Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range

Abstract Background Citrus bacterial canker is a disease that has severe economic impact on citrus industries worldwide and is caused by a few species and pathotypes of Xanthomonas. X. citri subsp. citri strain 306 (XccA306) is a type A (Asiatic) strain with a wide host range, whereas its variant X. citri subsp. citri strain Aw12879 (Xcaw12879, Wellington strain) is restricted to Mexican lime. Results To characterize the mechanism for the differences in host range of XccA and Xcaw, the genome of Xcaw12879 that was completed recently was compared with XccA306 genome. Effectors xopAF and avrGf1 are present in Xcaw12879, but were absent in XccA306. AvrGf1 was shown previously for Xcaw to cause hypersensitive response in Duncan grapefruit. Mutation analysis of xopAF indicates that the gene contributes to Xcaw growth in Mexican lime but does not contribute to the limited host range of Xcaw. RNA-Seq analysis was conducted to compare the expression profiles of Xcaw12879 and XccA306 in Nutrient Broth (NB) medium and XVM2 medium, which induces hrp gene expression. Two hundred ninety two and 281 genes showed differential expression in XVM2 compared to in NB for XccA306 and Xcaw12879, respectively. Twenty-five type 3 secretion system genes were up-regulated in XVM2 for both XccA and Xcaw. Among the 4,370 common genes of Xcaw12879 compared to XccA306, 603 genes in NB and 450 genes in XVM2 conditions were differentially regulated. Xcaw12879 showed higher protease activity than XccA306 whereas Xcaw12879 showed lower pectate lyase activity in comparison to XccA306. Conclusions Comparative genomic analysis of XccA306 and Xcaw12879 identified strain specific genes. Our study indicated that AvrGf1 contributes to the host range limitation of Xcaw12879 whereas XopAF contributes to virulence. Transcriptome analyses of XccA306 and Xcaw12879 presented insights into the expression of the two closely related strains of X. citri subsp. citri. Virulence genes including genes encoding T3SS components and effectors are induced in XVM2 medium. Numerous genes with differential expression in Xcaw12879 and XccA306 were identified. This study provided the foundation to further characterize the mechanisms for virulence and host range of pathotypes of X. citri subsp. citri.

Predicting dysthyroid optic neuropathy using computed tomography volumetric analyses of orbital structures

OBJECTIVE: To evaluate the ability of orbital apex crowding volume measurements calculated with multidetector-computed tomography to detect dysthyroid optic neuropathy. METHODS: Ninety-three patients with Graves' orbitopathy were studied prospectively. All of the patients underwent a complete neuro-ophthalmic examination and computed tomography scanning. Volumetric measurements were calculated from axial and coronal contiguous sections using a dedicated workstation. Orbital fat and muscle volume were estimated on the basis of their attenuation values (in Hounsfield units) using measurements from the anterior orbital rim to the optic foramen. Two indexes of orbital muscle crowding were calculated: i) the volumetric crowding index, which is the ratio between soft tissue (mainly extraocular muscles) and orbital fat volume and is based on axial scans of the entire orbit; and ii) the volumetric orbital apex crowding index, which is the ratio between the extraocular muscles and orbital fat volume and is based on coronal scans of the orbital apex. Two groups of orbits (with and without dysthyroid optic neuropathy) were compared. RESULTS: One hundred and two orbits of 61 patients with Graves' orbitopathy met the inclusion criteria and were analyzed. Forty-one orbits were diagnosed with Graves' orbitopathy, and 61 orbits did not have optic neuropathy. The two groups of orbits differed significantly with regard to both of the volumetric indexes (p<0.001). Although both indexes had good discrimination ability, the volumetric orbital apex crowding index yielded the best results with 92% sensitivity, 86% specificity, 81%/94% positive/negative predictive value and 88% accuracy at a cutoff of 4.14. CONCLUSION: This study found that the orbital volumetric crowding index was a more effective predictor of dysthyroid optic neuropathy than previously described computed tomography indexes were.

Genetic analyses of smoking initiation, persistence, quantity, and age-at-onset of regular cigarette use in Brazilian families: the Baependi Heart Study

Background: The purpose of this study was to estimate the genetic influences on the initiation of cigarette smoking, the persistence, quantity and age-at-onset of regular cigarette use in Brazilian families. Methods: The data set consisted of 1,694 individuals enrolled in the Baependi Heart Study. The heritability and the heterogeneity in genetic and environmental variance components by gender were estimated from variance components approaches, using the SOLAR (Sequential Oligogenic Linkage Analysis Routines) computer package. The mixed-effects Cox model was used for the genetic analysis of the age-at onset of regular cigarette use. Results: The heritability estimates were high (> 50%) for smoking initiation and were intermediate, ranging from 23.4 to 31.9%, for smoking persistence and quantity. Significant evidence for heterogeneity in variance components by gender was observed for smoking initiation and age-at-onset of regular cigarette use. Genetic factors play an important role in the interindividual variation of these phenotypes in females, while in males there is a predominant environmental component, which could be explained by greater social influences in the initiation of tobacco use. Conclusions: Significant heritabilities were observed in smoking phenotypes for both males and females from the Brazilian population. These data add to the literature and are concordant with the notion of significant biological determination in smoking behavior. Samples from the Baependi Heart Study may be valuable for the mapping of genetic loci that modulate this complex biological trait.

Influence of Growth Media and Temperature on Bacterial Adhesion to Polystyrene Surfaces

Bacterial adhesion to inert surfaces is a complex process influenced by environmental conditions. In this work, the influence of growth medium and temperature on the adhesion of Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Micrococcus luteus and Listeria monocytogenes to polystyrene surfaces was studied. Most bacteria demonstrated the highest adhesion when cultured in TSYEA, except S. marcescens, which showed to be positively influenced by the pigment production, favored in poor nutrient media (lactose and peptone agar). P. aeruginosa adhesion to polystyrene increased at low temperatures whatever the medium used. The culture medium influenced the surface properties of the bacteria as assessed by the MATS test.

Anatomical and ultrastructural analyses of in vitro organogenesis from root explants of commercial passion fruit (Passiflora edulis Sims)

This study aimed to characterize the anatomical events and ultrastructural aspects of direct and indirect in vitro organogenesis in Passiflora edulis. Root explants were cultured on induction medium, supplemented with 4.44 mu M 6-benzyladenine. Roots at different stages of development were collected and processed for observation by light microscopy and scanning and transmission electron microscopy. Patterns of direct and indirect regeneration were observed in the explants. During direct organogenesis, the organogenic buds and nodules, formed from meristemoids, originated from the pericycle regions distant from the cut surface. Completely differentiated buds were observed after 20 days of culture. During indirect organogenesis, bud formation occurred via meristemoids at the periphery of the calli, which differentiated from the cortical region of the initial explant. Regardless of the regeneration pattern, the meristemoids had similar ultrastructural characteristics; however, differences were reported in the nuclear shape of the cells of the meristemoids formed directly and indirectly. This study provides important information for enhancing the understanding and characterization of the organogenic process in non-meristematic explants and provides information on the use of roots as explants in genetic transformation protocols for this important tropical species.

Radiative transfer analyses of Titan's tropical atmosphere

Titan's optical and near-IR spectra result primarily from the scattering of sunlight by haze and its absorption by methane. With a column abundance of 92 km amagat (11 times that of Earth), Titan's atmosphere is optically thick and only similar to 10% of the incident solar radiation reaches the surface, compared to 57% on Earth. Such a formidable atmosphere obstructs investigations of the moon's lower troposphere and surface, which are highly sensitive to the radiative transfer treatment of methane absorption and haze scattering. The absorption and scattering characteristics of Titan's atmosphere have been constrained by the Huygens Probe Descent Imager/Spectral Radiometer (DISR) experiment for conditions at the probe landing site (Tomasko, M.G., Bezard, B., Doose, L., Engel, S., Karkoschka, E. 120084 Planet. Space Sci. 56, 624-247: Tomasko, M.G. et al. [2008b] Planet. Space Sci. 56, 669-707). Cassini's Visual and Infrared Mapping Spectrometer (VIMS) data indicate that the rest of the atmosphere (except for the polar regions) can be understood with small perturbations in the high haze structure determined at the landing site (Penteado, P.F., Griffith, CA., Tomasko, M.G., Engel, S., See, C., Doose, L, Baines, K.H., Brown, R.H., Buratti, B.J., Clark, R., Nicholson, P., Sotin, C. [2010]. Icarus 206, 352-365). However the in situ measurements were analyzed with a doubling and adding radiative transfer calculation that differs considerably from the discrete ordinates codes used to interpret remote data from Cassini and ground-based measurements. In addition, the calibration of the VIMS data with respect to the DISR data has not yet been tested. Here, VIMS data of the probe landing site are analyzed with the DISR radiative transfer method and the faster discrete ordinates radiative transfer calculation; both models are consistent (to within 0.3%) and reproduce the scattering and absorption characteristics derived from in situ measurements. Constraints on the atmospheric opacity at wavelengths outside those measured by DISR, that is from 1.6 to 5.0 mu m, are derived using clouds as diffuse reflectors in order to derive Titan's surface albedo to within a few percent error and cloud altitudes to within 5 km error. VIMS spectra of Titan at 2.6-3.2 mu m indicate not only spectral features due to CH4 and CH3D (Rannou, P., Cours, T., Le Mouelic, S., Rodriguez, S., Sotin, C., Drossart, P., Brown, R. [2010]. Icarus 208, 850-867), but also a fairly uniform absorption of unknown source, equivalent to the effects of a darkening of the haze to a single scattering albedo of 0.63 +/- 0.05. Titan's 4.8 mu m spectrum point to a haze optical depth of 0.2 at that wavelength. Cloud spectra at 2 mu m indicate that the far wings of the Voigt profile extend 460 cm(-1) from methane line centers. This paper releases the doubling and adding radiative transfer code developed by the DISR team, so that future studies of Titan's atmosphere and surface are consistent with the findings by the Huygens Probe. We derive the surface albedo at eight spectral regions of the 8 x 12 km(2) area surrounding the Huygens landing site. Within the 0.4-1.6 mu m spectral region our surface albedos match DISR measurements, indicating that DISR and VIMS measurements are consistently calibrated. These values together with albedos at longer 1.9-5.0 mu m wavelengths, not sampled by DISR, resemble a dark version of the spectrum of Ganymede's icy leading hemisphere. The eight surface albedos of the landing site are consistent with, but not deterministic of, exposed water ice with dark impurities. (C) 2011 Elsevier Inc. All rights reserved.

Sequence and Copy Number Analyses of HEXB Gene in Patients Affected by Sandhoff Disease: Functional Characterization of 9 Novel Sequence Variants

Sandhoff disease (SD) is a lysosomal disorder caused by mutations in the HEXB gene. To date, 43 mutations of HEXB have been described, including 3 large deletions. Here, we have characterized 14 unrelated SD patients and developed a Multiplex Ligation-dependent Probe Amplification (MLPA) assay to investigate the presence of large HEXB deletions. Overall, we identified 16 alleles, 9 of which were novel, including 4 sequence variation leading to aminoacid changes [c.626C>T (p.T209I), c.634C>A (p.H212N), c.926G>T (p.C309F), c.1451G>A (p.G484E)] 3 intronic mutations (c.1082+5G>A, c.1242+1G>A, c.1169+5G>A), 1 nonsense mutation c.146C>A (p.S49X) and 1 small in-frame deletion c.1260_1265delAGTTGA (p.V421_E422del). Using the new MLPA assay, 2 previously described deletions were identified. In vitro expression studies showed that proteins bearing aminoacid changes p.T209I and p.G484E presented a very low or absent activity, while proteins bearing the p.H212N and p.C309F changes retained a significant residual activity. The detrimental effect of the 3 novel intronic mutations on the HEXB mRNA processing was demonstrated using a minigene assay. Unprecedentedly, minigene studies revealed the presence of a novel alternative spliced HEXB mRNA variant also present in normal cells. In conclusion, we provided new insights into the molecular basis of SD and validated an MLPA assay for detecting large HEXB deletions.

Low-level laser therapy in collagenase-induced Achilles tendinitis in rats: Analyses of biochemical and biomechanical aspects

NSAIDs are widely prescribed and used over the years to treat tendon injuries despite its well-known long-term side effects. In the last years several animal and human trials have shown that low-level laser therapy (LLLT) presents modulatory effects on inflammatory markers, however the mechanisms involved are not fully understood. The aim of this study was to evaluate the short-term effects of LLLT or sodium diclofenac treatments on biochemical markers and biomechanical properties of inflamed Achilles tendons. Wistar rats Achilles tendons (n?=?6/group) were injected with saline (control) or collagenase at peritendinous area of Achilles tendons. After 1?h animals were treated with two different doses of LLLT (810?nm, 1 and 3?J) at the sites of the injections, or with intramuscular sodium diclofenac. Regarding biochemical analyses, LLLT significantly decreased (p?<?0.05) COX-2, TNF-a, MMP-3, MMP-9, and MMP-13 gene expression, as well as prostaglandin E2 (PGE2) production when compared to collagenase group. Interestingly, diclofenac treatment only decreased PGE2 levels. Biomechanical properties were preserved in the laser-treated groups when compared to collagenase and diclofenac groups. We conclude that LLLT was able to reduce tendon inflammation and to preserve tendon resistance and elasticity. (c) 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:19451951, 2012

Experimental analyses of the poly(vinyl chloride) foams' mechanical anisotropic behavior

Assessing a full set of mechanical properties is a rather complicate task in the case of foams, especially if material models must be calibrated with these results. Many issues, for example anisotropy and heterogeneity, influence the mechanical behavior. This article shows through experimental analyses how the microstructure affects different experimental setups and it also quantifies the degree of anisotropy of a poly(vinyl chloride) foam. Monotonic and cyclic experimental tests were carried out using standard compression specimens and non-standard tensile specimens. Results are complemented and compared with the aid of a digital image correlation technique and scanning electron microscopy analyses. Mechanical properties (e.g., elastic and plastic Poisson's ratios) are evaluated for compression and tensile tests, for two different material directions (normal and in-plane). The material is found to be transversely isotropic. Differences in the results of the mechanical properties can be as high as 100%, or even more depending on the technique used and the loading direction. Also, the experimental analyses show how the material's microstructure behavior, like the evolution of the herein identified yield fronts and a spring back phenomenon, can influence the phenomenological response and the failure mechanisms as well as the hardening curves. POLYM. ENG. SCI., 52:2654-2663, 2012. (C) 2012 Society of Plastics Engineers

Molecular and phylogenetic analyses of human Parvovirus B19 isolated from Brazilian patients with sickle cell disease and beta-thalassemia major and healthy blood donors

Human Parvovirus B19 (B19V) is a recognized cause of life-threatening conditions among patients with hemoglobinopathies. This study investigates B19V infection in patients with sickle cell disease and beta-thalassemia using different experimental approaches. A total of 183 individuals (144 with sickle cell disease and 39 with beta-thalassemia major) and 100 healthy blood donors were examined for B19V using anti-B19V IgG enzyme immunoassay, quantitative PCR, DNA sequencing, and phylogenetic analysis. Viremia was documented in 18.6% of patients and 1% of donors, and was generally characterized by low viral load (VL); however, acute infections were also observed. Anti-B19V IgG was detected in 65.9% of patients with sickle cell disease and in 60% of donors, whereas the patients with thalassemia exhibited relatively low seroreactivity. The seroprevalence varied among the different age groups. In patients, it progressively increased with age, whereas in donors it reached a plateau. Based on partial NS1 fragments, all isolates detected were classified as subgenotype 1A with a tendency to elicit genetically complex infections. Interestingly, quasispecies occurred in the plasma of not only patients but also donors with even higher heterogeneity. The partial NS1 sequence examined did not exhibit positive selection. Quantitation of B19V with a conservative probe is a technically and practically useful approach. The extensive spread of B19V subgenotype 1A in patients and donors and its recent introduction into the countryside of the Sao Paulo State, Brazil were demonstrated; however, it is difficult to establish a relationship between viral sequences and the clinical outcomes of the infection. J. Med. Virol. 84:16521665, 2012. (c) 2012 Wiley Periodicals, Inc.

Multivariate analyses of UV-Vis absorption spectral data from cachaca wood extracts: a model to classify aged Brazilian cachacas according to the wood species used

Multivariate analyses of UV-Vis spectral data from cachaca wood extracts provide a simple and robust model to classify aged Brazilian cachacas according to the wood species used in the maturation barrels. The model is based on inspection of 93 extracts of oak and different Brazilian wood species by a non-aged cachaca used as an extraction solvent. Application of PCA (Principal Components Analysis) and HCA (Hierarchical Cluster Analysis) leads to identification of 6 clusters of cachaca wood extracts (amburana, amendoim, balsamo, castanheira, jatoba, and oak). LDA (Linear Discriminant Analysis) affords classification of 10 different wood species used in the cachaca extracts (amburana, amendoim, balsamo, cabreuva-parda, canela-sassafras, castanheira, jatoba, jequitiba-rosa, louro-canela, and oak) with an accuracy ranging from 80% (amendoim and castanheira) to 100% (balsamo and jequitiba-rosa). The methodology provides a low-cost alternative to methods based on liquid chromatography and mass spectrometry to classify cachacas aged in barrels that are composed of different wood species.

Acoustic analyses of diadochokinesis in fluent and stuttering children

OBJECTIVES: The purpose of the study was to acoustically compare the performance of children who do and do not stutter on diadochokinesis tasks in terms of syllable duration, syllable periods, and peak intensity. METHODS: In this case-control study, acoustical analyses were performed on 26 children who stutter and 20 aged-matched normally fluent children (both groups stratified into preschoolers and school-aged children) during a diadochokinesis task: the repetition of articulatory segments through a task testing the ability to alternate movements. Speech fluency was assessed using the Fluency Profile and the Stuttering Severity Instrument. RESULTS: The children who stutter and those who do not did not significantly differ in terms of the acoustic patterns they produced in the diadochokinesis tasks. Significant differences were demonstrated between age groups independent of speech fluency. Overall, the preschoolers performed poorer. These results indicate that the observed differences are related to speech-motor age development and not to stuttering itself. CONCLUSIONS: Acoustic studies demonstrate that speech segment durations are most variable, both within and between subjects, during childhood and then gradually decrease to adult levels by the age of eleven to thirteen years. One possible explanation for the results of the present study is that children who stutter presented higher coefficients of variation to exploit the motor equivalence to achieve accurate sound production (i.e., the absence of speech disruptions).

Exploring the coordination chemistry of isomerizable terpyridine derivatives for successful analyses of cis and trans isomers by travelling wave ion mobility mass spectrometry

The photochemical cis-trans isomerization of the 4-{4-[2-(pyridin-4-yl)ethenyl]phenyl}-2,2': 6',2''-terpyridine ligand (vpytpy) was investigated by UV-vis, NMR and TWIM-MS. Ion mobility mass spectrometry was performed pursuing the quantification of the isomeric composition during photolysis, however an in-source trans-to-cis isomerization process was observed. In order to overcome this inherent phenomenon, the isomerization of the vpytpy species was suppressed by complexation, reacting with iron(II) ions, and forming the [Fe(vpytpy)(2)](2+) complex. The strategy of "freezing" the cis-trans isomerizable ligand at a given geometric conformation was effective, preventing further isomerization, thus allowing the distinction of each one of the isomers in the photolysed mixture. In addition, the experimental drift times were related to the calculated surface areas of the three possible cis-cis, cis-trans and trans-trans iron(II) complex isomers. The stabilization of the ligand in a given conformation also allows us to obtain the cis-cis and cis-trans complexes exhibiting the ligand in the metastable cis-conformation, as well as in the thermodynamically stable trans-conformation.

The consequences of growth hormone-releasing hormone receptor haploinsufficiency for bone quality and insulin resistance

Objective Growth hormone (GH)/insulin-like growth factor (IGF) axis and insulin are key determinants of bone remodelling. Homozygous mutations in the GH-releasing hormone receptor (GHRHR) gene (GHRHR) are a frequent cause of genetic isolated GH deficiency (IGHD). Heterozygosity for GHRHR mutation causes changes in body composition and possibly an increase in insulin sensitivity, but its effects on bone quality are still unknown. The objective of this study was to assess the bone quality and metabolism and its correlation with insulin sensitivity in subjects heterozygous for a null mutation in the GHRHR. Patients and methods A cross-sectional study was performed on 76 normal subjects (68.4% females) (N/N) and 64 individuals (64.1% females) heterozygous for a mutation in the GHRHR (MUT/N). Anthropometric features, quantitative ultrasound (QUS) of the heel, bone markers [osteocalcin (OC) and CrossLaps], IGF-I, glucose and insulin were measured, and homeostasis model assessment of insulin resistance (HOMAIR) was calculated. Results There were no differences in age or height between the two groups, but weight (P = 0.007) and BMI (P = 0.001) were lower in MUT/N. There were no differences in serum levels of IGF-I, glucose, T-score or absolute values of stiffness and OC, but insulin (P = 0.01), HOMAIR (P = 0.01) and CrossLaps (P = 0.01) were lower in MUT/N. There was no correlation between OC and glucose, OC and HOMAIR in the 140 individuals as a whole or in the separate MUT/N or N/N groups. Conclusions This study suggests that one allele mutation in the GHRHR gene has a greater impact on energy metabolism than on bone quality.

Mutational analyses of the signals involved in the subcellular location of DSCR1

Abstract Background Down syndrome is the most frequent genetic disorder in humans. Rare cases involving partial trisomy of chromosome 21 allowed a small chromosomal region common to all carriers, called Down Syndrome Critical Region (DSCR), to be determined. The DSCR1 gene was identified in this region and is expressed preferentially in the brain, heart and skeletal muscle. Recent studies have shown that DSCR1 belongs to a family of proteins that binds and inhibits calcineurin, a serine-threonine phosphatase. The work reported on herein consisted of a study of the subcellular location of DSCR1 and DSCR1-mutated forms by fusion with a green fluorescent protein, using various cell lines, including human. Results The protein's location was preferentially nuclear, independently of the isoform, cell line and insertion in the GFP's N- or C-terminal. A segment in the C-terminal, which is important in the location of the protein, was identified by deletion. On the other hand, site-directed mutational analyses have indicated the involvement of some serine and threonine residues in this event. Conclusion In this paper, we discuss the identification of amino acids which can be important for subcellular location of DSCR1. The involvement of residues that are prone to phosphorylation suggests that the location and function of DSCR1 may be regulated by kinases and/or phosphatases.