Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses

The Dengue has become a global public health threat, with over 100 million infections annually; to date there is no specific vaccine or any antiviral drug. The structures of the envelope (E) proteins of the four known serotype of the dengue virus (DENV) are already known, but there are insufficient molecular details of their structural behavior in solution in the distinct environmental conditions in which the DENVs are submitted, from the digestive tract of the mosquito up to its replication inside the host cell. Such detailed knowledge becomes important because of the multifunctional character of the E protein: it mediates the early events in cell entry, via receptor endocytosis and, as a class II protein, participates determinately in the process of membrane fusion. The proposed infection mechanism asserts that once in the endosome, at low pH, the E homodimers dissociate and insert into the endosomal lipid membrane, after an extensive conformational change, mainly on the relative arrangement of its three domains. In this work we employ all-atom explicit solvent Molecular Dynamics simulations to specify the thermodynamic conditions in that the E proteins are induced to experience extensive structural changes, such as during the process of reducing pH. We study the structural behavior of the E protein monomer at acid pH solution of distinct ionic strength. Extensive simulations are carried out with all the histidine residues in its full protonated form at four distinct ionic strengths. The results are analyzed in detail from structural and energetic perspectives, and the virtual protein movements are described by means of the principal component analyses. As the main result, we found that at acid pH and physiological ionic strength, the E protein suffers a major structural change; for lower or higher ionic strengths, the crystal structure is essentially maintained along of all extensive simulations. On the other hand, at basic pH, when all histidine residues are in the unprotonated form, the protein structure is very stable for ionic strengths ranging from 0 to 225 mM. Therefore, our findings support the hypothesis that the histidines constitute the hot points that induce configurational changes of E protein in acid pH, and give extra motivation to the development of new ideas for antivirus compound design.

Air quality simulations for Londrina region, Brazil

The objective of this work were apply and provide a preliminary evaluation of the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) performance, for Londrina region. We performed comparison with measurements obtained in meteorological stations. The model was configured to run with three domains with 27,9 and 3 km of grid resolution, using the ndown program and also was realized a simulation with the model configured to run with a single domain using a land use file based in a classified image for region of MODIS sensor. The emission files to supply the chemistry run were generated based in the work of Martins et al., 2012. RADM2 chemical mechanism and MADE/SORGAM modal aerosol models were used in the simulations. The results demonstrated that model was able to represent coherently the formation and dispersion of the pollution in Metropolitan Region of Londrina and also the importance of using the appropriate land use file for the region.

Notes and new taxa in Acanthoderini (Coleoptera: Cerambycidae: Lamiinae). V. Three new genera and notes on Irundisaua.

Generic characters of Irundisaua Martins & Galileo, 2005 are expanded (antennal formula, width of prosternal process inferior or equal to the diameter of procoxa, protibia enlarged and flattened) and two species are transferred from Acanthoderes Audinet-Serville, 1835: I. forsteri (Tippmann, 1960) comb. nov from Peru and Brazil (Amazonas) and I. ucayalensis (Tippmann,1960) comb. nov from Ecuador, Peru and Brazil (Amazonas).Three new genera are described: (1) Catuana gen. nov., type species, C. spinicornis (Tippmann, 1960) comb. nov, characterized by the mesosternal tubercle; (2) Mundeu gen. nov, type species, M. maculicollis (Bates, 1861) comb. nov, with rounded sides of protorax and expanded protibiae; (3) Urangaua gen. nov, with eyes divided and finelly granulated, length of antenomeres III-IV subequal to V-XI; the genus is proposed of two species: U. analis Melzer, 1935 comb. nov, type species, and U. subanalis (Zajciw,1964) comb. nov. A key to the species of Urangaua is added.

Characterization of Primary Isolates of HIV Type 1 CRF28_BF, CRF29_BF, and Unique BF Recombinants Circulating in Sao Paulo, Brazil

We report for the first time the genetic and biological characterization of 10 HIV-1 primary isolates representing CRF28_BF and CRF29_BF together with additional unique BF recombinant forms (URFs) obtained by PBMC cocultivation. Recombination is an important factor promoting the increase in the genetic diversity of HIV-1. Notably, more than 20% of HIV-1 sequences worldwide were recombinants. Several recombinant viruses were reported in Brazil, and six circulating recombinant forms (CRFs) have been identified (CRF28_BF, CRF29_BF, CRF31_BC, CRF39_BF, CRF40_BF, and CRF46_BF). CRF28_BF and CRF29_BF were found to infect almost 30% of the patients in Sao Paulo State. The near full-length genomes of these 10 primary isolates were amplified by nested PCR in three overlapping segments, purified, and sequenced. Three samples were related to CRF28_BF, three to CRF29_BF, and four were unique recombinant forms (URFs), as determined by their breakpoint profile determined with the jpHMM program. Additionally, the coreceptor usage of these isolates was investigated in vitro using GHOST assays, which revealed three dual-tropic (X4/R5) viruses, four lymphotropic (X4) viruses, and three macrophage-tropic (R5) viruses with different V3-loop motifs, which challenges the notion that GWGR-carrying viruses are macrophage-tropic only. In sum, we report a much-anticipated well-characterized panel of viruses representing CRF28_BF, CRF29_BF, and URFs from Sao Paulo State, Brazil.

Hollow-fiber liquid-phase microextraction of amphetamine-type stimulants in human hair samples

A fast method was optimized and validated in order to quantify amphetamine-type stimulants (amphetamine, AMP; methamphetamine, MAMP; fenproporex, FPX; 3,4-methylenedioxymethamphetamine, MDMA; and 3,4-methylenedioxyamphetamine, MDA) in human hair samples. The method was based in an initial procedure of decontamination of hair samples (50 mg) with dichloromethane, followed by alkaline hydrolysis and extraction of the amphetamines using hollow-fiber liquid-phase micro extraction (HF-LPME) in the three-phase mode. Gas chromatography-mass spectrometry (GC-MS) was used for identification and quantification of the analytes. The LoQs obtained for all amphetamines (around 0.05 ng/mg) were below the cut-off value (0.2 ng/mg) established by the Society of Hair Testing (SoHT). The method showed to be simple and precise. The intra-day and inter-day precisions were within 10.6% and 11.4%, respectively, with the use of only two deuteratecl internal standards (AMP-d5 and MDMA-d5). By using the weighted least squares linear regression (1/x(2)), the accuracy of the method was satisfied in the lower concentration levels (accuracy values better than 87%). Hair samples collected from six volunteers who reported regular use of amphetamines were submitted to the developed method. Drug detection was observed in all samples of the volunteers. (c) 2012 Elsevier B.V. All rights reserved.

Mandibular Angle Fracture Treated With New Three-Dimensional Grid Miniplate

Fractures of the mandibular angle deserve particular attention because they represent the highest percentage of mandibular fractures and have the highest postsurgical complication rate, making them the most challenging and unpredictable mandibular fractures to treat. Despite the evolution in the treatment of maxillofacial trauma and fixation methods, no single treatment modality has been revealed to be ideal for mandibular angle fractures. Several methods of internal fixation have been studied with great variation in complications rates, especially postoperative infections. Recently, new studies have shown reduction of postsurgical complications rates using three-dimensional plates to treat mandibular angle fractures. Nevertheless, only few surgeons have used this type of plate for the treatment of mandibular angle fractures. The aim of this clinical report was to describe a case of a patient with a mandibular angle fracture treated by an intraoral approach and a three-dimensional rectangular grid miniplate with 4 holes, which was stabilized with monocortical screws. The authors show a follow-up of 8 months, without infection and with occlusal stability.

Analysis of three Xanthomonas axonopodis pv. citri effector proteins in pathogenicity and their interactions with host plant proteins

Xanthomonas axonopodis pv. citri, the bacterium responsible for citrus canker, uses effector proteins secreted by a type III protein secretion system to colonize its hosts. Among the putative effector proteins identified for this bacterium, we focused on the analysis of the roles of AvrXacE1, AvrXacE2 and Xac3090 in pathogenicity and their interactions with host plant proteins. Bacterial deletion mutants in avrXacE1, avrXacE2 and xac3090 were constructed and evaluated in pathogenicity assays. The avrXacE1 and avrXacE2 mutants presented lesions with larger necrotic areas relative to the wild-type strain when infiltrated in citrus leaves. Yeast two-hybrid studies were used to identify several plant proteins likely to interact with AvrXacE1, AvrXacE2 and Xac3090. We also assessed the localization of these effector proteins fused to green fluorescent protein in the plant cell, and observed that they co-localized to the subcellular spaces in which the plant proteins with which they interacted were predicted to be confined. Our results suggest that, although AvrXacE1 localizes to the plant cell nucleus, where it interacts with transcription factors and DNA-binding proteins, AvrXacE2 appears to be involved in lesion-stimulating disease 1-mediated cell death, and Xac3090 is directed to the chloroplast where its function remains to be clarified.

Host-guest interactions between xanthones and water: the role of O-H center dot center dot center dot O, C-H center dot center dot center dot O, and pi center dot center dot center dot pi contacts in the channel- and cage-type frameworks

In this article were studied two xanthone derivatives known as 1,5-dihydroxy-8-methoxyxanthone (I) and 1,3,7-trihydroxy-8-methoxyxanthone (II), which show one water molecule into their crystal structures. In xanthone I, there are water wires contributing to build up channel-like cavities along the c axis, whereas in xanthone II the water is surrounded by three xanthone molecules forming a cage-type structure. The geometries of I and II were optimized using the density functional theory method with B3LYP functional, and the results were compared with crystal structure. Both theoretical and experimental investigations reveal a concordance between structural parameters, with the xanthone core presenting an almost flat conformation and substituents adopting the more stable orientations. In the two compounds, the hydroxyl group linked at position 1 is involved in a resonance-assisted hydrogen bond with the carbonyl group. Besides, the supramolecular arrangement of the host/guest systems are stabilized mainly by classical intermolecular hydrogen bonds (O-H center dot center dot center dot O) involving xanthone-to-water and xanthone-to-xanthone. In addition, C-H center dot center dot center dot O weak hydrogen bonds, as well as pi-pi interactions play an important role to stabilize the crystal self-assembly of xanthones I and II. The results reported here underline the role of inclusion of water molecules and their different arrangement into the crystal structure of two xanthone host/guest systems.

Characterization of selectivity and pharmacophores of type 1 sea anemone toxins by screening seven Na-v sodium channel isoforms

During their evolution, animals have developed a set of cysteine-rich peptides capable of binding various extracellular sites of voltage-gated sodium channels (VGSC). Sea anemone toxins that target VGSCs delay their inactivation process, but little is known about their selectivities. Here we report the investigation of three native type 1 toxins (CGTX-II, delta-AITX-Bcg1a and delta-AITX-Bcg1b) purified from the venom of Bunodosoma cangicum. Both delta-AITX-Bcg1a and delta-AITX-Bcg1b toxins were fully sequenced. The three peptides were evaluated by patch-clamp technique among Nav1.1-1.7 isoforms expressed in mammalian cell lines, and their preferential targets are Na(v)1.5 > 1.6 > 1.1. We also evaluated the role of some supposedly critical residues in the toxins which would interact with the channels, and observed that some substitutions are not critical as expected. In addition, CGTX-II and delta-AITX-Bcg1a evoke different shifts in activation/inactivation Boltzmann curves in Nav1.1 and 1.6. Moreover, our results suggest that the interaction region between toxins and VGSCs is not restricted to the supposed site 3 (S3-54 linker of domain IV), and this may be a consequence of distinct surface of contact of each peptide vs. targeted channel. Our data suggest that the contact surfaces of each peptide may be related to their surface charges, as CGTX-II is more positive than delta-AITX-Bcg1a and delta-AITX-Bcg1b. (C) 2011 Elsevier Inc. All rights reserved.

Redescriptions of two species and descriptions of three new species of the louse genus Bizarrifrons Eichler, 1938 (Phthiraptera: Ischnocera: Philopteridae)

Redescriptions of Bizarrifrons magus (Nitzsch [in Giebel], 1866), the type species of Bizarrifrons, and B. picturatus Carriker & Diaz-Ungria, 1961 are given based on material from their type hosts. The nymphal instars of these two species are described and illustrated for the first time. Also, three new species are named and described: B. latifrons, from the russet-backed oropendola, Psarocolius angustifrons alfredi (Des Murs, 1856); B. wecksteini, from the Amazonian oropendola, Psarocolius b. bifasciatus (Spix, 1824); and B. quasisymmetricus, from the solitary cacique, Cacicus solitarius (Vieillot, 1816) (Passeriformes: Icteridae). Two species-groups are proposed, and a checklist and a key for the species of Bizarrifrons are also included. Sequences of a portion of the mitochondrial cytochrome oxidase I (COI) and the nuclear elongation factor 1 alpha (EF-1 alpha) genes for two species are given for the first time in this genus.

Three time-based scale formulations for the two-stage lot sizing and scheduling in process industries

In this paper, we propose three novel mathematical models for the two-stage lot-sizing and scheduling problems present in many process industries. The problem shares a continuous or quasi-continuous production feature upstream and a discrete manufacturing feature downstream, which must be synchronized. Different time-based scale representations are discussed. The first formulation encompasses a discrete-time representation. The second one is a hybrid continuous-discrete model. The last formulation is based on a continuous-time model representation. Computational tests with state-of-the-art MIP solver show that the discrete-time representation provides better feasible solutions in short running time. On the other hand, the hybrid model achieves better solutions for longer computational times and was able to prove optimality more often. The continuous-type model is the most flexible of the three for incorporating additional operational requirements, at a cost of having the worst computational performance. Journal of the Operational Research Society (2012) 63, 1613-1630. doi:10.1057/jors.2011.159 published online 7 March 2012

Equid herpesvirus type-1 exhibits neurotropism and neurovirulence in a mouse model

Intranasal inoculation of equid herpesvirus type-1 (EHV-1) Brazilian strains A4/72 and A9/92 induced an acute and lethal infection in four different inbred mouse strains. Clinical and neurological signs appeared between the 2nd and 3rd day post inoculation (dpi) and included weight loss, ruffled fur, a hunched posture, crouching in corners, nasal and ocular discharges, dyspnoea, dehydration and increased salivation. These signs were followed by increased reactivity to external stimulation, seizures, recumbency and death. The virus was recovered consistently from the brain and viscera of all mice with neurological signs. Histopathological changes consisted of leptomeningitis, focal haemorrhage, ventriculitis, neuronal degeneration and necrosis, neuronophagia, non-suppurative inflammation, multifocal gliosis and perivascular infiltration of polymorphonuclear and mononuclear cells. Immunohistochemical examination demonstrated that EHV-1 strains A4/72 and A9/92 replicated in neurons of the olfactory bulb, the cortex and the hippocampus. In contrast, mice inoculated with the EHV-1 Brazilian strain A3/97 showed neither weight loss nor apparent clinical or neurological signs; however, the virus was recovered consistently from their lungs at 3 dpi. These three EHV-1 strains showed distinct degrees of virulence and tissue tropism in mice. EHV-1 strains A4/72 and A9/92 exhibited a high degree of central nervous system tropism with neuroinvasion and neurovirulence. EHV-1 strain A3/97 was not neurovirulent despite being detected in the brains of infected BALB/c nude mice. These findings indicate that several inbred mouse strains are susceptible to neuropathogenic EHV-1 strains and should be useful models for studying the pathogenesis and mechanisms contributing to EHV-induced myeloencephalopathy in horses. (C) 2011 Elsevier Ltd. All rights reserved.

Three Postpartum Antiretroviral Regimens to Prevent Intrapartum HIV Infection

BACKGROUND The safety and efficacy of adding antiretroviral drugs to standard zidovudine prophylaxis in infants of mothers with human immunodeficiency virus (HIV) infection who did not receive antenatal antiretroviral therapy (ART) because of late identification are unclear. We evaluated three ART regimens in such infants. METHODS Within 48 hours after their birth, we randomly assigned formula-fed infants born to women with a peripartum diagnosis of HIV type 1 (HIV-1) infection to one of three regimens: zidovudine for 6 weeks (zidovudine-alone group), zidovudine for 6 weeks plus three doses of nevirapine during the first 8 days of life (two-drug group), or zidovudine for 6 weeks plus nelfinavir and lamivudine for 2 weeks (three-drug group). The primary outcome was HIV-1 infection at 3 months in infants uninfected at birth. RESULTS A total of 1684 infants were enrolled in the Americas and South Africa (566 in the zidovudine-alone group, 562 in the two-drug group, and 556 in the three-drug group). The overall rate of in utero transmission of HIV-1 on the basis of Kaplan-Meier estimates was 5.7% (93 infants), with no significant differences among the groups. Intrapartum transmission occurred in 24 infants in the zidovudine-alone group (4.8%; 95% confidence interval [CI], 3.2 to 7.1), as compared with 11 infants in the two-drug group (2.2%; 95% CI, 1.2 to 3.9; P=0.046) and 12 in the three-drug group (2.4%; 95% CI, 1.4 to 4.3; P=0.046). The overall transmission rate was 8.5% (140 infants), with an increased rate in the zidovudine-alone group (P=0.03 for the comparisons with the two-and three-drug groups). On multivariate analysis, zidovudine monotherapy, a higher maternal viral load, and maternal use of illegal substances were significantly associated with transmission. The rate of neutropenia was significantly increased in the three-drug group (P < 0.001 for both comparisons with the other groups). CONCLUSIONS In neonates whose mothers did not receive ART during pregnancy, prophylaxis with a two-or three-drug ART regimen is superior to zidovudine alone for the prevention of intrapartum HIV transmission; the two-drug regimen has less toxicity than the three-drug regimen. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development [NICHD] and others; ClinicalTrials.gov number, NCT00099359.)

Identification of Regions Involved in Substrate Binding and Dimer Stabilization within the Central Domains of Yeast Hsp40 Sis1

Protein folding, refolding and degradation are essential for cellular life and are regulated by protein homeostatic processes such those that involve the molecular chaperone DnaK/Hsp70 and its co-chaperone DnaJ. Hsp70 action is initiated when proteins from the DnaJ family bind an unfolded protein for delivery purposes. In eukaryotes, the DnaJ family can be divided into two main groups, Type I and Type II, represented by yeast cytosolic Ydj1 and Sis1, respectively. Although sharing some unique features both members of the DnaJ family, Ydj1 and Sis1 are structurally and functionally distinct as deemed by previous studies, including the observation that their central domains carry the structural and functional information even in switched chimeras. In this study, we combined several biophysical tools for evaluating the stability of Sis1 and mutants that had the central domains (named Gly/Met rich domain and C-terminal Domain I) deleted or switched to those of Ydj1 to gain insight into the role of these regions in the structure and function of Sis1. The mutants retained some functions similar to full length wild-type Sis1, however they were defective in others. We found that: 1) Sis1 unfolds in at least two steps as follows: folded dimer to partially folded monomer and then to an unfolded monomer. 2) The Gly/Met rich domain had intrinsically disordered characteristics and its deletion had no effect on the conformational stability of the protein. 3) The deletion of the C-terminal Domain I perturbed the stability of the dimer. 4) Exchanging the central domains perturbed the conformational stability of the protein. Altogether, our results suggest the existence of two similar subdomains in the C-terminal domain of DnaJ that could be important for stabilizing each other in order to maintain a folded substrate-binding site as well as the dimeric state of the protein.

Clinical microscopic analysis of protaper retreatment system efficacy considering root canal thirds using three endodontic sealers

To evaluate the efficacy of ProTaper Universal rotary retreatment system and the influence of sealer type on the presence of filling debris in the reinstrumented canals viewed in an operative clinical microscope. Forty-five palatal root canals of first molars were filled with gutta-percha and one of the following sealers: G1, EndoFill; G2, AH Plus; G3, Sealapex. The canals were then reinstrumented with ProTaper Universal rotary system. Roots were longitudinally sectioned and examined under an operative clinical microscope (10x), and the amount of filling debris on canal walls was analyzed using the AutoCAD 2004 software. A single operator used a specific software tool to outline the canal area and the filling debris area in each third (cervical, middle, and apical), as well as the total canal area. Data were analyzed by Kruskal-Wallis test and Tukey test at P < 0.05. Sealapex demonstrated significant differences in the average of filling debris area/canal among the 3 thirds. This group revealed that apical third showed more debris than the both cervical and middle third (P < 0.0001). Endofill presented significantly more filling debris than Sealapex in the cervical third (P < 0.05). In the middle (P = 0.12) and apical third (P = 0.10), there were no differences amongst groups. Debris was left in all canal thirds, regardless of the retreatment technique. The greatest differences between techniques and sealers were found in the cervical third. Microsc. Res. Tech. 75:12331236, 2012. (C) 2012 Wiley Periodicals, Inc.