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.

Some questions about the Metropolitan Areas in Buenos Aires, Sao Paulo and Santiago regions

Among the numerous problems that are common to the Latin-American metropolises, such as the deep socio-spatial segregation, the impressive territorial fragmentation and the real estate valorisation that overvalues some territories, whilst it depreciates others, we have chosen to focus on the management of the metropolitan regions. That question clearly indicates that due to the great current changes of the economical restructuring - a process that strengthened the capitalist logic of social development - the traditional form of thinking urban planning has found its limits. Consequently, this issue of metropolitan management shows the need to look for new ways of metropolitan administration that can answer to the The main metropolitan regions of South America: Buenos Aires, Sao Paulo and Santiago form our references to characterize the recent changes from a territorial point of view on the one hand; and relative to the new determinations of the metropolis on the other hand. This leads us to discuss the challenges that metropolitan management face in a scenario of governability fragmentation.

Non-Detection of Human Herpesvirus 8 (HHV-8) DNA in HHV-8-Seropositive Blood Donors from Three Brazilian Regions

Human herpesvirus 8 (HHV-8), also known as Kaposi's sarcoma-associated herpesvirus (KSHV), is the etiologic agent of all forms of Kaposi's sarcoma, primary effusion lymphoma and the plasmablastic cell variant of multicentric Castleman disease. In endemic areas of sub-Saharan Africa, blood transfusions have been associated with a substantial risk of HHV-8 transmission. By contrast, several studies among healthy blood donors from North America have failed to detect HHV-8 DNA in samples of seropositive individuals. In this study, using a real-time PCR assay, we investigated the presence of HHV-8 DNA in whole-blood samples of 803 HHV-8 blood donors from three Brazilian states (Sao Paulo, Amazon, Bahia) who tested positive for HHV-8 antibodies, in a previous multicenter study. HHV-8 DNA was not detected in any sample. Our findings do not support the introduction of routine HHV-8 screening among healthy blood donors in Brazil. (WC = 140).

The Genomic Ancestry of Individuals from Different Geographical Regions of Brazil Is More Uniform Than Expected

Based on pre-DNA racial/color methodology, clinical and pharmacological trials have traditionally considered the different geographical regions of Brazil as being very heterogeneous. We wished to ascertain how such diversity of regional color categories correlated with ancestry. Using a panel of 40 validated ancestry-informative insertion-deletion DNA polymorphisms we estimated individually the European, African and Amerindian ancestry components of 934 self-categorized White, Brown or Black Brazilians from the four most populous regions of the Country. We unraveled great ancestral diversity between and within the different regions. Especially, color categories in the northern part of Brazil diverged significantly in their ancestry proportions from their counterparts in the southern part of the Country, indicating that diverse regional semantics were being used in the self-classification as White, Brown or Black. To circumvent these regional subjective differences in color perception, we estimated the general ancestry proportions of each of the four regions in a form independent of color considerations. For that, we multiplied the proportions of a given ancestry in a given color category by the official census information about the proportion of that color category in the specific region, to arrive at a ""total ancestry"" estimate. Once such a calculation was performed, there emerged a much higher level of uniformity than previously expected. In all regions studied, the European ancestry was predominant, with proportions ranging from 60.6% in the Northeast to 77.7% in the South. We propose that the immigration of six million Europeans to Brazil in the 19(th) and 20(th) centuries - a phenomenon described and intended as the ""whitening of Brazil"" -is in large part responsible for dissipating previous ancestry dissimilarities that reflected region-specific population histories. These findings, of both clinical and sociological importance for Brazil, should also be relevant to other countries with ancestrally admixed populations.

The stellar content of obscured Galactic giant H II regions. VI. W51A

We present K-band spectra of newly born OB stars in the obscured Galactic giant H II region W51A and approximate to 0.8 '' angular resolution images in the J, H, and K(S)-bands. Four objects have been spectroscopically classified as O-type stars. The mean spectroscopic parallax of the four stars gives a distance of 2.0 +/- 0.3 kpc (error in the mean), significantly smaller than the radio recombination line kinematic value of 5.5 kpc or the values derived from maser proper motion observations (6-8 kpc). The number of Lyman continuum photons from the contribution of all massive stars (NLyc approximate to 1.5 x 10(50) s(-1)) is in good agreement with that inferred from radio recombination lines (NLyc = 1.3 x 10(50) s(-1)) after accounting for the smaller distance derived here. We present analysis of archival high angular resolution images (NAOS CONICA at VLT and T-ReCS at Gemini) of the compact region W51 IRS 2. The K(S)-band images resolve the infrared source IRS 2 indicating that it is a very young compact H II region. Sources IRS 2E was resolved into compact cluster (within 660 AU of projected distance) of three objects, but one of them is just bright extended emission. W51d1 and W51d2 were identified with compact clusters of three objects (maybe four in the case of W51d1) each one. Although IRS 2E is the brightest source in the K-band and at 12.6 mu m, it is not clearly associated with a radio continuum source. Our spectrum of IRS 2E shows, similar to previous work, strong emission in Br gamma and He I, as well as three forbidden emission lines of Fe III and emission lines of molecular hydrogen (H(2)) marking it as a massive young stellar object.

THE STELLAR CONTENT OF OBSCURED GALACTIC GIANT H II REGIONS. VII. W3

Spectrophotometric distances in the K band have been reported by different authors for a number of obscured Galactic H II regions. Almost 50% of them show large discrepancies compared to the classical method using radial velocities measured in the radio spectral region. In order to provide a crucial test of both methods, we selected a target that does not present particular difficulty for any method and which has been measured by as many techniques as possible. The W3 star-forming complex, located in the Perseus arm, offers a splendid opportunity for such a task. We used the Near-Infrared Integral Field Spectrograph on the Frederick C. Gillett Gemini North telescope to classify candidate ""naked photosphere"" OB stars based on Two Micron All Sky Survey photometry. Two of the targets are revealed to be mid-O-type main-sequence stars leading to a distance of d = 2.20 kpc. This is in excellent agreement with the spectrophotometric distance derived in the optical band (d = 2.18 pc) and with a measurement of the W3 trigonometric parallax (d = 1.95 kpc). Such results confirm that the spectrophotometric distances in the K band are reliable. The radio-derived kinematic distance, on the contrary, gives a distance twice as large (d = 4.2 kpc). This indicates that this region of the Perseus arm does not follow the Galactic rotation curve, and this may also be the case for other H II regions for which discrepancies have been found.

Mycoflora and Co-Occurrence of Fumonisins and Aflatoxins in Freshly Harvested Corn in Different Regions of Brazil

Natural mycoflora and co-occurrence of fumonisins (FB(1), FB(2)) and aflatoxins (AFB(1), AFB(2), AFG(1) and AFG(2)) in freshly harvested corn grain samples from four regions of Brazil were investigated. Fusarium verticillioides was predominant in all samples. Analysis of fumonisins showed that 98% of the samples were contaminated with FB(1) and 74.5% with FB(1) + FB(2), with toxin levels ranging from 0.015 to 9.67 mu g/g for FB(1) and from 0.015 to 3.16 mu g/g for FB(2). Twenty-one (10.5%) samples were contaminated with AFB(1), seven (3.5%) with AFB(2) and only one (0.5%) with AFG(1) and AFG(2). Co-contamination with aflatoxins and fumonisins was observed in 7% of the samples. The highest contamination of fumonisins and aflatoxins was observed in Nova Odessa (SP) and Varzea Grande (MT), respectively. The lowest contamination of these mycotoxins was found in Varzea Grande and Nova Odessa, respectively.

Naturally-acquired humoral immune responses against the N- and C-termini of the Plasmodium vivax MSP1 protein in endemic regions of Brazil and Papua New Guinea using a multiplex assay

Background: Progress towards the development of a malaria vaccine against Plasmodium vivax, the most widely distributed human malaria parasite, will require a better understanding of the immune responses that confer clinical protection to patients in regions where malaria is endemic. Methods: Glutathione S-transferase (GST) and GST-fusion proteins representing the N-terminus of the merozoite surface protein 1 of P. vivax, PvMSP1-N, and the C-terminus, PvMSP1-C, were covalently coupled to BioPlex carboxylated beads. Recombinant proteins and coupled beads were used, respectively, in ELISA and Bioplex assays using immune sera of P. vivax patients from Brazil and PNG to determine IgG and subclass responses. Concordances between the two methods in the seropositivity responses were evaluated using the Kappa statistic and the Spearman's rank correlation. Results: The results using this methodology were compared with the classical microtitre enzyme-linked immnosorbent assay ( ELISA), showing that the assay was sensitive, reproducible and had good concordance with ELISA; yet, further research into different statistical analyses seems desirable before claiming conclusive results exclusively based on multiplex assays. As expected, results demonstrated that PvMSP1 was immunogenic in natural infections of patients from different endemic regions of Brazil and Papua New Guinea ( PNG), and that age correlated only with antibodies against the C-terminus part of the molecule. Furthermore, the IgG subclass profiles were different in these endemic regions having IgG3 predominantly recognizing PvMSP1 in Brazil and IgG1 predominantly recognizing PvMSP1 in PNG. Conclusions: This study validates the use of the multiplex assay to measure naturally-acquired IgG antibodies against the merozoite surface protein 1 of P. vivax.

Phase transitions and regions of stability in Reissner-Nordstrom holographic superconductors

The phase transition of Reissner-Nordstrom AdS(4) interacting with a massive charged scalar field has been further revisited. We found exactly one stable and one unstable quasinormal mode region for the scalar field. The two of them are separated by the first marginally stable solution.

No-match ORESTES explored as tumor markers

Sequencing technologies and new bioinformatics tools have led to the complete sequencing of various genomes. However, information regarding the human transcriptome and its annotation is yet to be completed. The Human Cancer Genome Project, using ORESTES (open reading frame EST sequences) methodology, contributed to this objective by generating data from about 1.2 million expressed sequence tags. Approximately 30 of these sequences did not align to ESTs in the public databases and were considered no-match ORESTES. On the basis that a set of these ESTs could represent new transcripts, we constructed a cDNA microarray. This platform was used to hybridize against 12 different normal or tumor tissues. We identified 3421 transcribed regions not associated with annotated transcripts, representing 83.3 of the platform. The total number of differentially expressed sequences was 1007. Also, 28 of analyzed sequences could represent noncoding RNAs. Our data reinforces the knowledge of the human genome being pervasively transcribed, and point out molecular marker candidates for different cancers. To reinforce our data, we confirmed, by real-time PCR, the differential expression of three out of eight potentially tumor markers in prostate tissues. Lists of 1007 differentially expressed sequences, and the 291 potentially noncoding tumor markers were provided.

MPC for tracking zone regions

This paper deals with the problem of tracking target sets using a model predictive control (MPC) law. Some MPC applications require a control strategy in which some system outputs are controlled within specified ranges or zones (zone control), while some other variables - possibly including input variables - are steered to fixed target or set-point. In real applications, this problem is often overcome by including and excluding an appropriate penalization for the output errors in the control cost function. In this way, throughout the continuous operation of the process, the control system keeps switching from one controller to another, and even if a stabilizing control law is developed for each of the control configurations, switching among stable controllers not necessarily produces a stable closed loop system. From a theoretical point of view, the control objective of this kind of problem can be seen as a target set (in the output space) instead of a target point, since inside the zones there are no preferences between one point or another. In this work, a stable MPC formulation for constrained linear systems, with several practical properties is developed for this scenario. The concept of distance from a point to a set is exploited to propose an additional cost term, which ensures both, recursive feasibility and local optimality. The performance of the proposed strategy is illustrated by simulation of an ill-conditioned distillation column. (C) 2010 Elsevier Ltd. All rights reserved.

TESA-blot for the diagnosis of Chagas disease in dogs from co-endemic regions for Trypanosoma cruzi, Trypanosoma evansi and Leishmania chagasi

We standardized serodiagnosis of dogs infected with Trypanosoma cruzi using TESA (trypomastigote excreted-secreted antigen)-blot developed for human Chagas disease. TESA-blot showed 100% sensitivity and specificity. In contrast, ELISA using TESA (TESA-ELISA) or epimastigotes (epi-ELISA) as antigen yielded 100% sensitivity but specificity of 94.1% and 49.4%, respectively. When used in field studies in an endemic region for Chagas disease, visceral leishmaniasis and Trypanosoma evansi (Mato Grosso do Sul state, Central Brazil), positivities were 9.3% for TESA-blot, 10.7% for TESA-ELISA and 32% for epi-ELISA. Dogs from a non-endemic region for these infections (Rondonia state, western Amazonia) where T cruzi is enzootic showed positivity of 4.5% for TESA-blot and epi-ELISA and 6.8% for TESA-ELISA. Sera from urban dogs from Santos, Sao Paulo, where these diseases are absent, yielded negative results. TESA-blot was the only method that distinguished dogs infected with T cruzi from those infected with Leishmania chagasi and/or Trypanosoma evansi. (C) 2009 Published by Elsevier B.V.

Occurrence of phytoplasma associated with sugarcane yellow leaf syndrome in three regions of Sao Paulo State, Brazil

Sugarcane yellow leaf syndrome caused serious damage to crops in the Sao Paulo State, Brazil, in the 1990`s. The syndrome was also reported in other countries and investigations into the etiology revealed an association between the disease and virus and/or phytoplasma. The disease is potentially important and occurs endemically in that State, and for this reason the present study was conducted in order to demonstrate the occurrence of phytoplasma in three traditional sugarcane-producing areas, in Sao Paulo State, through molecular detection From naturally infected plants. Symptomatic plants belonging to varieties SP71-6163, SP71-6180 and SP89-1115 were sampled from Piracicaba, Jau and Ribeirao Preto, and total DNA was extracted from foliar tissues. Nested PCR was conducted with primer pairs P1/ Tint-16F2n/R2, and the amplified products were analyzed by electrophoresis on agarose gels. Amplified DNA fragments of 1.2 kb evidenced the presence of phytoplasma in 36% of symptomatic plants and revealed its Occurrence in all sampled regions. The results demonstrated that phytoplasma is associated with the disease and that it is important to keep a safe inspection of nurseries and monitoring plants in the field, as well as to Select Sugarcane genotypes with a good level of resistance in breeding programs.

A plateau detected in lead accumulation in subsurface deciduous enamel from individuals exposed to lead may be useful to identify children and regions exposed to higher levels of lead

In a previous study, we showed 4 times more lead in surface deciduous enamel (1.9-5.9 mu m) of a notoriously contaminated area (Bauru, Sao Paulo State, Brazil) in comparison to samples from a region with no lead contamination described (Ribeirao Preto, Sao Paulo State, Brazil). The samples from the more superficial enamel (1.9-3.18 mu m) showed higher amounts of lead and the highest variability, while in the subsurface enamel (3.18-5.9 mu m) a plateau in lead content was detected in children living in the contaminated environment (around 600 mu g/g). Here we expand our previous study, and use only samples obtained from subsurface enamel (Ribeirao Preto, n = 186; Bauru, n = 20). We tried to distinguish regions with more children with lead above the threshold of 600 mu g/g of lead in enamel. We tested whether differences in the percentage of children with ""high"" lead (>= 600 mu g/g) could be observed among the different Kindergartens studied in Ribeirao Preto. We also tested whether these results were different from the ones provided by conventional comparison of the data. Ribeirao Preto showed almost 4 times less lead than Bauru (p < 0.0001), and a statistically significant difference was found only in Ribeirao Preto between Kindergarten 2 and 5 (p<0.01). Twelve percent of the children from Ribeirao Preto had ""high"" lead, while 55% of the children from Bauru did so. However, when we looked at the percentages of children with ""high"" lead in each Kindergarten, and compared them, a whole new picture emerged, in which we could see children with ""high"" lead concentrated mainly in 3 Kindergartens from Ribeirao Preto, with Kindergarten 5 with 33% of the children with ""high"" lead, being statistically different from all Kindergartens, except 4 and 6. The threshold of 600 mu g/g of lead in subsurface enamel was tentatively settled here after the plateau seen in exposed children, and enabled us to identify locations with more children exposed to a higher amount of lead. (C) 2008 Elsevier Inc. All rights reserved.