MiRNA expression profiles at different developmental stages by hierarchical clustering and STC analysis.

<p>(A) We found 116 miRNAs that were differentially expressed among the four developmental stages (<i>p</i><0.05). Red indicates a gene that is highly expressed at that stage. Green indicates opposite gene that is lowly expressed at that stage. MiRNA expression was analyzed using the STC method, and 26 model profiles were defined. Three gene expression patterns were significant (<i>p</i><0.05) (red boxes). (B–D) Pair-wise comparisons revealed that 37 miRNAs were differentially expressed (<i>p</i><0.05) between E35 and E45, 4 between E45 and E50, and 40 between E50 and E60. (E–G) miRNA expression profiles 2, 23, and 25 in tooth germ tissue. The horizontal axis represents time, and the vertical axis shows the time series of miRNA expression after log-normalized transformation.</p

MicroRNAome and Expression Profile of Developing Tooth Germ in Miniature Pigs

<div><p>MicroRNAs (miRNAs) play important roles in the regulation of rodent tooth development, but little is known about their role in tooth development in large mammals. We identified 637 unique miRNA sequences in a large-scale screen for miRNA expression profiles in the developing lower deciduous molars of miniature pigs (<em>Sus scrofa</em>) using Illumina Solexa deep sequencing. These candidate miRNAs and another 105 known <em>Sus scrofa</em> miRNAs were included in the custom-designed microarray and used to analyze the miRNA expression profile in the bud, cap, early bell, and late bell stages of tooth development. Microarray analysis revealed 166 transcripts that were differentially expressed in the four stages. Bioinformatic analysis identified 18 key miRNAs, including let-7f, miR-128, miR-200b, and miR-200c, that might play key roles in tooth development. Taken together, our results not only identified the specific microRNAome and expression profile in developing lower deciduous molars of the miniature pig, but they also provided useful information for investigating the molecular mechanism of tooth development in the miniature pig.</p> </div

Analysis of sequencing data.

<p>To obtain mappable sequences from raw sequencing data, we used a series of digital filters to remove various unmappable sequencing reads. (A) Unique families of sequences were generated by sorting raw sequencing reads. “Impure” sequences were then removed by sample preparation, sequencing chemistry and processes, and the optical digital resolution of the sequencer detector. Unique sequences were pulled from selected databases, including mRNA, rRNA, tRNA, snRNA, snoRNA, and Repbase databases. (B) (<i>i</i>) A length filter was used to retain unique sequences of 16–26 nt. (<i>ii</i>) Sequences with copy numbers greater than the predefined cut-off number (default = 3) were also retained. (C) After masking the adaptor sequences and removing contaminated reads, the 92.65% mappable clean reads were processed for advanced analysis. (D) The unique mapped sequences were grouped as “unique sequences mapped to selected species pre-miRNAs in miRbase, and further mapped to pig genome and EST,” and divided into six groups.</p

BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria

Gram-negative bacteria utilize secretion systems to export substrates into their surrounding environment or directly into neighboring cells. These substrates are proteins that function to promote bacterial survival: by facilitating nutrient collection, disabling competitor species or, for pathogens, to disable host defenses. Following a rapid development of computational techniques, a growing number of substrates have been discovered and subsequently validated by wet lab experiments. To date, several online databases have been developed to catalogue these substrates but they have limited user options for in-depth analysis, and typically focus on a single type of secreted substrate. We therefore developed a universal platform, BastionHub, that incorporates extensive functional modules to facilitate substrate analysis and integrates the five major Gram-negative secreted substrate types (i.e. from types I–IV and VI secretion systems). To our knowledge, BastionHub is not only the most comprehensive online database available, it is also the first to incorporate substrates secreted by type I or type II secretion systems. By providing the most up-to-date details of secreted substrates and state-of-the-art prediction and visualized relationship analysis tools, BastionHub will be an important platform that can assist biologists in uncovering novel substrates and formulating new hypotheses

Key miRNA in tooth germ.

<p>Key miRNA in tooth germ.</p

MicroRNA-gene network.

<p>Circular nodes represent genes, and rounded rectangle nodes represent miRNAs. The size of the nodes represents the power of the interrelation among the nodes, and edges between two nodes represent interactions between genes. The more edges a gene has, the more genes that interact with it, and the more central a role it has within the network. (A) The top five key miRNAs in the human network were hsa-miR-200b, hsa-miR-200c, hsa-miR-429, hsa-miR-381, and hsa-let-7f. The top five key mRNAs were SP1, ACVR2B, IGF1R, SMAD2, and ERBB4. (B) The top five key miRNAs in the mouse network were mmu-miR-381, mmu-let-7f, mmu-miR-128, mmu-miR-200b, and mmu-miR-200c. The top five key mRNAs were Ets1, Igf1r, Nr3c1, Sp1, and Frs2.</p

Additional file 6: of Identification of differential microRNA expression during tooth morphogenesis in the heterodont dentition of miniature pigs, SusScrofa

Expression patterns of miRNAs in the four types of teeth during three tooth developmental stages revealed by in situ hybridization. (A1–C4) At E40, miR-107 was expressed in both the epithelium and mesenchyme of the incisor, canine and molar, but expression in the premolar was not detected by in situ hybridization (A1–A4). At E50, localization of miR-107 in all four types of teeth stayed the same, but the expression level was more restricted in the inner enamel epithelium in the incisor, canine, and molar (B1–B4). At E60, mir-107 expression in the premolar increased significantly; in the premolar as in the other three types of teeth, the location was restricted in the inner enamel epithelium (C1–C4). (D1–F4) At E40, miR-133b was expressed in the both epithelium and mesenchyme of all four types of teeth, with a higher signal in the incisor and a lower signal in the other three types of teeth (D1–D4). At E50, miR-133b expression in all four types of teeth stayed the same, but with a lower signal in the incisor (E1–E4). At E60, expression was more restricted in the inner enamel epithelium and increased expression was found in the premolar and molar (F1–F4). Scale bar, 200 μm. Di, first deciduous incisor; Dc, deciduous canine; Dpm, second deciduous premolar; Dm, deciduous molar; E40, embryonic day 40; E50, embryonic day 50; E60, embryonic day 60. (PDF 4755 kb

Additional file 4: of Identification of differential microRNA expression during tooth morphogenesis in the heterodont dentition of miniature pigs, SusScrofa

Detectable transcripts in different type tooth germ during different development stages. (DOC 1429 kb