Role of SoxB binding sites in the regulation of <i>cyp26a1</i> expression in the anterior neural plate (ANP).

<p>(A) Representation of the cANE region in the zebrafish genome; 3 predicted SoxB binding sites are indicated; the green channel represents the intensity of the anti-Sox2 ChipSeq signal in this region according to [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150639#pone.0150639.ref034" target="_blank">34</a>]. (B) A logo representing the composite consensus binding site for SoxB/Oct factors [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150639#pone.0150639.ref033" target="_blank">33</a>] is aligned with the predicted Sox binding site (Sox_BS1) overlapping Motif1 (cANE 45–59). The mutSox TT->CC mutation destroying the Sox-binding half-site is indicated. (C-F) egfp in situ hybridization representing enhancer activity of cANE ΔSoxBS2-3, where both Sox_BS2 and Sox_BS3 have been deleted (C), compared with intact cANE (D), at the 90% epiboly stage, and enhancer activity of Motif1 mutation mutSox (F) in 1–222 context compared with wild type 1–222 (E), at the 75% epiboly stage. Dorsal views; anterior is to the left. (G) RT-PCR relative quantification of total <i>egfp</i> expression stable transgenic embryos for constructs cANE (1–310), 81–310, 1–222 and 1–222 mutSox, as well as non transgenic embryos (Ctl); error bars represent SEM; units are arbitrary.</p

Characterization of cANE activity as an early neural plate specific enhancer.

<p>(A-I,A’-I’) Compared expression patterns of <i>cyp26a1</i> (A-I) and <i>egfp</i> driven by cANE (A’-I’) during early embryonic development. (J) Double in situ hybridization showing <i>barhl2</i> expression domain (blue) exactly filling the gap in the <i>cyp26a1</i> expression domain (red). (A,B,C,E,G,A’,B’,C’,E’,G’) are lateral views. (d,f,h,I,D’,f’,h’,I’) are animal pole views. White arrowheads: anterior neural plate. Black arrowheads: blastoderm marginal zone. Arrows in (H-J): gap in the anterior neural plate domain of <i>cyp26a1</i> expression. All stages are indicated in the pictures. (k,k’,l,l’) The effect of 100 nM retinoic acid (RA) treatment between 2,5 hpf and 8,5 hpf on on stable transgenic cANE_endo:::<i>egfp</i> (K-K’) and cANE::<i>egfp</i> (L-L’) expression. (M) EGFP fluorescence in a 12 hpf stable transgenic cANE:::<i>egfp</i> embryo. Lateral view with dorsal to the left. (N) Schematic representation of cANE and all three reported retinoic acid responsive elements (R1, R2, R3) identified previously. cANE is located from -504 bp to -195 bp relative to <i>cyp26a1</i> ATG codon. An: animal, Vg: vegetal; V: ventral; D: dorsal, A: anterior, P: posterior, L: left, R: right, CTRL: control embryo, RA: retinoic-acid treated embryo.</p

Conservation of vertebrate <i>cyp26a1</i> promoter region with zebrafish cANE.

<p>Alignment of 4 teleostean (tetraodon, fugu, stickleback and medaka) and mouse and human <i>cyp26a1</i> promoter regions orthologous to zebrafish cANE. The most conserved regions are outlined with red (predicted SoxB binding sites 2 and 3) or purple (conserved block1,2,3) boxes. The green (Motif1) and blue (predicted SoxB binding site 1) boxed sequences lie in the non-evolutionarily conserved region of zebrafish cANE. Numbers correspond to nucleotide coordinates within the 310 nt zebrafish cANE.</p

Detailed dissection of cANE by transient expression of deletion constructs in zebrafish embryos.

<p>(A) Schematic view of the constructs used for dissection of the cANE module. All constructs contain one single fragment (black) from the cANE module, placed immediately upstream of the <i>gata2</i> minimal promoter, except for construct cANE_endo, where the <i>gata2</i> promoter is replaced by the <i>cyp26a1</i> endogenous promoter. Numbers correspond to nucleotide coordinates within the 310 nt zebrafish cANE. The hatched block (Motif1) represents the 12-bp difference between constructs 39–310 and 50–310; the highly conserved blocks are indicated by checkered patterns. (B-K) Enhancer activity of the cANE deletions shown in (A), assayed by <i>egfp</i> in situ hybridization in transient or stable (labelled Tg()) transgenic embryos. All embryos are between stages 10.5 and 11 hpf, viewed from the animal pole, with anterior on the left.</p

Introduction

It is an introduction of CIFOR's research in Bulungan, Kalimantan with the Ministry of Forestry in Indonesia and ITTO. CIFOR's strategic research is focused on policy issues to enable more informed, productive, sustainable and equitable decisions about the management and use of forests. CIFOR works closely with ITTO and FORDA (the Forestry Research and Development Agency, Ministry of Forestry, Indonesia) as important strategic partners in the Bulungan model forest project phase 1, 1997-2001. The aim of the research is to carry out a systematic investigation of how to achieve forest sustainability for a 'large forest landscape' in the humid tropics, where diverse, rapidly changing and often conflicting land use demand exist. The specific objectives of the activities conducted with ITTO support are: 1) Assessment of the effect of reduced-impact logging (RIL) on biodiversity, conservation, ecology and socio-economics, 2) Assessment of rural development trends and future policy options including the effects of macro-level development activities on people dependent on the forest

Additional file 2: of Sequence variation and functional analysis of a FRIGIDA orthologue (BnaA3.FRI) in Brassica napus

Sequence variations and haplotypes of BnaA3.FRI in 30 B. napus. (XLSX 14 kb

Asymmetric Flasklike Hollow Carbonaceous Nanoparticles Fabricated by the Synergistic Interaction between Soft Template and Biomass

The soft template method is broadly applied to the fabrication of hollow-structured nanomaterials. However, due to the instability and the typical spherical shape of these soft templates, the resultant particles have a spherical morphology with a wide size distribution. Herein, we developed a sustainable route to fabricate asymmetric flasklike hollow carbonaceous structures with a highly uniform morphology and a narrow size distribution using the soft template method. A dynamic growth mechanism induced by the synergetic interactions between template and biomass is proposed. The precursors (ribose) provide an acidic environment for sodium oleate during the hydrothermal process in which oleic acid nanoemulsions are initially formed and serve as both template and benign solvent for the amphiphilic derivatives of the precursor. Simultaneously, the cosurfactant P123 facilitates the uniform dispersion of the nanoemulsion and is believed to cause the carbonaceous shells to rupture, providing openings through which the intermediates can enter. These subtle interactions facilitate the formation of the flasklike, asymmetric, hollow, carbonaceous nanoparticles. Furthermore, this unique structure contributes to the high surface area (2335 m² g^–1) of the flasklike carbon particles, which enhances the performance of supercapacitors. These findings may open up an exciting field for exploring anisotropic carbonaceous nanomaterials and for understanding the related mechanisms to provide guidance for the design of increasingly complex carbonaceous materials

Additional file 1: of Sequence variation and functional analysis of a FRIGIDA orthologue (BnaA3.FRI) in Brassica napus

Accession information of the 174 B. napus and their BnaA3.FRI haplotypes. (XLSX 20 kb

Additional file 9: of Sequence variation and functional analysis of a FRIGIDA orthologue (BnaA3.FRI) in Brassica napus

Variance of phenotype for flowering time of all the transgenic lines harboring different BnaA3.FRI haplotypes and Col-0. (A) The phenotype at flowering stage, (B) days to flowering; (C) rosette leaf numbers at bolting stage. Letters indicate significant differences according to t-test (α = 0.05) (TIFF 1290 kb

Additional file 4: of Sequence variation and functional analysis of a FRIGIDA orthologue (BnaA3.FRI) in Brassica napus

Primers used in this study. (XLSX 12 kb