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.

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.

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

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).

Contributions from the systematic review of economic evaluations: the case of childhood hepatitis A vaccination in Brazil

The aim of this study was to present the contributions of the systematic review of economic evaluations to the development of a national study on childhood hepatitis A vaccination. A literature review was performed in EMBASE, MEDLINE, WOPEC, HealthSTAR, SciELO and LILACS from 1995 to 2010. Most of the studies (8 of 10) showed favorable cost-effectiveness results. Sensitivity analysis indicated that the most important parameters for the results were cost of the vaccine, hepatitis A incidence, and medical costs of the disease. Variability was observed in methodological characteristics and estimates of key variables among the 10 studies reviewed. It is not possible to generalize results or transfer epidemiological estimates of resource utilization and costs associated with hepatitis A to the local context. Systematic review of economic evaluation studies of hepatitis A vaccine demonstrated the need for a national analysis and provided input for the development of a new decision-making model for Brazil.