Genetic variability and demographic history of Heliothis virescens (Lepidoptera: Noctuidae) populations from Brazil inferred by mtDNA sequences

Intra-and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton-and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's F-S parameters. In addition, high values of haplotype diversity ((H) over cap) and low values of nucleotide diversity (pi), combined with a high number of low frequency haplotypes and values of theta(pi)<theta(W), suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.

Diversity and Adaptation of Human Respiratory Syncytial Virus Genotypes Circulating in Two Distinct Communities: Public Hospital and Day Care Center

HRSV is one of the most important pathogens causing acute respiratory tract diseases as bronchiolitis and pneumonia among infants. HRSV was isolated from two distinct communities, a public day care center and a public hospital in Sao Jose do Rio Preto - SP, Brazil. We obtained partial sequences from G gene that were used on phylogenetic and selection pressure analysis. HRSV accounted for 29% of respiratory infections in hospitalized children and 7.7% in day care center children. On phylogenetic analysis of 60 HRSV strains, 48 (80%) clustered within or adjacent to the GA1 genotype; GA5, NA1, NA2, BA-IV and SAB1 were also observed. SJRP GA1 strains presented variations among deduced amino acids composition and lost the potential O-glycosilation site at amino acid position 295, nevertheless this resulted in an insertion of two potential O-glycosilation sites at positions 296 and 297. Furthermore, a potential O-glycosilation site insertion, at position 293, was only observed for hospital strains. Using SLAC and MEME methods, only amino acid 274 was identified to be under positive selection. This is the first report on HRSV circulation and genotypes classification derived from a day care center community in Brazil.

Phylogeny of Lundia (Bignoniaceae) based on ndhF and PepC sequences

The circumscription of genera belonging to tribe Bignonieae (Bignoniaceae) has traditionally been complex, with only a few genera having stable circumscriptions in the various classification systems proposed for the tribe. The genus Lundia, for instance, is well characterized by a series of morphological synapomorphies and its circumscription has remained quite stable throughout its history. Despite the stable circumscription of Lundia, the circumscription of species within the genus has remained problematic. This study aims to reconstruct the phylogeny of Lundia in order to refine species circumscriptions, gain a better understanding of relationships between taxa, and identify potential morphological synapomorphies for species and major clades. We sampled 26 accessions representing 13 species of Lundia, and 5 outgroups, and reconstructed the phylogeny of the genus using a chloroplast (ndhF) and a nuclear marker (PepC). Data derived from sequences of the individual loci were analyzed using parsimony and Bayesian inference, and the combined molecular dataset was analyzed with Bayesian methods. The monophyly of Lundia nitidula, a species with a particularly complex circumscription, was tested using Shimodaira-Hasegawa (SH) test and the approximately unbiased test for phylogenetic tree selection (AU test). In addition, 40 morphological characters were mapped onto the tree that resulted from the analysis of the combined molecular dataset in order to identify morphological synapomorphies of individual species and major clades. Lundia and most species currently recognized within the genus were strongly supported as monophyletic in all analyses. One species, Lundia nitidula, was not resolved as monophyletic, but the monophyly of this species was not rejected by the AU and SH tests. Lundia sect. Eriolundia is resolved as paraphyletic in all analyses, while Lundia sect. Eulundia is monophyletic and supported by the same morphological characters traditionally used to circumscribe this section. The phylogeny of Lundia contributed important information for a better circumscription of species and served as basis the taxonomic revision of the genus.

In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements

In silico analyses of Leishmania spp. genome data are a powerful resource to improve the understanding of these pathogens' biology. Trypanosomatids such as Leishmania spp. have their protein-coding genes grouped in long polycistronic units of functionally unrelated genes. The control of gene expression happens by a variety of posttranscriptional mechanisms. The high degree of synteny among Leishmania species is accompanied by highly conserved coding sequences (CDS) and poorly conserved intercoding untranslated sequences. To identify the elements involved in the control of gene expression, we conducted an in silico investigation to find conserved intercoding sequences (CICS) in the genomes of L major, L infantum, and L braziliensis. We used a combination of computational tools, such as Linux-Shell, PERL and R languages, BLAST, MSPcrunch, SSAKE, and Pred-A-Term algorithms to construct a pipeline which was able to: (i) search for conservation in target-regions, (ii) eliminate CICS redundancy and mask repeat elements, (iii) predict the mRNA's extremities, (iv) analyze the distribution of orthologous genes within the generated LeishCICS-clusters, (v) assign GO terms to the LeishCICS-clusters. and (vi) provide statistical support for the gene-enrichment annotation. We associated the LeishCICS-cluster data, generated at the end of the pipeline, with the expression profile oft. donovani genes during promastigote-amastigote differentiation, as previously evaluated by others (GEO accession: GSE21936). A Pearson's correlation coefficient greater than 0.5 was observed for 730 LeishCICS-clusters containing from 2 to 17 genes. The designed computational pipeline is a useful tool and its application identified potential regulatory cis elements and putative regulons in Leishmania. (C) 2012 Elsevier B.V. All rights reserved.

MRKAd5 HIV-1 Gag/Pol/Nef Vaccine-Induced T-Cell Responses Inadequately Predict Distance of Breakthrough HIV-1 Sequences to the Vaccine or Viral Load

Background: The sieve analysis for the Step trial found evidence that breakthrough HIV-1 sequences for MRKAd5/HIV-1 Gag/Pol/Nef vaccine recipients were more divergent from the vaccine insert than placebo sequences in regions with predicted epitopes. We linked the viral sequence data with immune response and acute viral load data to explore mechanisms for and consequences of the observed sieve effect. Methods: Ninety-one male participants (37 placebo and 54 vaccine recipients) were included; viral sequences were obtained at the time of HIV-1 diagnosis. T-cell responses were measured 4 weeks post-second vaccination and at the first or second week post-diagnosis. Acute viral load was obtained at RNA-positive and antibody-negative visits. Findings: Vaccine recipients had a greater magnitude of post-infection CD8+ T cell response than placebo recipients (median 1.68% vs 1.18%; p = 0.04) and greater breadth of post-infection response (median 4.5 vs 2; p = 0.06). Viral sequences for vaccine recipients were marginally more divergent from the insert than placebo sequences in regions of Nef targeted by pre-infection immune responses (p = 0.04; Pol p = 0.13; Gag p = 0.89). Magnitude and breadth of pre-infection responses did not correlate with distance of the viral sequence to the insert (p. 0.50). Acute log viral load trended lower in vaccine versus placebo recipients (estimated mean 4.7 vs 5.1) but the difference was not significant (p = 0.27). Neither was acute viral load associated with distance of the viral sequence to the insert (p>0.30). Interpretation: Despite evidence of anamnestic responses, the sieve effect was not well explained by available measures of T-cell immunogenicity. Sequence divergence from the vaccine was not significantly associated with acute viral load. While point estimates suggested weak vaccine suppression of viral load, the result was not significant and more viral load data would be needed to detect suppression.

Genetic transformation of Citrus sinensis with Citrus tristeza virus (CTV) derived sequences and reaction of transgenic lines to CTV infection

Transgenic Citrus sinensis (L.) Osb. plants, cvs. Valencia and Hamlin, expressing Citrus tristeza virus (CTV) derived sequences were obtained by genetic transformation. The gene constructs were pCTV-CP containing the 25 kDa major capsid protein gene (CTV-CP), pCTV-dsCP containing the same CTV-CP gene in an intron-spliced hairpin construct, and pCTV-CS containing a 559 nt conserved region of the CTV genome. The transgenic lines were identified by PCR and the transgene integration was confirmed by Southern blot. Transgene mRNA could be detected in most transgenic lines containing pCTV-CP or pCTV-CS transgene. The mRNA of pCTV-dsCP transgene was almost undetectable, with very light bands in most analyzed plants. The transgene transcription appears to be closely linked to the type of gene construct. The virus challenge assays reveals that all transgenic lines were infected. However, it was possible to identify propagated clones of transgenic plants of both cultivars studied with a low virus titer, with values similar to the non-inoculated plants (negative control). These results suggested that the transgenic plants present some level of resistance to virus replication. The higher number of clones with low virus titer and where mRNA could not be detected or was presented in a very light band was found for pCTV-dsCP-derived transgenic lines.

The effect of implant design on insertion torque and immediate micromotion

Objectives: To evaluate the effect of insertion torque on micromotion to a lateral force in three different implant designs. Material and methods: Thirty-six implants with identical thread design, but different cutting groove design were divided in three groups: (1) non-fluted (no cutting groove, solid screw-form); (2) fluted (901 cut at the apex, tap design); and (3) Blossomt (Patent pending) (non-fluted with engineered trimmed thread design). The implants were screwed into polyurethane foam blocks and the insertion torque was recorded after each turn of 901 by a digital torque gauge. Controlled lateral loads of 10N followed by increments of 5 up to 100N were sequentially applied by a digital force gauge on a titanium abutment. Statistical comparison was performed with two-way mixed model ANOVA that evaluated implant design group, linear effects of turns and displacement loads, and their interaction. Results: While insertion torque increased as a function of number of turns for each design, the slope and final values increased (Po0.001) progressively from the Blossomt to the fluted to the non-fluted design (M +/- standard deviation [SD] = 64.1 +/- 26.8, 139.4 +/- 17.2, and 205.23 +/- 24.3 Ncm, respectively). While a linear relationship between horizontal displacement and lateral force was observed for each design, the slope and maximal displacement increased (Po0.001) progressively from the Blossomt to the fluted to the non-fluted design (M +/- SD 530 +/- 57.7, 585.9 +/- 82.4, and 782.33 +/- 269.4 mm, respectively). There was negligible to moderate levels of association between insertion torque and lateral displacement in the Blossomt, fluted and non-fluted design groups, respectively. Conclusion: Insertion torque was reduced in implant macrodesigns that incorporated cutting edges, and lesser insertion torque was generally associated with decreased micromovement. However, insertion torque and micromotion were unrelated within implant designs, particularly for those designs showing the least insertion torque.

Abundance and Genetic Diversity of nifH Gene Sequences in Anthropogenically Affected Brazilian Mangrove Sediments

Although mangroves represent ecosystems of global importance, the genetic diversity and abundance of functional genes that are key to their functioning scarcely have been explored. Here, we present a survey based on the nifH gene across transects of sediments of two mangrove systems located along the coast line of Sao Paulo state (Brazil) which differed by degree of disturbance, i.e., an oil-spill-affected and an unaffected mangrove. The diazotrophic communities were assessed by denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR), and clone libraries. The nifH gene abundance was similar across the two mangrove sediment systems, as evidenced by qPCR. However, the nifH-based PCR-DGGE profiles revealed clear differences between the mangroves. Moreover, shifts in the nifH gene diversities were noted along the land-sea transect within the previously oiled mangrove. The nifH gene diversity depicted the presence of nitrogen-fixing bacteria affiliated with a wide range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and also a group of anaerobic sulfate-reducing bacteria. We also detected a unique mangrove-specific cluster of sequences denoted Mgv-nifH. Our results indicate that nitrogen-fixing bacterial guilds can be partially endemic to mangroves, and these communities are modulated by oil contamination, which has important implications for conservation strategies.

Influence of Pleural Drain Insertion in Lung Function of Patients Undergoing Coronary Artery Bypass Grafting

Background and objectives: Longitudinal, prospective, randomized, blinded Trial to assess the influence of pleural drain (non-toxic PVC) site of insertion on lung function and postoperative pain of patients undergoing coronary artery bypass grafting in the first three days post-surgery and immediately after chest tube removal. Method: Thirty six patients scheduled for elective myocardial revascularization with cardiopulmonary bypass (CPB) were randomly allocated into two groups: SX group (subxiphoid) and IC group (intercostal drain). Spirometry, arterial blood gases, and pain tests were recorded. Results: Thirty one patients were selected, 16 in SX group and 15 in IC group. Postoperative (PO) spirometric values were higher in SX than in IC group (p < 0.05), showing less influence of pleural drain location on breathing. PaO2 on the second PO increased significantly in SX group compared with IC group (p < 0.0188). The intensity of pain before and after spirometry was lower in SX group than in IC group (p < 0.005). Spirometric values were significantly increased in both groups after chest tube removal. Conclusion: Drain with insertion in the subxiphoid region causes less change in lung function and discomfort, allowing better recovery of respiratory parameters.

ZETA DETERMINANT FOR DOUBLE SEQUENCES OF SPECTRAL TYPE

We study the spectral functions, and in particular the zeta function, associated to a class of sequences of complex numbers, called of spectral type. We investigate the decomposability of the zeta function associated to a double sequence with respect to some simple sequence, and we provide a technique for obtaining the first terms in the Laurent expansion at zero of the zeta function associated to a double sequence.

Totally implantable venous catheters: insertion via internal jugular vein with pocket implantation in the arm is an alternative for diseased thoracic walls

Purpose: Insertion of totally implantable catheters via deep vessels that drain into the superior vena cava results in a lower incidence of venous thrombosis and infection as compared to catheters inserted into femoral and arm veins. Superior vena cava obstruction and inadequacy of the thoracic wall are conditions that prevent reservoir implantation in the chest wall. In this article, we describe a technical innovation that enables the pocket to be fixed in the arm while still allowing access to be achieved via the internal jugular vein. Method: The procedure reported maintains the use of the internal jugular vein for access even when the patient's chest is not suited for reservoir implantation, which is localized in the arm. Results: The procedure was successful and no complications occurred. The position of the catheter tip did not alter with arm movement. Conclusion: The implantation of a port reservoir in the arm following venous access via the internal jugular vein is both safe and convenient.

Mini-implant insertion based on tooth crown references: a guide-free technique

Mini-implant insertion requires accurate surgical technique. This study shows an insertion technique using only tooth crown references; its scientific basis is evaluated radiographically. The sample consisted of 213 inter-radicular septa, evaluated in 53 bitewing radiographs. The proximal contour of adjacent tooth crowns was used to define septum width. The midpoint of the septum width was linked to the interdental contact point to determine septum midline. The distances from septum midline to "mesial and distal teeth were measured to evaluate the septum midline centralization degree in two different septum heights. The difference between mesial and distal distances represented the septum midline deviation degree. The mesial and distal distances were compared by t-tests, and the septum midline deviation was correlated with septum height using Pearson's correlation test. The mesial and distal distances were not statistically different in the midpoint of the septum height, but they were different at the apical septum height. There was a moderate correlation (r = 0.45) between septum midline deviation and septum height. The tooth crown references evaluated on interproximal radiographs determine a high centralization degree of the septum midline on which the insertion site could be defined. The greater centralization degree was observed at the coronal septum area.

Phylogenetic analysis of complete genome sequences of hepatitis B virus from an Afro-Colombian community: presence of HBV F3/A1 recombinant strain

Background: Hepatitis B virus (HBV) infection is one of the most prevalent viral infections in humans and represents a serious public health problem. In Colombia, our group reported recently the presence of subgenotypes F3, A2 and genotype G in Bogota. The aim of this study was to characterize the HBV genotypes circulating in Quibdo, the largest Afro-descendant community in Colombia. Sixty HBsAg-positive samples were studied. A fragment of 1306 bp (S/POL) was amplified by nested PCR. Positive samples to S/POL fragment were submitted to PCR amplification of the HBV complete genome. Findings: The distribution of HBV genotypes was: A1 (52.17%), E (39.13%), D3 (4.3%) and F3/A1 (4.3%). An HBV recombinant strain subgenotype F3/A1 was found for the first time. Conclusions: This study is the first analysis of complete HBV genome sequences from Afro-Colombian population. It was found an important presence of HBV/A1 and HBV/E genotypes. A new recombinant strain of HBV genotype F3/A1 was reported in this population. This fact may be correlated with the introduction of these genotypes in the times of slavery.

Mechanical Performance of Cylindrical and Dual-Core Pedicle Screws After Repeated Insertion

Study Design. Ex vivo study of the mechanical performance of cylindrical and dual-core pedicle screws after insertion, removal, and reinsertion in the same hole. Objective. To evaluate the effect of repeated use of same screw hole on the insertion torque and the retentive strength of the cylindrical and dual-core screws. Summary of Background Data. Insertion and removal of pedicle screws is sometimes necessary during surgical procedure to assess the integrity of the pilot-hole wall. However, this maneuver may compromise the implant-holding capacity. Methods. Sixty thoracolombar vertebrae (T13-L5), harvested from 10 healthy calves, were used to insert 2 different designs of pedicle screws: cylindrical (5.0-mm outer diameter) and dual-core screws (5.2-mm outer diameter). Three experimental groups were created on the basis of the number of insertions of the screws and 2 subgroups were established according to the core pedicle screw design (dual-core and cylindrical). The insertion torque was measured during initial insertion, second insertion, and third insertion. Pullout screw tests were performed using a universal testing machine to evaluate the pullout strength after initial insertion, second insertion, and third insertion. Results. Significant reductions of 38% in mean insertion torque and 30% in mean pullout strength of dual-core screw were observed between the initial insertion and the third insertion. The cylindrical screw observed significant reductions of 52.5% in mean insertion torque and 42.3% in mean pullout strength between the initial insertion and the third insertion. A reduction of mean insertion torque and pullout strength between the first insertion and the second insertion but without significance was also observed for both types of screws. Conclusion. Insertions and reinsertion of either cylindrical or dual-core pedicle screws have compromised insertion torque and pullout strength of the implants as measured by mechanical tests.

Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii

Abstract Background Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C. Results We have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein. Conclusion We have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.