with polarized light (lambda 400-2000 nm, 20 or 40 J/cm(2)/session, 40 mW/cm(2), 2.4 J/cm(2)/min, 5.5-cm beam diameter). Background: Uncontrolled diabetes mellitus causes severe disruption of the body's metabolism, including healing. Polarized light sources have been shown to be effective in improving healing in many situations. Animals and Methods: Diabetes mellitus was induced with streptozotocin (60 mg/kg) in 45 male Wistar albino rats, and a third-degree burn (1.5 by 1.5 cm) was created on the dorsum of each animal under general anesthesia. The animals were randomly distributed into three groups: control, 20 J/cm(2), and 40 J/cm(2). Each group was then divided into three subgroups based on time of death (7, 14, 21 d). Phototherapy (20 or 40 J/cm(2) per session) was carried out immediately after the burning and repeated daily until the day before death. Following animal death, specimens were removed, embedded in paraffin, sectioned, and stained with hematoxylin and eosin (HE) or Sirius Red or immunomarked with CK AE1/AE3 antibody. Qualitative and semiquantitative analyses were performed under light microscopy. The results were statistically analyzed. Results: The animals treated with 20 J/cm(2) showed significant differences with regard to revascularization and re-epithelialization. Although the 40 J/cm(2) group showed stimulation of fibroblastic proliferation as an isolated feature, no other difference from the control was observed. Conclusion: Our results suggest that the use of polarized light at 20 J/cm(2) effectively improves the healing of third-degree burns on diabetic animals at both early and late stages of repair.

Dynamics and constraints of the massive graviton dark matter flat cosmologies

We discuss the dynamics of the Universe within the framework of the massive graviton cold dark matter scenario (MGCDM) in which gravitons are geometrically treated as massive particles. In this modified gravity theory, the main effect of the gravitons is to alter the density evolution of the cold dark matter component in such a way that the Universe evolves to an accelerating expanding regime, as presently observed. Tight constraints on the main cosmological parameters of the MGCDM model are derived by performing a joint likelihood analysis involving the recent supernovae type Ia data, the cosmic microwave background shift parameter, and the baryonic acoustic oscillations as traced by the Sloan Digital Sky Survey red luminous galaxies. The linear evolution of small density fluctuations is also analyzed in detail. It is found that the growth factor of the MGCDM model is slightly different (similar to 1-4%) from the one provided by the conventional flat Lambda CDM cosmology. The growth rate of clustering predicted by MGCDM and Lambda CDM models are confronted to the observations and the corresponding best fit values of the growth index (gamma) are also determined. By using the expectations of realistic future x-ray and Sunyaev-Zeldovich cluster surveys we derive the dark matter halo mass function and the corresponding redshift distribution of cluster-size halos for the MGCDM model. Finally, we also show that the Hubble flow differences between the MGCDM and the Lambda CDM models provide a halo redshift distribution departing significantly from the those predicted by other dark energy models. These results suggest that the MGCDM model can observationally be distinguished from Lambda CDM and also from a large number of dark energy models recently proposed in the literature.

Spectroscopic variabilities in lambda Pavonis

Aims. We investigate the time-varying patterns in line profiles, V/R, and radial velocity of the Be star HD 173948 (lambda Pavonis). Methods. Time series analyses of radial velocity, V/R, and line profiles of He I, Fe II, and Si II were performed with the Cleanest algorithm. An estimate of the stellar rotation frequency was derived from the stellar mass and radius in the Roche limit by adopting an aspect angle i derived from the fittings of non-LTE model spectra affected by rotation. The projected rotation velocity, necessary as input for the spectral synthesis procedure, was evaluated from the Fourier transform of the rotation profiles of all neutral helium lines in the optical range. Results. Emission episodes in Balmer and He i lines, as well as V/R cyclic variations, are reported for spectra observed in year 1999, followed by a relatively quiescent phase (2000) and then again a new active epoch (2001). From time series analyses of line profiles, radial velocities, and V/R ratios, four signals with high confidence levels are detected: nu(1) = 0.17 +/- 0.02, nu(2) = 0.49 +/- 0.05, nu(3) = 0.82 +/- 0.03, and nu(4) = 1.63 +/- 0.04 c/d. We interpret nu 4 as a non-radial pulsation g-mode, nu 3 as a signal related to the orbital timescale of ejected material, which is near the theoretical rotation frequency 0.81 c/d inferred from the fitting of the models taken into account for gravity darkening. The signals nu(1) and nu(2) are viewed as aliases of nu(3) and nu(4).