Genome Sequence Resource of 'Candidatus Liberibacter asiaticus' strain 9PA From Brazil.

'Candidatus Liberibacter asiaticus', an unculturable α-proteobacterium, is associated with citrus huanglongbing (HLB), a devastating disease threatening citrus production in Brazil and worldwide. In this study, a draft whole-genome sequence of 'Ca. L. asiaticus' strain 9PA from a sweet orange (cultivar Pera) tree collected in São Paulo State, Brazil, is reported. The 9PA genome is 1,231,881 bp, including two prophages, with G+C content of 36.7%. This is the first report of a whole-genome sequence of 'Ca. L. asiaticus' from Brazil or South America. The 9PA genome sequence will enrich 'Ca. L. asiaticus' genome resources and facilitate HLB research and control in Brazil and the world.

A combined experimental and numerical approach to the assessment of floc settling velocity using fractal geometry.

Sedimentation processes are fundamental to solids/liquid separation in water and wastewater treatment, and therefore a robust understanding of the settlement characteristics of mass fractal aggregates (flocs) formed in the flocculation stage is fundamental to optimized settlement tank design and operation. However, the use of settling as a technique to determine aggregates' traits is limited by current understanding of permeability. In this paper, we combine experimental and numerical approaches to assess settling velocities of fractal aggregates. Using a non-intrusive in situ digital image-based method, three- and two-dimensional fractal dimensions were calculated for kaolin-based flocs. By considering shape and fractal dimension, the porosity, density and settling velocities of the flocs were calculated individually, and settling velocities compared with those of spheres of the same density using Stokes' law. Shape analysis shows that the settling velocities for fractal aggregates may be greater or less than those for perfect spheres. For example, fractal aggregates with floc fractal dimension, Df = 2.61, floc size, df > 320 µm and dp = 7.5 µm settle with lower velocities than those predicted by Stokes' law; whilst, for Df = 2.33, all aggregates of df > 70 µm and dp = 7.5 µm settled below the velocity calculated by Stokes' law for spheres. Conversely, fractal settling velocities were higher than spheres for all the range of sizes, when Df of 2.83 was simulated. The ratio of fractal aggregate to sphere settling velocity (the former being obtained from fractal porosity and density considerations), varied from 0.16 to 4.11 for aggregates in the range of 10 and 1,000 µm, primary particle size of 7.5 µm and a three-dimensional fractal dimension between 2.33 and 2.83. However, the ratio decreases to the range of 0.04-2.92 when primary particle size changes to 1.0 µm for the same fractal dimensions. Using the floc analysis technique developed here, the results demonstrate the difference in settlement behaviour between the approach developed here and the traditional Stokes' law approach using solid spheres. The technique and results demonstrate the improvements in understanding, and hence value to be derived, from an analysis based on fractal, rather than Euclidean, geometry when considering flocculation and subsequent clarification performance.

Direct and transdentinal biostimulatory effects of grape seed extract rich in proanthocyanidin on pulp cells.

AIM: To evaluate the potential biostimulatory effects of grape seed extract (GSE) on a primary culture of human pulp cells. METHODOLOGY: Human molars were used to obtain the primary pulp cell culture and 0.5-mm dentine discs. For GSE direct exposure, dose-response (0.0065-6.5%) and time response (1-60 min of contact) were examined. For transdentinal exposure, 0.65% of GSE was tested for 24 h. Cellular metabolism, nitric oxide and collagen production, and cell morphology alterations were assessed at periods of 24 and 72 h. After cell differentiation and direct exposure to GSE, the total protein production (TP), alkaline phosphatase activity (ALP) and formation of mineralization nodules (MN) were assessed. The results were analysed by parametric tests or non-parametric tests (α = 0.05). RESULTS: The lower concentration of GSE tested (0.0065%) was associated with an increase in cellular metabolism, a reduction in the production of nitric oxide and an increase in extracellular matrix synthesis (collagen). Distinct behaviours were observed for the different concentrations, without a reduction of cellular metabolism >10% compared with the control, either when applied directly or transdentinally. SEM revealed no significant change in cell morphology, except for the positive control (H2 O2 ). There was no difference in TP, ALP or MN between the control group and the group exposed to GSE. CONCLUSIONS: Treatment with grape seed extract, even at the highest concentration and longest period, caused neither direct nor transdentinal cytotoxic effects on human pulp cells. Grape seed extract components may play a biostimulatory role and protect dental pulp cells when in direct contact.

Antimicrobial activity of prodigiosin isolated from Serratia marcescens UFPEDA 398.

Prodigiosin is an alkaloid and natural red pigment produced by Serratia marcescens. Prodigiosin has antimicrobial, antimalarial and antitumor properties and induces apoptosis in T and B lymphocytes. These properties have piqued the interest of researchers in the fields of medicine, pharmaceutics and different industries. The aim of the present study was to evaluate the antimicrobial activity of prodigiosin against pathogenic micro-organisms. The red pigments produced by S. marcescens exhibited absorption at 534 nm, Rf of 0.59 and molecular weight of 323 m/z. Antimicrobial activity was tested against oxacillin-resistant Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Enterococcus faecalis, Streptococcus pyogenes, Acinetobacter sp. and oxacillin-resistant S. aureus. The standard antibiotics employed were ampicillin, chloramphenicol, gentamicin and oxacillin. The disc-diffusion tests demonstrated significant inhibition zones for S. aureus (35 ± 0.6), E. faecalis (22 ± 1.0) and S. pyogenes (14 ± 0.6). However, prodigiosin showed resistance to E. coli, P. aeruginosa and acinetobacter, where no significant formation of inhibitory halos were observed. We determined the inhibitory minimum concentrations and bactericidal for 20 strains of oxacillin-resistant S. aureus (ORSA). The pattern was the antibiotic oxacillin. The minimum inhibitory concentrations observed ranged from 1, 2 and 4.0 µg/mL, respectively, while the minimum bactericidal concentrations ranged from 2, 4, 8 and 16 µg/mL. The S. marcescens prodigiosin produced by showed bactericidal and bacteriostatic effect showing promising antimicrobial activity and suggesting future studies regarding its applicability in antibiotics therapies directed ORSA.

A new sheep model with automatized analysis of biomaterial-induced bone tissue regeneration.

Presently, several bone graft substitutes are being developed or already available for clinical use. However, the limited number of clinical and in vivo trials for direct comparison between these products may complicate this choice. One of the main reasons for this scarcity it is the use of models that do not readily allow the direct comparison of multiple bone graft substitutes, due especially to the small number of implantation sites. Although sheep cancellous bone models are now well established for these purposes, the limited availability of cancellous bone makes it difficult to find multiple comparable sites within a same animal. These limitations can be overcome by the monocortical model here proposed as it consists in 5-6 holes (5 mm Ø), in the femoral diaphysis, with similar bone structure, overlying soft tissue and loading pattern for all defects. Associated to this model, it is also described a fast histomorphometric analysis method using a computer image segmentation test (Threshold method) to assess bone regeneration parameters. The information compiled through the experimental use of 45 sheep in several studies allowed determining that this ovine model has the potential to demonstrate differences in bone-forming performance between various scaffolds. Additionally, the described histomorphometric method is fast, accurate and reproducible.

Identification of a novel subtype of feline immunodeficiency virus in a population of naturally infected felines in the Brazilian Federal District.

The feline immunodeficiency virus (FIV) is a retrovirus that is found worldwide, and it can be assigned to six subtypes (A, B, C, D, E, and a putative subtype F) based on sequencing analysis of the env and gag genes. Subtypes A and B are the most common worldwide. In Brazil, several authors have isolated only subtype B, and its prevalence differs markedly among investigated populations. Blood samples from 200 domestic felines from the Federal District in Brazil were analyzed by PCR. Samples that tested positive for FIV were then cloned, sequenced, and analyzed phylogenetically and statistically. The results represent the first description of FIV infection in the Central Region of Brazil and suggest that only 2 % of felines in this region are positive for the virus. In addition, the analysis showed that one out of the four positive samples that we detected could not be assigned to any of the six classical subtypes. This sample was taken as a putative novel subtype of the FIV virus. The remaining three positive samples were assigned to subtype B, with differences existing among these samples.

Use of poly(DL-lactide-ε-caprolactone) membranes and mesenchymal stem cells from the Wharton's jelly of the umbilical cord for promoting nerve regeneration in axonotmesis: in vitro and in vivo analysis.

Cellular systems implanted into an injured nerve may produce growth factors or extracellular matrix molecules, modulate the inflammatory process and eventually improve nerve regeneration. In the present study, we evaluated the therapeutic value of human umbilical cord matrix MSCs (HMSCs) on rat sciatic nerve after axonotmesis injury associated to Vivosorb® membrane. During HMSCs expansion and differentiation in neuroglial-like cells, the culture medium was collected at 48, 72 and 96 h for nuclear magnetic resonance (NMR) analysis in order to evaluate the metabolic profile. To correlate the HMSCs ability to differentiate and survival capacity in the presence of the Vivosorb® membrane, the [Ca(2+)]i of undifferentiated HMSCs or neuroglial-differentiated HMSCs was determined by the epifluorescence technique using the Fura-2AM probe. The Vivosorb® membrane proved to be adequate and used as scaffold associated with undifferentiated HMSCs or neuroglial-differentiated HMSCs. In vivo testing was carried out in adult rats where a sciatic nerve axonotmesis injury was treated with undifferentiated HMSCs or neuroglial differentiated HMSCs with or without the Vivosorb® membrane. Motor and sensory functional recovery was evaluated throughout a healing period of 12 weeks using sciatic functional index (SFI), extensor postural thrust (EPT), and withdrawal reflex latency (WRL). Stereological analysis was carried out on regenerated nerve fibers. In vitro investigation showed the formation of typical neuroglial cells after differentiation, which were positively stained for the typical specific neuroglial markers such as the GFAP, the GAP-43 and NeuN. NMR showed clear evidence that HMSCs expansion is glycolysis-dependent but their differentiation requires the switch of the metabolic profile to oxidative metabolism. In vivo studies showed enhanced recovery of motor and sensory function in animals treated with transplanted undifferentiated and differentiated HMSCs that was accompanied by an increase in myelin sheath. Taken together, HMSC from the umbilical cord Wharton jelly might be useful for improving the clinical outcome after peripheral nerve lesion.

Photochemistry and desorption induced by X-rays in water rich astrophysical ice analogs: implications for the moon Enceladus and other frozen space environments.

Soft X-rays are an important agent for chemical processing in the Solar System and in the interstellar medium. The photolysis and photodesorption processes of H2O-rich ices triggered by soft X-rays was, experimentally, addressed in this paper. The experiments were performed at the Brazilian synchrotron facility LNLS/CNPEN employing broadband radiation (from 6 to 2000 eV; mainly soft X-rays and a small fraction of VUV) in solid samples at temperatures of 20 and 80 K. The icy samples were monitored by infrared spectroscopy. We determined the effective destruction cross section (in the order 10-18 cm2) as well as the formation cross section for the new species produced after the irradiation. Among them, we list OCN-, CO, CO3, CH3OH, H2O2, HCOO-, NH4 +, HCONH2 and CH3HCO, mostly formed in the experiment at 80 K. The chemical equilibrium stage was characterized and molecular abundances were quantified. In addition, we discuss a methodology to estimate the amount of unknown species in the ice produced by photolysis. The samples reach chemical equilibrium at fluences around 2-3 × 1018 cm-2. Timescales for reaching chemical equilibrium in space environments illuminated by X-rays were given, as well as the desorption yields induced by X-rays. The astrophysical implication on the surface chemistry and desorption processes at the moon Enceladus are provided.

Use of hybrid chitosan membranes and N1E-115 cells for promoting nerve regeneration in an axonotmesis rat model.

Many studies have been dedicated to the development of scaffolds for improving post-traumatic nerve regeneration. The goal of this study was to develop and test hybrid chitosan membranes to use in peripheral nerve reconstruction, either alone or enriched with N1E-115 neural cells. Hybrid chitosan membranes were tested in vitro, to assess their ability in supporting N1E-115 cell survival and differentiation, and in vivo to assess biocompatibility as well as to evaluate their effects on nerve fiber regeneration and functional recovery after a standardized rat sciatic nerve crush injury. Functional recovery was evaluated using the sciatic functional index (SFI), the static sciatic index (SSI), the extensor postural thrust (EPT), the withdrawal reflex latency (WRL) and ankle kinematics. Nerve fiber regeneration was assessed by quantitative stereological analysis and electron microscopy. All chitosan membranes showed good biocompatibility and proved to be a suitable substrate for plating the N1E-115 cellular system. By contrast, in vivo nerve regeneration assessment after crush injury showed that the freeze-dried chitosan type III, without N1E-115 cell addition, was the only type of membrane that significantly improved posttraumatic axonal regrowth and functional recovery. It can be thus suggested that local enwrapping with this type of chitosan membrane may represent an effective approach for the improvement of the clinical outcome in patients receiving peripheral nerve surgery.

Neural cell transplantation effects on sciatic nerve regeneration after a standardized crush injury in the rat.

The goal of the present study was to assess whether in vitro-differentiated N1E-115 cells supported by a collagen membrane would enhance rat sciatic nerve regeneration after a crush injury. To set up an appropriate experimental model for investigating the effects of neural cell transplantation, we have recently described the sequence of functional and morphologic changes occurring after a standardized sciatic nerve crush injury with a nonserrated clamp. Functional recovery was evaluated using the sciatic functional index, the static sciatic index, the extensor postural thrust, the withdrawal reflex latency, and ankle kinematics. In addition, histomorphometric analysis was carried out on regenerated nerve fibers by means of the 2D-disector method. Based on the results of the EPT and of some of the ankle locomotor kinematic parameters analyzed, the hypothesis that N1E-115 cells may enhance nerve regeneration is partially supported although histomorphometry disclosed no significant difference in nerve fiber regeneration between the different experimental groups. Therefore, results suggest that enrichment of equine type III collagen membrane with the N1E-115 cellular system in the rat sciatic nerve crush model may support recovery, at least in terms of motor function. The discrepancy between functional and morphological results also suggests that the combined use of functional and morphological analysis should be recommended for an overall assessment of recovery in nerve regeneration studies.

Muscle thickness and echo-intensity changes of the quadriceps femoris muscle during a strength training program.

INTRODUCTION: Ultrasound (US) has an important role in musculoskeletal (MSK) evaluation, allowing the study of muscle morphology and function. Muscle thickness (MT) and muscle echo-intensity (EI) are two important parameters that may quantify muscle structural adaptations to a variety of stimuli. The aim was to explore the potential of quantitative US imaging for assessing the adaptations and responses of the muscle tissue to increased contractile activity using B-mode US. This study was centred on the quadriceps femoris muscle contractile activity on MT and EI. METHODS AND MATERIALS: Twenty-eight young male adults participated in the study, divided in a control group and two training groups performing concentric or eccentric strength training, respectively. The effect of a 15-week strength program was studied on MT and EI in several regions of the heads of the quadriceps femoris using B-mode US. All images acquisitions and measurements were done by the same experience sonographer. RESULTS: Strength training resulted in an increase of MT at all muscles and sites (p < 0.05), except the VM. Strength training failed in changing EI in most of the quadriceps femoris, except in the VI and some regions of the VL. No statistically significant differences were observed in our quantitative US parameters between concentric and eccentric training (p > 0.05). CONCLUSION: These results emphasise the value of MT as a quantifiable muscle US method for evaluating muscle adaptation to exercise training. However, the inconsistency of the EI values indicates that more studies are needed to develop it as an accurate diagnostic tool.

Long-term functional and morphological assessment of a standardized rat sciatic nerve crush injury with a non-serrated clamp.

We have recently described the sequence of functional and morphologic changes occurring after a standardized sciatic nerve crush injury. An 8-week post-injury time was used because this end point is the far most used. Unexpectedly, both functional and morphological data revealed that animals had still not recovered to normal pre-injury levels. Therefore, the present study was designed in order to prolong the observation up to 12 weeks. Functional recovery was evaluated using sciatic functional index (SFI), static sciatic index (SSI), extensor postural thrust (EPT), withdrawal reflex latency (WRL) and ankle kinematics. In addition, quantitative morphology was carried out on regenerated nerve fibers. A full functional recovery was predicted by SFI/SSI, EPT and WRL but not all ankle kinematics parameters. Moreover, only two morphological parameters (myelin thickness/axon diameter ratio and fiber/axon diameter ratio) returned to normal values. Data presented in this paper provide a baseline for selecting the adequate end-point and methods of recovery assessment for a rat sciatic nerve crush study and suggest that the combined use of functional and morphological analysis should be recommended in this experimental model.

Dynamics of the Davydov-Scott monomer in a thermal bath: comparison of the full quantum and semiclassical approaches.

The quantum state diffusion equation is applied to the problem of energy transfer in proteins. Lindblad operators, capable of coupling the full quantum Davydov-Scott monomer to a thermal bath, are derived. Numerical simulations with the QSD equation show that the Lindblad operators derived do recreate the exact equilibrium ensemble for the Davydov-Scott monomer. Comparison of the results obtained with the full quantum and with the semiclassical systems shows that, at biological temperatures, the latter provides a good approximation of the former.

Pacific Islands Families Study: risk factors associated with otitis media with effusion among Pacific 2-year-old children.

OBJECTIVE: This study examined the risk factors associated with middle ear disease in a cohort of Pacific 2-year-old children residing in New Zealand. METHODS: The data were gathered as part of the Pacific Island Families: first 2 years of life (PIF) study in which 656 2-year-old were screened using tympanometry to identify children at risk for otitis media with effusion (OME) and other otological disorders. RESULTS: Within this 2-year-old cohort of Pacific children, one set of factors significantly associated with OME was clustered around the respiratory and auditory health of the child over the past year. OME was more likely for children who were regularly suffering from fluid/pus discharge from ears (OR=2.10, 95% CI: 1.01-4.35), children with five or more coughs/colds in the last year (OR=1.90, 95% CI: 1.22-3.00), and children who frequently/constantly snored (OR=2.60, 95% CI: 1.09-6.23) to have OME. Those children who were treated at home for breathing problems were more that two times more likely to have OME (OR=2.61, 95% CI: 1.55-4.42). A second set of factors was clustered around environmental risks that exposed children to a large number of other children. Children who attended a day care centre for more than 20h were five times more likely (OR=5.21, 95% CI: 2.90-9.35) and those who regularly attended church (OR=2.78, 95% CI: 1.05-7.40) were almost three times more likely to have OME. CONCLUSIONS: These findings portray a child compromised by persistent ear infections and general coughs and colds as being at increased risk of contracting OME. In line with international research these findings raise questions about the negative child health effects associated with the day care environment for young children.

Reproducibility of ultrasound-derived muscle thickness and echo-intensity for the entire quadriceps femoris muscle.

INTRODUCTION: Muscle thickness (MT) and muscle echo-intensity (EI) allow the study of skeletal muscle adaptive changes with ultrasound. This study investigates the intra- and inter-session reliability and agreement of MT and EI measurements for each of the four heads of the quadriceps femoris in transverse and longitudinal scans, using two sizes for the region of interest (ROI); EI measurements only. METHODS: Three B-mode images from two views were acquired from each head of quadriceps femoris from twenty participants (10 females) in two sessions, 7 days apart. EI was measured using a large and a small ROI. Reliability was examined with the mixed two-way intra-class correlation coefficient (ICC), the standard error of mean (SEM) and the smallest detectable change (SDC). Bland-Altman's plots were used to study agreement. RESULTS: High to very high inter-session ICC values were found for MT for all muscle heads, particularly for measurements from transverse scans. For EI measurement, ICC values ranged from low to high, with higher ICC values seen with the largest ROI. SDC values ranged between 0.19 and 0.53 cm for MT and between 3.73 and 18.56 arbitrary units (a.u.) for two ROIs. Good agreement existed between MT measurements made in both scans. A small bias and larger 95% limits of agreement were seen for EI measurements collected with the two ROI sizes. CONCLUSION: Ultrasound measures of MT and EI show moderate to very high reliability. The reliability and agreement of MT and EI measurements are improved in transverse scans and with larger ROIs.

Venous flow during manual lymphatic drainage applied to different regions of the lower extremity in people with and without chronic venous insufficiency: a cross-sectional study.

OBJECTIVES: To evaluate the effect of manual lymphatic drainage (MLD) on venous flow when applied to the medial and lateral aspects of the thigh and leg in patients with chronic venous insufficiency (CVI) and healthy subjects. DESIGN: Cross-sectional study. SETTING: Participants were assessed in a school-based health community attendant service. PARTICIPANTS: Fifty-seven subjects participated in this study {mean age: 43 [standard deviation (SD) 14] years, 38 women and 19 men}. Of these, 28 subjects had CVI [mean age 47 (SD 12) years] and 29 subjects did not have CVI [mean age 39 (14) years]. INTERVENTION: MLD was applied by a certificated physical therapist to the medial and lateral aspects of the thigh and leg. MAIN OUTCOME MEASUREMENTS: Cross-sectional area; blood flow velocities in the femoral vein, great saphenous vein, popliteal vein and small saphenous vein at baseline and during MLD, measured by duplex ultrasound. RESULTS: Flow volume in the femoral vein increased from baseline [5.19 (SD 3.25)cm3/second] when MLD was applied to the medial [7.03 (SD 3.65)cm3/second; P≤0.001; mean difference -1.69; 95% confidence interval (CI) -2.42 to -0.97] and lateral [6.16 (SD 3.35)cm3/second; P≤0.001; mean difference -1.04; 95% CI -1.70 to -0.39] aspects of the thigh. Venous flow augmentation in the femoral vein and great saphenous vein was higher when MLD was applied to the medial aspect of the thigh (P<0.001), while MLD had a similar effect on venous blood flow regardless of whether it was applied to the medial or the lateral aspect of the leg (P=0.731). CONCLUSIONS: MLD increases blood flow in deep and superficial veins. MLD should be applied along the route of the venous vessels for improved venous return.

Comparison of redox and D29 phage methods for detection of isoniazid and rifampicin resistance in Mycobacterium tuberculosis.

Rapid, accurate and inexpensive methods are essential to detect drug-resistant Mycobacterium tuberculosis and allow timely application of effective treatment and precautions to prevent transmission. The proportion method, the MTT and Alamar Blue redox methods, and the D29 mycobacteriophage assay, were compared for their ability to detect resistance to isoniazid and rifampicin. When tested against a panel of known M. tuberculosis strains, the redox methods and the D29 assay showed good sensitivity and specificity compared to the proportion method, suggesting that they could be useful alternatives for identifying multidrug resistance in M. tuberculosis.

Dynamics of a nonconserving Davydov monomer.

The Davydov-Scott model describes the transfer of energy along hydrogen-bonded chains, like those that stabilize the structure of alpha helices. It is based on the hypothesis that amide I excitations are created (by the hydrolysis of ATP, for instance) and kept in the system. Recent experimental results confirm that the energy associated with amide I excitations does indeed last for tens of picoseconds in proteins and model systems. However, the Davydov-Scott model cannot describe the conversion of that energy into work, because it conserves the number of excitations. With the aim of describing conformational changes, we consider, in this paper, a nonconserving generalization of the model, which is found to describe essentially a contraction of the hydrogen bond adjacent to the site where an excitation is present. Unlike the one-site Davydov-Scott model, that contraction is time dependent because the number of excitations is not conserved. However, considering the time average of the dynamical variables, the results reported here tend to the known results of the Davydov-Scott model.

Pacific Islands families study: the prevalence of chronic middle ear disease in 2-year-old Pacific children living in New Zealand.

OBJECTIVE: The aim of this study was to determine the prevalence of chronic middle ear disease in 2-year-old Pacific children living in New Zealand. METHODS: The data were gathered as part of the Pacific Islands Families: First Two Years of Life (PIF) Study in which 1001 two year olds were screened using tympanometry to identify children at risk for otitis media with effusion (OME) and other otological disorders. Those failing the screening tests were referred to Manukau Superclinic where they had a further tympanometry test, and if they failed this test, were followed up with a comprehensive otological examination by an otolaryngologist using otomicroscopy and pneumatic otoscopy. RESULTS: Bilateral otitis media with effusion (OME) was the most common abnormality detected (N=102) with further cases of unilateral OME (N=8), and unilateral OME resolving (N=2). Other cases of OME were associated with acute otitis media (AOM), impacted wax (N=1), perforation (N=1), and mild retraction (N=2). Overall there were 118 children with unilateral or bilateral OME. AOM of any form was seen in nine cases. Retraction of the tympanic membrane was seen in 26 cases. The population prevalence among Pacific 2-year-old children was estimated as 25.4% for OME, 1.9% for AOM, and 26.9% for OME or AOM. CONCLUSIONS: These findings reveal that over 25% of Pacific Island 2-year-old were affected by OME and recommend the consideration of national screening for OME and other otological disorders at this earlier age.