Assessment of Color Perception and Preference with Eye-Tracking Analysis in a Dental Treatment Environment.

Nowadays, medical facilities are developing their treatment environment to provide better services to their patients. In particular, dental hospitals have been considered uncomfortable and uninviting spaces, which needs to change so that people can visit easily and feel more relaxed. However, only a few systematic studies have reported on the demand for building a comfortable space. This study aimed to investigate gaze characteristics based on a color preference survey of the dental unit chair, which has the most influence on spatial perception in the dental treatment environment, using an eye tracking technique for color. The results of this study showed that the color perception by eye tracking and the color preference by survey did not tend to match. The color most viewed by a majority of subjects was pink, which attracted a high level of attention, regardless of personal preference. In addition, for the psychological color images associated with color preference, the subjects tended to prefer images such as warmth, friendliness, and calmness. This appeared to reflect the psychology of the subjects who wished to replace their feelings of anxiety or fear when going to the dental hospital with comfort and tranquility. Therefore, colors that can provide comfort and tranquility to patients should be considered first as visual elements (e.g., brown) in creating a dental treatment environment.

Mechanical Assessment of Fatigue Characteristics between Single- and Multi-Directional Cyclic Loading Modes on a Dental Implant System.

Mechanical testing based on ISO 14801 standard is generally used to evaluate the performance of the dental implant system according to material and design changes. However, the test method is difficult to reflect on the clinical environment because the ISO 14801 standard does not take into account the various loads from different directions during chewing motion. In addition, the fracture pattern of the implant system can occur both in the horizontal and the vertical directions. Therefore, the purpose of this study was to compare fatigue characteristics and fracture patterns between single directional loading conditions based on the ISO 14801 standard and multi-directional loading condition. Firstly, the static test was performed on five specimens to derive the fatigue load, and the fatigue load was chosen as 40% of the maximum load measured in the static test. Subsequently, the fatigue test was performed considering the single axial/occlusal (AO), AO with facial/lingual (AOFL) and AO with mesial/distal (AOMD) directions, and five specimens were used for each fatigue loading modes. In order to analyze the fatigue characteristics, the fatigue cycle at the time of specimen fracture and displacement change of the specimen every 500 cycles were measured. Field emission scanning electron microscopy (FE-SEM) was used to analyze the fracture patterns and the fracture surface. Compared to the AO group, the fatigue cycle of the AOFL and AOMD groups showed lower about five times, while the displacement gradually increased with every 500 cycles. From FE-SEM results, there were no different surface morphology characteristics among three groups. However, the AOMD group showed a vertical slip band. Therefore, our results suggest that the multi-directional loading mode under the worst-case environment can reproduce the vertical fracture pattern in the clinical situation and may be essential to reflect on the dental implant design including connection types and surface treatments.

Optimized Dental Implant Fixture Design for the Desirable Stress Distribution in the Surrounding Bone Region: A Biomechanical Analysis.

The initial stability of a dental implant is known to be an indicator of osseointegration at immediate loading upon insertion. Implant designs have a fundamental role in the initial stability. Although new designs with advanced surface technology have been suggested for the initial stability of implant systems, verification is not simple because of various assessment factors. Our study focused on comparing the initial stability between two different implant systems via design aspects. A simulated model corresponding to the first molar derived from the mandibular bone was constructed. Biomechanical characteristics between the two models were compared by finite element analysis (FEA). Mechanical testing was also performed to derive the maximum loads for the two implant systems. CMI IS-III active (IS-III) had a more desirable stress distribution than CMI IS-II active (IS-II) in the surrounding bone region. Moreover, IS-III decreased the stress transfer to the nerve under the axial loading direction more than IS-II. Changes of implant design did not affect the maximum load. Our analyses suggest that the optimized design (IS-III), which has a bigger bone volume without loss of initial fixation, may minimize the bone damage during fixture insertion and we expect greater effectiveness in older patients.

Protective Effects of Melon Extracts on Bone Strength, Mineralization, and Metabolism in Rats with Ovariectomy-Induced Osteoporosis.

A polyphenolic extract from melon (Cucumis melo L.), as a potential source of natural antioxidants, has been reported to have a positive effect on osteoblast activity. In this study, the protective effects of heat-treated melon extract (ECO-A) on bone strength, mineralization, and metabolism were examined in osteoporotic rat models. Osteoporosis was induced by ovariectomy (OVX) in female rats and then maintained for 8 weeks, along with the ingestion of phosphate-buffered saline (PBS, OVXP) or ECO-A (OVXE) for an additional 4 weeks. At a pre-determined timepoint, bone strengths, as well as bone mineral contents (BMC) and the density (BMD) of femurs and/or lumbar spines extracted from each animal, were measured by a mechanical test and dual-energy X-ray absorptiometry, respectively. Moreover, several biochemical markers for bone turnover were analyzed by respective colorimetric assay kits in addition to clinical analyses. The maximum load and stiffness of femurs from the OVXE group were found to be significantly higher than the other groups. Furthermore, the OVXE group showed significantly higher BMC, BMD, and bone volume than the OVX and OVXP groups, which were comparable to the non-OVX (sham) group. The levels of bone formation and resorption markers in the OVXE group were similar to the sham group, but significantly different from other groups. In conclusion, these results suggest that ECO-A can play potentially positive roles in the protection of bone loss in rats with OVX-induced osteoporosis.

Prediction of Host-Specific Genes by Pan-Genome Analyses of the Korean Ralstonia solanacearum Species Complex.

The soil-borne pathogenic Ralstonia solanacearum species complex (RSSC) is a group of plant pathogens that is economically destructive worldwide and has a broad host range, including various solanaceae plants, banana, ginger, sesame, and clove. Previously, Korean RSSC strains isolated from samples of potato bacterial wilt were grouped into four pathotypes based on virulence tests against potato, tomato, eggplant, and pepper. In this study, we sequenced the genomes of 25 Korean RSSC strains selected based on these pathotypes. The newly sequenced genomes were analyzed to determine the phylogenetic relationships between the strains with average nucleotide identity values, and structurally compared via multiple genome alignment using Mauve software. To identify candidate genes responsible for the host specificity of the pathotypes, functional genome comparisons were conducted by analyzing pan-genome orthologous group (POG) and type III secretion system effectors (T3es). POG analyses revealed that a total of 128 genes were shared only in tomato-non-pathogenic strains, 8 genes in tomato-pathogenic strains, 5 genes in eggplant-non-pathogenic strains, 7 genes in eggplant-pathogenic strains, 1 gene in pepper-non-pathogenic strains, and 34 genes in pepper-pathogenic strains. When we analyzed T3es, three host-specific effectors were predicted: RipS3 (SKWP3) and RipH3 (HLK3) were found only in tomato-pathogenic strains, and RipAC (PopC) were found only in eggplant-pathogenic strains. Overall, we identified host-specific genes and effectors that may be responsible for virulence functions in RSSC in silico. The expected characters of those genes suggest that the host range of RSSC is determined by the comprehensive actions of various virulence factors, including effectors, secretion systems, and metabolic enzymes.

Finite Element Analysis of Novel Separable Fixture for Easy Retrievement in Case with Peri-Implantitis.

Peri-implantitis is a common complication following dental implant placement, which may lead to bone loss and fixation failure. With the conventional fixture, it is difficult to perfectly clear-up the infection. To solve this, we have designed a separable fixture of which the top part is replaceable. This study aimed to compare the structural and biomechanical stability of the separable and conventional fixture. A single surgical model corresponding to the first molar in a virtual mandible model and conventional/separable implants were reproduced to compare the biomechanical characteristics of the implants using finite element analysis (FEA). The loading condition was 200N preload in the first step, and 100N (Axial), 100N (15°), and 30N (45°) in the second step. The stress distribution on the cortical bone in the separable implant was lower than the conventional implant. In particular, the Peak von Mises Stress (PVMS) values of the separable implant under lateral load was found to be about twice as low as that of the conventional implant. In this study, we suggest that the separable implant has an equivalent biomechanical stability compared to the conventional implant, is easy to retrieve in the case of peri-implantitis, and has an excellent initial stability after the surgery when used in stage 2.

Analysis of Genetic and Pathogenic Diversity of Ralstonia solanacearum Causing Potato Bacterial Wilt in Korea.

The Ralstonia solanacearum species complex (RSSC) can be divided into four phylotypes, and includes phenotypically diverse bacterial strains that cause bacterial wilt on various host plants. This study used 93 RSSC isolates responsible for potato bacterial wilt in Korea, and investigated their phylogenetic relatedness based on the analysis of phylotype, biovar, and host range. Of the 93 isolates, twenty-two were identified as biovar 2, eight as biovar 3, and sixty-three as biovar 4. Applied to the phylotype scheme, biovar 3 and 4 isolates belonged to phylotype I, and biovar 2 isolates belonged to phylotype IV. This classification was consistent with phylogenetic trees based on 16S rRNA and egl gene sequences, in which biovar 3 and 4 isolates clustered to phylotype I, and biovar 2 isolates clustered to phylotype IV. Korean biovar 2 isolates were distinct from biovar 3 and 4 isolates pathologically as well as genetically - all biovar 2 isolates were nonpathogenic to peppers. Additionally, in host-determining assays, we found uncommon strains among biovar 2 of phylotype IV, which were the tomato-nonpathogenic strains. Since tomatoes are known to be highly susceptible to RSSC, to the best of our knowledge this is the first report of tomato-nonpathogenic potato strains. These results imply the potential prevalence of greater RSSC diversity in terms of host range than would be predicted based on phylogenetic analysis.

Time-resolved pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae.

BACKGROUND: Plant-pathogen interactions at early stages of infection are important to the fate of interaction. Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight, which is a devastating disease in rice. Although in vivo and in vitro systems have been developed to study rice-Xoo interactions, both systems have limitations. The resistance mechanisms in rice can be better studied by the in vivo approach, whereas the in vitro systems are suitable for pathogenicity studies on Xoo. The current in vitro system uses minimal medium to activate the pathogenic signal (expression of pathogenicity-related genes) of Xoo, but lacks rice-derived factors needed for Xoo activation. This fact emphasizes the need of developing a new in vitro system that allow for an easy control of both pathogenic activation and for the experiment itself. RESULTS: We employed an in vitro system that can activate pathogenicity-related genes in Xoo using rice leaf extract (RLX) and combined the in vitro assay with RNA-Seq to analyze the time-resolved genome-wide gene expression of Xoo. RNA-Seq was performed with samples from seven different time points within 1 h post-RLX treatment and the expression of up- or downregulated genes in RNA-Seq was validated by qRT-PCR. Global analysis of gene expression and regulation revealed the most dramatic changes in functional categories of genes related to inorganic ion transport and metabolism, and cell motility. Expression of many pathogenicity-related genes was induced within 15 min upon contact with RLX. hrpG and hrpX expression reached the maximum level within 10 and 15 min, respectively. Chemotaxis and flagella biosynthesis-related genes and cyclic-di-GMP controlling genes were downregulated for 10 min and were then upregulated. Genes related to inorganic ion uptake were upregulated within 5 min. We introduced a non-linear regression fit to generate continuous time-resolved gene expression levels and tested the essentiality of the transcriptionally upregulated genes by a pathogenicity assay of lesion length using single-gene knock-out Xoo strains. CONCLUSIONS: The in vitro system combined with RNA-Seq generated a genome-wide time-resolved pathogenic gene expression profile within 1 h of initial rice-Xoo interactions, demonstrating the expression order and interaction dependency of pathogenic genes. This combined system can be used as a novel tool to study the initial interactions between rice and Xoo during bacterial blight progression.

Transcriptome-Based Identification of Differently Expressed Genes from Xanthomonas oryzae pv. oryzae Strains Exhibiting Different Virulence in Rice Varieties.

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight (BB) in rice (Oryza sativa L.). In this study, we investigated the genome-wide transcription patterns of two Xoo strains (KACC10331 and HB1009), which showed different virulence patterns against eight rice cultivars, including IRBB21 (carrying Xa21). In total, 743 genes showed a significant change (p-value < 0.001 in t-tests) in their mRNA expression levels in the HB1009 (K3a race) strain compared with the Xoo KACC10331 strain (K1 race). Among them, four remarkably enriched GO terms, DNA binding, transposition, cellular nitrogen compound metabolic process, and cellular macromolecule metabolic process, were identified in the upregulated genes. In addition, the expression of 44 genes was considerably higher (log2 fold changes > 2) in the HB1009 (K3a race) strain than in the Xoo KACC10331 (K1 race) strain. Furthermore, 13 and 12 genes involved in hypersensitive response and pathogenicity (hrp) and two-component regulatory systems (TCSs), respectively, were upregulated in the HB1009 (K3a race) strain compared with the Xoo KACC10331 (K1 race) strain, which we determined using either quantitative real-time PCR analysis or next-generation RNA sequencing. These results will be helpful to improve our understanding of Xoo and to gain a better insight into the Xoo-rice interactions.

Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation.

Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.

PCR-based assay for rapid and specific detection of the new Xanthomonas oryzae pv. oryzae K3a race using an AFLP-derived marker.

We describe the development of a polymerase chain reaction method for the rapid, precise, and specific detection of the Xanthomonas oryzae pv. oryzae (Xoo) K3a race, the bacterial blight pathogen of rice. The specific primer set was designed to amplify a genomic locus derived from an amplified fragment length polymorphism specific for the K3a race. The 1,024 bp amplicon was generated from the DNA of 13 isolates of Xoo K3a races out of 119 isolates of other races, pathovars, and Xanthomonas species. The assay does not require isolated bacterial cells or DNA extraction. Moreover, the pathogen was quickly detected in rice leaf 2 days after inoculation with bacteria and at a distance of 8 cm from the rice leaf 5 days later. The results suggest that this PCR-based assay will be a useful and powerful tool for the detection and identification of the Xoo K3a race in rice plants as well as for early diagnosis of infection in paddy fields.

Functional analysis of the aroC gene encoding chorismate synthase from Xanthomonas oryzae pathovar oryzae.

Xanthomonas oryzae pv. oryzae causes bacterial blight in rice, and this bacterial blight has been widely found in the major rice-growing areas. We constructed a transposon mutagenesis library of X. oryzae pv. oryzae and identified a mutant strain (KXOM9) that is deficient for pigment production and virulence. Furthermore, the KXOM9 mutant was unable to grow in minimal medium lacking aromatic amino acids. Thermal asymmetric interlaced-PCR and sequence analysis of KXOM9 revealed that the transposon was inserted into the aroC gene, which encodes a chorismate synthase in various bacterial pathogens. In planta growth assays revealed that bacterial growth of the KXOM9 mutant in rice leaves was severely reduced. Genetic complementation of this mutant with a 7.9-kb fragment containing aroC restored virulence, pigmentation, and prototrophy. These results suggest that the aroC gene plays a crucial role in the growth, attenuation of virulence, and pigment production of X. oryzae pv. oryzae.

Electrophoretic karyotyping and construction of a bacterial artificial chromosome library of the winter mushroom Flammulina velutipes.

An electrophoretic karyotype of Korean Flammulina velutipes was obtained using contour-clamped homogeneous electric field (CHEF) gel electrophoresis. The monokaryotic progenies (4019-20 and 4019-18) and a dikaryotic strain (4019-2018) had 6-8 chromosomes, with sizes ranging from 1.6 to 5.8 megabase (Mb) pairs. Among the 3 strains that were examined, strain 4019-20 resolved into at least 7 chromosomes, with a total genome size of approximately 26.7Mb. We selected several chromosome-specific genes from the cDNA library of F. velutipes using Southern hybridization analysis. In order to determine the whole genome sequence, we constructed a bacterial artificial chromosome (BAC) library of the 4019-20 strain. The BAC library comprised 3840 clones, and the insert size ranged from 60 to 228kb, with an average size of 136kb.

Virulence analysis and gene expression profiling of the pigment-deficient mutant of Xanthomonas oryzae pathovar oryzae.

Xanthomonas oryzae pathovar oryzae (Xoo) causes bacterial blight disease in rice (Oryza sativa L.). For a study of function, we constructed a random insertion mutant library of Xoo using a Tn5 transposon and isolated the mutant strain (M11; aroK::Tn5) that had extremely low pigment production. In addition, M11 had decreased virulence against the susceptible rice cultivar IR24. Thermal asymmetric interlaced-PCR and sequence analysis of M11 revealed that the transposon was inserted into the aroK gene (which encodes a shikimate kinase). To investigate the expression patterns of the pigment- and virulence-deficient mutant, DNA microarray analysis was performed. In addition, reverse transcriptase-PCR was performed to confirm the expression levels of several genes, including the aro genes of the aroK mutant. Our findings reveal that several crucial genes for virulence, including cellulase and hypersensitive response and pathogenicity (hrp) genes, were regulated by mutations in the aroK gene.

Molecular analysis of the hrp gene cluster in Xanthomonas oryzae pathovar oryzae KACC10859.

Xanthomonas oryzae pathovar oryzae is the causal agent of rice bacterial blight. The plant pathogenic bacterium X. oryzae pv. oryzae expresses a type III secretion system that is necessary for both the pathogenicity in susceptible hosts and the induction of the hypersensitive response in resistant plants. This specialized protein transport system is encoded by a 32.18kb hrp (hypersensitive response and pathogenicity) gene cluster. The hrp gene cluster is composed of nine hrp, nine hrc (hrp conserved) and eight hpa (hrp-associated) genes and is controlled by HrpG and HrpX, which are known as regulators of the hrp gene cluster. Before mutational analysis of these hrp genes, the transcriptional linkages of the core region of the hrp gene cluster from hpaB to hrcC of the X. oryzae pv. oryzae KACC10859 was determined and the non-polarity of EZTn5 insertional mutagenesis was demonstrated by reverse transcription polymerase chain reaction. Pathogenicity assays of these non-polar hrp mutants were carried out on the susceptible rice cultivar, Milyang-23. According to the results of these assays, all hrp-hrc, except hrpF, and hpaB mutants lost their pathogenicity, which indicates that most hrp-hrc genes encode essential pathogenicity factors. On the other hand, most hpa mutants showed decreased virulence in a different pattern, i.e., hpa genes are not essential but are important for pathogenicity.

Analysis of virulence and growth of a purine auxotrophic mutant of Xanthomonas oryzae pathovar oryzae.

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight of rice. A random insertional mutant library of Xoo KACC10331 was constructed using a Tn5-derived transposon, and the virulence of the mutants against the susceptible rice cultivar IR24 was assayed. After the virulence assay, the M793 (purD::Tn5) mutant that had reduced virulence against the rice plants was isolated. Thermal asymmetric interlaced-PCR and sequence analysis revealed that the transposon was inserted into the purD gene (encodes a phosphoribosylamine-glycine ligase) of the M793 mutant. The reverse transcriptase-PCR assay revealed that the mutation of the purD gene did not affect the expression of other purine biosynthesis genes. However, the M793 mutant required exogenous purines and thiamine for growth in minimal media. These results indicate that the purD gene plays a crucial role in the growth and virulence of Xoo.

Construction of a bacterial artificial chromosome library and characterization of hrp/hrc gene cluster of Pseudomonas syringae pathovar tagetis LMG5090.

Pseudomonas syringae pv. tagetis causes apical chlorosis of several plant species in the Asteraceae, including marigold. As a means to facilitate the isolation of pathogenicity genes and to characterize the genome of this bacterium, we have constructed a bacterial artificial chromosome library of P. syringae pv. tagetis strain LMG5090. The library consists of 1,536 clones with insert size ranging from 30 to 160 kb and an average size of 86 kb. Based upon colony hybridization, the BAC clone 420E23 containing the hrp/hrc gene cluster encoding the type III secretion system was identified from this library and subsequently shotgun sequenced. The hrp/hrc gene cluster of P. syringae pv. tagetis has a 23 kb sequence which contains 27 open reading frames. Comparative analysis of the hrp/hrc gene cluster of P. syringae pv. tagetis LMG5090, P. syringae pv. tomato DC3000, P. syringae pv. syringae B728a, and P. syringae pv. phaseolicola 1448A revealed that the entire hrp/hrc gene cluster of P. syringae pv. tagetis is conserved and identically arranged in all four pathovars.

The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice.

The nucleotide sequence was determined for the genome of Xanthomonas oryzae pathovar oryzae (Xoo) KACC10331, a bacterium that causes bacterial blight in rice (Oryza sativa L.). The genome is comprised of a single, 4 941 439 bp, circular chromosome that is G + C rich (63.7%). The genome includes 4637 open reading frames (ORFs) of which 3340 (72.0%) could be assigned putative function. Orthologs for 80% of the predicted Xoo genes were found in the previously reported X.axonopodis pv. citri (Xac) and X.campestris pv. campestris (Xcc) genomes, but 245 genes apparently specific to Xoo were identified. Xoo genes likely to be associated with pathogenesis include eight with similarity to Xanthomonas avirulence (avr) genes, a set of hypersensitive reaction and pathogenicity (hrp) genes, genes for exopolysaccharide production, and genes encoding extracellular plant cell wall-degrading enzymes. The presence of these genes provides insights into the interactions of this pathogen with its gramineous host.