OrchidBase 4.0: a database for orchid genomics and molecular biology.

BACKGROUND: The Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic information of this plant. Previously, we established OrchidBase, which contains expressed sequence tags (ESTs) from different tissues and developmental stages of Phalaenopsis as well as biotic and abiotic stress-treated Phalaenopsis. The database includes floral transcriptomic sequences from 10 orchid species across all the five subfamilies of Orchidaceae. DESCRIPTION: Recently, the whole-genome sequences of Apostasia shenzhenica, Dendrobium catenatum, and Phalaenopsis equestris were de novo assembled and analyzed. These datasets were used to develop OrchidBase 4.0, including genomic and transcriptomic data for these three orchid species. OrchidBase 4.0 offers information for gene annotation, gene expression with fragments per kilobase of transcript per millions mapped reads (FPKM), KEGG pathways and BLAST search. In addition, assembled genome sequences and location of genes and miRNAs could be visualized by the genome browser. The online resources in OrchidBase 4.0 can be accessed by browsing or using BLAST. Users can also download the assembled scaffold sequences and the predicted gene and protein sequences of these three orchid species. CONCLUSIONS: OrchidBase 4.0 is the first database that contain the whole-genome sequences and annotations of multiple orchid species. OrchidBase 4.0 is available at http://orchidbase.itps.ncku.edu.tw/.

Chromosome-scale assembly of the Kandelia obovata genome.

The mangrove Kandelia obovata (Rhizophoraceae) is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia. Herein, a chromosome-level reference genome of K. obovata based on PacBio, Illumina, and Hi-C data is reported. The high-quality assembled genome size is 177.99 Mb, with a contig N50 value of 5.74 Mb. A large number of contracted gene families and a small number of expanded gene families, as well as a small number of repeated sequences, may account for the small K. obovata genome. We found that K. obovata experienced two whole-genome polyploidization events: one whole-genome duplication shared with other Rhizophoreae and one shared with most eudicots (γ event). We confidently annotated 19,138 protein-coding genes in K. obovata and identified the MADS-box gene class and the RPW8 gene class, which might be related to flowering and resistance to powdery mildew in K. obovata and Rhizophora apiculata, respectively. The reference K. obovata genome described here will be very useful for further molecular elucidation of various traits, the breeding of this coastal shelterbelt species, and evolutionary studies with related taxa.

[Effect of self-made colloid paste on gingival retraction in dogs].

PURPOSE: To evaluate the efficiency of self-made paste on gingival retraction in dogs as well as its potential clinical application. METHODS: Forty teeth from two mature dogs were prepared with 0.5 mm wide shoulder in the lip and buccal sides of the teeth, and then divided into four groups randomly. The gingival grooves of the four groups were filled with self-made colloid paste, Expasyl gingival retraction paste, gingival retraction cord, and medicated (15.5% Fe2SO4 solution) gingival retraction cord, respectively. The gingival grooves models before and after gingival retraction were analyzed using the image precise mapper instrument; the gingival width and height of the gingival groove were compared using SAS6.12 software package. RESULTS: The changes of gingival width of the gingival groove before and after gingival retraction were not significant between the four groups. However, the gingival height of the gingival groove in the medicated gingival retraction cord group increased significantly [(0.423 + or - 0.348) mm before gingival retraction and (0.623 + or - 0.278) mm after gingival retraction] compared with the other three groups. CONCLUSIONS: The self-made colloid paste for gingival retraction is efficient like Expasyl gingival retraction paste and gingival retraction cord with potential clinical application, while the medicated gingival retraction cord can induce gingival shrinkage. Supported by Research Fund of Science and Technology Bureau of Huangpu District,Shanghai.

[The influence of Streptococcus sanguis on corrosion resistance of magnetic retainer].

PURPOSE: To study the effect of Streptococcus sanguis on corrosion resistance of magnetic retainers in which are encapsulated with stainless steel artificial saliva. METHODS: A magnetic retainer was put in one culture flask,which was filled with artificial saliva.Ten of them were added Streptococcus sanguis suspension,the others were added PBS as control.The culture flasks were cultivated in incubator(36 degrees centigrade). 5 ml suspension was dislodged from each flask at the 3rd, 10th and 20th day. The quantity of Fe(3+) and Mn(2+) was detected.Statistical analysis of paired t test was performed with SPSS10.0 software package. RESULTS: When Streptococcus sanguis existed, the quantity of Fe(3+) and Mn(2+) was significantly higher than that in the control (P<0.01). CONCLUSION: The existence of Streptococcus sanguis destroys the corrosion resistance of magnetic retainers remarkably.

[The efficacy of dental plaque removed by using sonic electric toothbrush in children].

PURPOSE: To evaluate the efficacy of using sonic electric toothbrush to clean the teeth and control dental plaque in children. METHODS: 50 children aged 6 to 7 years old were selected and divided into 2 groups according to the use of sonic electric toothbrush and traditional manual toothbrush (control group). The numbers of dental plaque surface and PLI before and after tooth brushing were recorded. The data of the two groups were analyzed with SPSS10.0 software package for student's t test and chi(2) test. RESULTS: The ratio of dental plaque removal was 70.22% by using sonic electric toothbrush and 39.08% in the control group. The efficacy of dental plaque removal on the lingual and mesial buccal surface by using sonic electric toothbrush was 2 times greater than the control group. The PLI and the ratio of dental plaque removal were significantly different between the 2 groups (P<0.001). CONCLUSIONS: Sonic electric toothbrush can help children effectively remove dental plaque. It's an efficient instrument for oral care of children.

[Analysis of conservative therapies for posterior teeth with longitudinal fractures.].

PURPOSE: To explore the ideal method for conservative therapies of posterior teeth with longitudinal fracture. METHODS: The records of 297 cases undergoing conservative treatment of posterior teeth with longitudinal fracture were analyzed regarding to the position, etiology and the time of treatment from fracture and the causes of failure. RESULTS: 258 cases were conserved effectively and 39 cases were extracted due to failure.16 cases had failure 1 week after treatment. All the patients were followed up for 2 to 10 years, and the rate of success was 86.87%. CONCLUSION: With fixed early and appropriate treatment, the teeth can be conserved effectively and exert good masticatory function .