A Novel Diagnostic Target in the Hepatitis C Virus Genome

Background

Detection and quantification of hepatitis C virus (HCV) RNA is integral to diagnostic and therapeutic regimens. All molecular assays target the viral 5′-noncoding region (5′-NCR), and all show genotype-dependent variation of sensitivities and viral load results. Non-western HCV genotypes have been under-represented in evaluation studies. An alternative diagnostic target region within the HCV genome could facilitate a new generation of assays.

Methods and Findings

In this study we determined by de novo sequencing that the 3′-X-tail element, characterized significantly later than the rest of the genome, is highly conserved across genotypes. To prove its clinical utility as a molecular diagnostic target, a prototype qualitative and quantitative test was developed and evaluated multicentrically on a large and complete panel of 725 clinical plasma samples, covering HCV genotypes 1–6, from four continents (Germany, UK, Brazil, South Africa, Singapore). To our knowledge, this is the most diversified and comprehensive panel of clinical and genotype specimens used in HCV nucleic acid testing (NAT) validation to date. The lower limit of detection (LOD) was 18.4 IU/ml (95% confidence interval, 15.3–24.1 IU/ml), suggesting applicability in donor blood screening. The upper LOD exceeded 10⁻⁹ IU/ml, facilitating viral load monitoring within a wide dynamic range. In 598 genotyped samples, quantified by Bayer VERSANT 3.0 branched DNA (bDNA), X-tail-based viral loads were highly concordant with bDNA for all genotypes. Correlation coefficients between bDNA and X-tail NAT, for genotypes 1–6, were: 0.92, 0.85, 0.95, 0.91, 0.95, and 0.96, respectively; X-tail-based viral loads deviated by more than 0.5 log10 from 5′-NCR-based viral loads in only 12% of samples (maximum deviation, 0.85 log10). The successful introduction of X-tail NAT in a Brazilian laboratory confirmed the practical stability and robustness of the X-tail-based protocol. The assay was implemented at low reaction costs (US$8.70 per sample), short turnover times (2.5 h for up to 96 samples), and without technical difficulties.

Conclusion

This study indicates a way to fundamentally improve HCV viral load monitoring and infection screening. Our prototype assay can serve as a template for a new generation of viral load assays. Additionally, to our knowledge this study provides the first open protocol to permit industry-grade HCV detection and quantification in resource-limited settings.     

Structural insights into enzyme-substrate interaction and characterization of enzymatic intermediates of organic hydroperoxide resistance protein from Xylella fastidiosa

Organic hydroperoxide resistance proteins (Ohr) belong to a family of proteins that possess thiol-dependent peroxidase activity endowed by reactive cysteine residues able to reduce peroxides. The crystal structure of Ohr from Xylella fastidiosa in complex with polyethylene glycol, providing insights into enzyme-substrate interactions is described herein. In addition, crystallographic studies, molecular modeling and biochemical assays also indicated that peroxides derived from long chain fatty acids could be the biological substrates of Ohr. Because different oxidation states of the reactive cysteine were present in the Ohr structures from X. fastidiosa, Pseudomonas aeruginosa and Deinococcus radiodurans it was possible to envisage a set of snapshots along the coordinate of the enzyme-catalyzed reaction. The redox intermediates of X. fastidiosa Ohr observed in the crystals were further characterized in solution by electrospray ionization mass spectrometry and by biochemical approaches. In this study, the formation of an intramolecular disulfide bond and oxidative inactivation through the formation of a sulfonic acid derivative was unequivocally demonstrated for the first time. Because Ohr proteins are exclusively present in bacteria, they may represent promising targets for therapeutical drugs. In this regard, the structural and functional analyses of Ohr presented here might be very useful.     

Morpho-physiology and maize grain yield under periodic soil flooding in successive selection cycles

This study was carried out to evaluate maize plants of different recurrent selection cycles of the variety (Zea mays L.—Saracura-BRS-4154) regarded to genetic gains, morphophysiology, and grain yield, achieved over the selection cycles under intermittent flooding of the soil. This variety has the capacity to survive and produce in temporarily flooded soils and was developed by the National Maize and Sorghum Research Center (EMBRAPA). The experiment was conducted in greenhouse by using ten alternating selection cycles (Cycle 1–18) and BR 107 a variety known for its susceptibility to flooding. The flooding initiated at six-leaf stage by applying 50 mm of water three times a week. At flowering, the following parameters were evaluated: rate of leaf photosynthesis, stomatal conductance, intercellular CO₂ concentration, transpiration rate, photosynthetically active leaf area, root porosity, relative chlorophyll content, grain yield, harvest index, ear length, and interval between male and female flowering. Yield as a function of root porosity and photosynthesis were also evaluated. An index was created in this study, in order to help the discussion of the characteristics evaluated, it was called “Relative Tolerance Value—RTV”, only gaseous exchange measurements was not included in this index. By the way, it was observed throughout the selection cycles an increase in all gaseous exchange parameters, being the cycle 18, the one which presented the greatest averages. RTV for leaf area showed the greatest values for cycles 7 and 18, whereas root porosity, chlorophyll relative content, and harvest index, the greater RTV values were found in cycles 17 and 18. The largest grain yield RTV was observed in cycle 7, followed by cycles 13, 15, and 18. Flooding resulted in longer Anthesis-Silking Interval, especially for the first cycles. At flooding condition, grain yield was strongly related to root porosity (R ² = 0.66). These results showed that the selection cycles of “Saracura” maize improved some morphophysiologic characters, which favor their survival in flooded environments, also resulting in higher productivity.     

Evaluation of the synergistic potential of vancomycin combined with other antimicrobial agents against methicillin-resistant Staphylococcus aureus and coagulase-negative Staphylococcus spp strains

Methicillin-resistant Staphylococcus aureus (MRSA) and coagulase-negative Staphylococcus spp (CNS) are the most common pathogens that cause serious long term infections in patients. Despite the existence of new antimicrobial agents, such as linezolid, vancomycin (VAN) remains the standard therapy for the treatment of infections caused by these multidrug-resistant strains. However, the use of VAN has been associated with a high frequency of therapeutic failures in some clinical scenarios, mainly with decreasing concentration of VAN. This work aims to evaluate the synergic potential of VAN plus sulfamethoxazole/trimethoprim (SXT), VAN plus rifampin (RIF) and VAN plus imipenem (IPM) in sub-minimum inhibitory concentrations against 22 clinical strains of MRSA and CNS. The checkerboard method showed synergism of VAN/RIF and VAN/SXT against two and three of the 22 strains, respectively. The combination of VAN with IPM showed synergistic effects against 21 out of 22 strains by the E-test method. Four strains were analyzed by the time-kill curve method and synergistic activity was observed with VAN/SXT, VAN/RIF and especially VAN/IPM in sub-inhibitory concentrations. It would be interesting to determine if synergy occurs in vivo. Evidence of in vivo synergy could lead to a reduction of the standard VAN dosage or treatment time.     

Catalytic properties of thioredoxin immobilized on superparamagnetic nanoparticles

Thioredoxin (Trx1), a very important protein for regulating intracellular redox reactions, was immobilized on iron oxide superparamagnetic nanoparticles previously coated with 3-aminopropyltriethoxysilane (APTS) via covalent coupling using the EDC (1-ethyl-3-{3-dimethylaminopropyl}carbodiimide) method. The system was extensively characterized by atomic force microscopy, vibrational and magnetic techniques. In addition, gold nanoparticles were also employed to probe the exposed groups in the immobilized enzyme based on the SERS (surface enhanced Raman scattering) effect, confirming the accessibility of the cysteines residues at the catalytic site. For the single coated superparamagnetic nanoparticle, by monitoring the enzyme activity with the Ellman reagent, DTNB = 5,5′-dithio-bis(2-15 nitrobenzoic acid), an inhibitory effect was observed after the first catalytic cycle. The inhibiting effect disappeared after the application of an additional silicate coating before the APTS treatment, reflecting a possible influence of unprotected iron-oxide sites in the redox kinetics. In contrast, the doubly coated system exhibited a normal in-vitro kinetic activity, allowing a good enzyme recovery and recyclability.     

Ascorbate uptake is decreased in the hippocampus of ageing rats

Ascorbate, an intracellular antioxidant, has been considered critical for neuronal protection against oxidant stress, which is supported especially by in vitro studies. Besides, it has been demonstrated an age-related decrease in brain ascorbate levels. The aims of the present study were to investigate ascorbate uptake in hippocampal slices from old Wistar rats, as well as its neuroprotective effects in in vitro and in vivo assays. Hippocampal slices from male Wistar rats aged 4, 11 and 24 months were incubated with radiolabeled ascorbate and incorporated radioactivity was measured. Hippocampal slices from rats were incubated with different concentrations of ascorbate and submitted to H(2)O(2)-induced injury, cellular damage and S100B protein levels were evaluated. The effect of chronic administration of ascorbate on cellular oxidative state and astrocyte biochemical parameters in the hippocampus from 18-months-old Wistar rats was also studied. The ascorbate uptake was decreased in hippocampal slices from old-aged rats, while supplementation with ascorbate (2 weeks) did not modify any tested oxidative status in the hippocampus and the incubation was unable to protect hippocampal slices submitted to oxidative damage (H(2)O(2)) from old rats. Our data suggest that the decline of ascorbate uptake might be involved in the brain greater susceptibility to oxidative damage with advancing age and both in vitro and vivo assays suggest that ascorbate supplementation did not protect hippocampal cells.     

Effect of Prophylactic Low Level Laser Therapy on Oral Mucositis: A Systematic Review and Meta-Analysis

Background

Objective was to determine whether prophylactic low level laser therapy (LLLT) reduces the risk of severe mucositis as compared to placebo or no therapy.

Methods

MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials were searched until February 2014 for randomized controlled trials (RCTs) comparing prophylactic LLLT with placebo or no therapy in patients with cancer or undergoing hematopoietic stem cell transplantation (HSCT). All analyses used random effects models.

Results

Eighteen RCTs (1144 patients) were included. Prophylactic LLLT reduced the overall risk of severe mucositis (risk ratio (RR) 0.37, 95% confidence interval (CI) 0.20 to 0.67; P = 0.001). LLLT also reduced the following outcomes when compared to placebo/no therapy: severe mucositis at the time of anticipated maximal mucositis (RR 0.34, 95% CI 0.20 to 0.59), overall mean grade of mucositis (standardized mean difference −1.49, 95% CI −2.02 to −0.95), duration of severe mucositis (weighted mean difference −5.32, 95% CI −9.45 to −1.19) and incidence of severe pain (RR 0.26, 95% CI 0.18 to 0.37).

Conclusion

Prophylactic LLLT reduced severe mucositis and pain in patients with cancer and HSCT recipients. Future research should identify the optimal characteristics of LLLT and determine feasibility in the clinical setting.     

A new species of Curimatopsis Steindachner (Characiformes: Curimatidae) from the Rio Nhamundá, Amazon basin

A new species of Curimatopsis is described from the Rio Nhamundá, Amazon basin in northern Brazil. The new species is distinguished from congeners by the presence of a distinctive concentration of dark pigmentation over the entire lower lobe of the caudal fin, reticulate pattern of body pigmentation, lower jaw longer than and overlapping the anterior portion of the upper jaw, crescent‐shaped posterior nostril and by morphometric and meristic data. Comments on the phylogenetic position of the new species within Curimatopsis are also provided.     

An integrative ichnological and taphonomic approach in a transgressive–regressive cycle: a case study from Devonian of Paraná Basin,Brazil

The palaeoenvironmental context of a section of the Devonian Ponta Grossa Formation (Paraná Basin) was examined using an integrated ichnological and taphonomic approach. Three taphofacies (T‐A, T‐B and T‐C) and six ichnofabrics are recognized. T‐A is mainly composed of disarticulated organisms and is associated with Chondrites, Planolites‐Palaeophycus, Asterosoma‐Zoophycos and Asterosoma‐Chondrites ichnofabrics, representing the Cruziana ichnofacies. The upward increase in diversity and abundance of body fossils for Taphofacies A can be explained by changes in sedimentation rates during aggradational to progradational phases. T‐B beds, represented by articulated brachiopods, occur in distal tempestites associated with the Skolithos ichnofabric (Skolithos ichnofacies) and represent higher hydrodynamic energy and oxygenation than in T‐A. Taphofacies C, characterized by a mix of articulated and disarticulated organisms, generally lacks bioturbation except for Chondrites ichnofabrics occurring only at the bed tops, suggesting low substrate oxygenation and low‐energy conditions. T‐C indicates the maximum transgression in the T‐R cycle, characterizing it as a good indicator of maximum flooding surfaces. The composite Asterosoma‐Teichichnus ichnofabric (bioturbation degree 5) occurs in layers without body fossils and represents suites of the Cruziana ichnofacies. This likely reflects intense intrastratal activity at all substrate levels, which facilitated the oxygenation of the substrate disallowing the preservation of organism remains. This observation indicates that the bioturbation is an important factor controlling the loss of taphonomic information within the TAZ, mainly when associated with detritus‐feeding trace fossils.