Integration of the PDF signaling model with the known PTTH signaling pathway.

<p>Solid lines indicate demonstrated or highly likely pathways, and dashed lines indicate hypothetical pathways. Gαs: G protein αs subunit, AC: adenylate cyclase, AMP: adenosine monophosphate, cAMP: cyclic AMP, EPAC: exchange protein directly activated by cAMP, eIF4e: eukaryotic translation initiation factor 4E, 4E-BP: eIF4E binding protein, TOR: target of rapamycin, PKA: protein kinase A, PKC: protein kinase C, PI3K: phosphatidylinositol 3-kinase, AKT: protein kinase B, CREB: cAMP response element-binding protein, MAPK: mitogen-activated protein kinase, ERK: extracellular signal-regulated kinase, MEK: MAP kinase kinase, Raf: MAP kinase kinase kinase, S6: ribosomal protein S6, p70S6K: 70 kDa S6 kinase, PLC: phospholipase C, DAG: diacylglycerol, IP₃: inositol 1,4,5-trisphosphate, IP₃R: IP₃ receptor, CaM: calmodulin.</p

Pigment Dispersing Factor Regulates Ecdysone Biosynthesis via <i>Bombyx</i> Neuropeptide G Protein Coupled Receptor-B2 in the Prothoracic Glands of <i>Bombyx mori</i>

<div><p>Ecdysone is the key hormone regulating insect growth and development. Ecdysone synthesis occurs in the prothoracic glands (PGs) and is regulated by several neuropeptides. Four prothoracicotropic and three prothoracicostatic factors have been identified to date, suggesting that ecdysone biosynthesis is intricately regulated. Here, we demonstrate that the neuropeptide pigment dispersing factor (PDF) stimulates ecdysone biosynthesis and that this novel signaling pathway partially overlaps with the prothoracicotropic hormone (PTTH) signaling pathway. We performed transcriptome analysis and focused on receptors predominantly expressed in the PGs. From this screen, we identified a candidate orphan G protein coupled receptor (GPCR), <i>Bombyx</i> neuropeptide GPCR-B2 (BNGR-B2). <i>BNGR-B2</i> was predominantly expressed in ecdysteroidogenic tissues, and the expression pattern in the PGs corresponded to the ecdysteroid titer in the hemolymph. Furthermore, we identified PDF as a ligand for BNGR-B2. PDF stimulated ecdysone biosynthesis in the PGs, but the stimulation was only observed in the PGs during a specific larval stage. PDF did not affect the transcript level of known ecdysone biosynthetic enzymes, and inhibiting transcription did not suppress ecdysone biosynthesis, suggesting that the effects of PDF might be mediated by translational regulation and/or post-translational modification. In addition, the participation of protein kinase A (PKA), phosphatidylinositol 3-kinase (PI3K), target of rapamycin (TOR) and eukaryotic translation initiation factor 4E (eIF4E)-binding protein (4E-BP) in the PDF signaling pathway was discovered.</p></div

Signaling pathways involved in PDF-induced ecdysone biosynthesis.

<p>(A) Effect of PDF on the transcript level of ecdysone biosynthesis-related enzymes in the PGs. PGs of V7 larvae were treated with or without PDF. The transcript levels of <i>nvd</i>, <i>nm-g</i>, <i>spo</i>, <i>phm</i>, <i>dib</i> and <i>sad</i> were quantified with Q-PCR. Each datum point represents the mean ±SEM (n = 3). (B-D) Effect of (B) transcript inhibitor (actinomycin D: ActD, 10 µM), (C) PKA inhibitor (H-89, 0.1 mM) and (D) translation inhibitor (cycloheximide: CHX, 0.2 mM) on PDF-induced ecdysone biosynthesis. Each datum point represents the mean ±SEM (n = 10). (E, F) Effect of (E) PI3K inhibitor (LY294002: LY, 50 µM) and (F) TOR inhibitor (rapamycin: Rap, 10 µM) on PDF-induced ecdysone biosynthesis. Each datum point represents the mean ±SEM (n = 3 and 4). Statistically significant differences were evaluated by Student's <i>t</i>-test (***P<0.001, **P<0.01). (G) Effect of PDF on the levels of p-ERK and p-4E-BP in cultured PGs. The phosphorylated proteins were examined by immunoblotting, and α-tubulin was used as a loading control. (H, I) Effect of (H) PI3K inhibitor (LY294002: LY, 50 µM) and (I) PKA inhibitor (H-89, 0.1 mM) on p-4E-BP levels in cultured PGs. The phosphorylated proteins were examined by immunoblotting, and α-tubulin was used as a loading control.</p

Screening of candidate receptors.

<p>(A) Tissue distribution of <i>BNGR-B2</i>. The expression of <i>BNGR-B2</i> was measured by RT-PCR in the selected tissues from gut-purged fifth instar larvae (p50T strain). PG: prothoracic gland, BR: brain, FB: fat body, MT: Malpighian tubule, ASG: anterior silk gland, MG: midgut, TE: testis and OV: ovary. (B) Developmental profile of <i>BNGR-B2</i> in the PGs. The expression of <i>BNGR-B2</i> was measured by Q-PCR. The timing of molting, gut purge and pupation in our rearing conditions is indicated with arrows. Each datum point represents the mean ±SEM (n = 3). The dashed line indicates the outline of the hemolymph ecdysteroid titer described by Koyama et al., 2004 (4th instar), Sakurai et al., 1998 (5th instar) and Kaneko et al., 2006 (5th instar). (A, B) <i>RpL3</i> was used as an internal standard.</p

Characterization of BNGR-B2.

<p>(A) Phylogenetic relationship of BNGR-B2 and highly homologous receptors. The tree was generated based on the amino acid sequences of selected regions with the neighbor-joining method using the ClustalX multiple alignment program and a bootstrap value of 1000 trials for each branch position. The indicated numbers are the bootstrap values as a percentage of 1000 replicates, and the scale bar indicates 0.05 changes per residue. Bootstrap values greater than 50% are indicated. The <i>Mus musculus</i> calcitonin receptor (CR) was used as an outgroup. (B) Ligand-binding analysis of BNGR-B2 by examining the change in intracellular cAMP levels. BNGR-B2-expressing HEK293 cells were treated with 1 µM of the candidate BNGR-B2 ligands (PDF and DH31). Each datum point represents the mean ±SEM (n = 5). Statistically significant differences were evaluated by Student's <i>t</i>-test (***P<0.001).</p

Dinuclear Ruthenium(III)–Ruthenium(IV) Complexes, Having a Doubly Oxido-Bridged and Acetato- or Nitrato-Capped Framework

Dinuclear ruthenium complexes in a mixed-valence state of Ru^III–Ru^IV, having a doubly oxido-bridged and acetato- or nitrato-capped framework, [{Ru^III,IV(ebpma)}₂(μ-O)₂(μ-L)]­(PF₆)₂ [ebpma = ethylbis­(2-pyridylmethyl)­amine; L = CH₃COO^– (<b>1</b>), NO₃^– (<b>2</b>)], were synthesized. In aqueous solutions, the diruthenium complex <b>1</b> showed multiple redox processes accompanied by proton transfers depending on the pH. The protonated complex of <b>1</b>, which is described as <b>1</b>_<b>H+</b>, was obtained

Additional file 6: of Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs

Multiple alignment of sequences found with each motif. Sequences found by searching with the motifs were aligned by Infernal and shown in Stockholm format. Refseq ID of the origin of the sequence, positions of the 3′ UTR in the mRNAs of the Refseq ID, and positions of the sequence found by motif searching was shown in the left column. Common secondary structure (SS_cons) and consensus sequence (RF) are also shown. (PDF 214 kb

Dinuclear Ruthenium(III)–Ruthenium(IV) Complexes, Having a Doubly Oxido-Bridged and Acetato- or Nitrato-Capped Framework

Dinuclear ruthenium complexes in a mixed-valence state of Ru^III–Ru^IV, having a doubly oxido-bridged and acetato- or nitrato-capped framework, [{Ru^III,IV(ebpma)}₂(μ-O)₂(μ-L)]­(PF₆)₂ [ebpma = ethylbis­(2-pyridylmethyl)­amine; L = CH₃COO^– (<b>1</b>), NO₃^– (<b>2</b>)], were synthesized. In aqueous solutions, the diruthenium complex <b>1</b> showed multiple redox processes accompanied by proton transfers depending on the pH. The protonated complex of <b>1</b>, which is described as <b>1</b>_<b>H+</b>, was obtained

Gene expression profiles and schematic representation of the method.

<p>A. Log fold change in gene expression levels of 1047 genes showing greater than 2-fold up-regulation in dendritic cells on LPS stimulation at 7 time points. The orange blocks illustrate the partitioning of the genes into 3 groups based on the time of their highest fold change - T1: 0.5–1 hour, T2: 2–4 hours, T3: 6–8 hours, used to identify the most probable paths between them within the molecular network. B. Schematic representation of the minimum cost network flow optimization used to predict an optimal sub-network in active DCs from a large molecular network containing protein-protein interactions, protein-DNA interactions and post-translational modifications. The sub-network is obtained by optimizing the flow from the auxiliary source node (S) to the auxiliary sink node (T) such that it includes edges with the lowest edge cost, A, (highest edge reliability) and the highest edge capacity, C, (greatest fold change in expression of adjacent genes). The predicted minimum cost flow path (in red) passes through at least one of genes A and B which show altered expression between 0.5–1 hour, followed by one or more of the genes E and F with significant change in expression between 2–4 hours, before finally passing through at least one of the genes, I and J, with altered expression between 6–8 hours.</p

Additional file 4: of TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis

Percent occurrence of core promoter motifs in various core promoter classes. (DOC 26 kb