Genome assembly, resequencing and genome-wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry.

Flowering cherry is a very popular species around the world. High-quality genome resources for different elite cultivars are needed, and the understanding of their origins and the regulation of key ornamental traits are limited for this tree. Here, a high-quality chromosome-scale genome of Prunus campanulata 'Plena' (PCP), which is a native and elite flowering cherry cultivar in China, was generated. The contig N50 of the genome was 18.31 Mb, and 99.98% of its contigs were anchored to eight chromosomes. Furthermore, a total of 306 accessions of flowering cherry germplasm and six lines of outgroups were collected. Resequencing of these 312 lines was performed, and 761 267 high-quality genomic variants were obtained. The origins of flowering cherry were predicted, and these 306 accessions could be classified into three clades, A, B and C. According to phylogenetic analysis, we predicted two origins of flowering cherry. Flowering cherry in clade A originated in southern China, such as in the Himalayan Mountains, while clades B and C originated in northeastern China. Finally, a genome-wide association study of flower colour was performed for all 312 accessions of flowering cherry germplasm. A total of seven quantitative trait loci (QTLs) were identified. One gene encoding glycosylate transferase was predicted as the candidate gene for one QTL. Taken together, our results provide a valuable genomic resource and novel insights into the origin, evolution and flower colour variations of flowering cherry.

Genome-Wide Identified MADS-Box Genes in Prunus campanulata 'Plena' and Theirs Roles in Double-Flower Development.

The MADS-box gene family plays key roles in flower induction, floral initiation, and floral morphogenesis in flowering plants. To understand their functions in the double-flower formation of Prunus campanulata 'Plena' (hereafter referred to as PCP), which is an excellent flowering cherry cultivar, we performed genome-wide identification of the MADS-box gene family. In this study, 71 MADS-box genes were identified and grouped into the Mα, Mß, Mγ and MIKC subfamilies according to their structures and phylogenetic relationships. All 71 MADS-box genes were located on eight chromosomes of PCP. Analysis of the cis-acting elements in the promoter region of MADS-box genes indicated that they were associated mainly with auxin, abscisic acid, gibberellin, MeJA (methyl jasmonate), and salicylic acid responsiveness, which may be involved in floral development and differentiation. By observing the floral organ phenotype, we found that the double-flower phenotype of PCP originated from petaloid stamens. The analysis of MIKC-type MADS-box genes in PCP vegetative and floral organs by qRT-PCR revealed six upregulated genes involved in petal development and three downregulated genes participating in stamen identity. Comparative analysis of petaloid stamens and normal stamens also indicated that the expression level of the AG gene (PcMADS40) was significantly reduced. Thus, we speculated that these upregulated and downregulated genes, especially PcMADS40, may lead to petaloid stamen formation and thus double flowers. This study lays a theoretical foundation for MADS-box gene identification and classification and studying the molecular mechanism underlying double flowers in other ornamental plants.

Mechanistic aspects of photo-induced formation of peroxide ions on the surface of cubic Ln2O3 (Ln = Nd, Sm, Gd) under oxygen.

The photo-induced formation of peroxide ions on the surface of cubic Ln2O3 (Ln = Nd, Sm, Gd) was studied by in situ microprobe Raman spectroscopy using a 325 nm laser as excitation source. It was found that the Raman bands of peroxide ions at 833-843 cm(-1) began to grow at the expense of the Ln(3+)-O(2-) bands at 333-359 cm(-1) when the Ln2O3 samples under O2 were continuously irradiated with a focused 325 nm laser beam at temperatures between 25-150 °C. The intensity of the peroxide Raman band was found to increase with increasing O2 partial pressure, whereas no peroxide band was detected on the Ln2O3 under N2 as well as on the samples first irradiated with laser under Ar or N2 followed by exposure to O2 in the dark. The experiments using (18)O as a tracer further confirmed that the peroxide ions are generated by a photo-induced reaction between O2 and the lattice oxygen (O(2-)) species in Ln2O3. Under the excitation of 325 nm UV light, the transformation of O2 to peroxide ions on the surface of the above lanthanide sesquioxides can even take place at room temperature. Basicity of the lattice oxygen species on Ln2O3 also has an impact on the peroxide formation. Higher temperature or laser irradiation power is required to initiate the reaction between O2 and O(2-) species of weaker basicity.

Metal-organic frameworks constructed from monomeric, dimeric and trimeric phenanthroline citrate zinc building units.

Adduct of mononuclear and dinuclear citrate zinc complex [Zn(Hcit)(phen)(H2O)][Zn2(Hcit)(phen)2(H2O)3]·13.5H2O (1) and its aggregate [Zn3(Hcit)2(phen)4]n·14nH2O (2) (H4cit = citric acid, phen = 1,10-phenanthroline) were synthesized in weak acidic solutions. The former was obtained from the reaction of zinc nitrate, citric acid and phenanthroline in a molar ratio of 3 : 2 : 3, while a slightly excess of phenanthroline results in the formation of the polymeric product 2 in a molar ratio of 3 : 2 : 4. Transformation of 1 to 2 was finished by the reaction of 1 with an equimolar of phenanthroline in 72% yield. Reverse conversion of 2 to 1 is obtained in 77% yield, showing an equilibrium between 1 and 2. Neutral compound 1 consists of one monomeric anionic unit [Zn(Hcit)(phen)(H2O)]- and one dimeric cationic unit [Zn2(Hcit)(phen)2(H2O)3]+ that connect each other by strong hydrogen bonds [O6⋯O4w 2.636(2); O7⋯O3w 2.630(3) Å]. In 2, the citrate ligand links each trinuclear unit [Zn3(Hcit)2(phen)4] to generate an infinite 1D chain that extents into a 3D supramolecular structure by intra- and inter-molecular hydrogen bonds. Moreover, 1 and 2 exhibit strong fluorescence at room temperature.

CD200Fc attenuates inflammatory responses and maintains barrier function by suppressing NF-κB pathway in cigarette smoke extract induced endothelial cells.

BACKGROUND: Recent evidence suggests that CD200 fusion protein (CD200Fc), a CD200R1 agonist may attenuate inflammatory responses in autoimmune diseases and neuro-degeneration. While, little is known about the function of CD200Fc in cigarette smoke extract (CSE)-induced mouse Cardiac Microvascular Endothelial Cells (mCMECs). The present study was designed to elucidate the effects of CD200Fc on CSE-induced vascular endothelial barrier (VEB) dysfunction and inflammatory responses, which is a highly clinically relevant model of smoking related cardiovascular diseases. METHODS: mCMECs were pre-treated with 1, 10 and 100µg/ml CD200Fc for 24h respectively, and then treated with 250µg/ml CSE for different times (24h or 120min). The transepithelial electrical resistance (TEER) and transport of fluorescent markers were used to measure VEB function in CSE-induced mCMECs. Western blot and immunofluorescent staining analysis were used to detect the expression of tight junction proteins, such as Zona Occludens-1 (ZO-1) and Claudin-1 in CSE-induced mCMECs. We measured the expression of pro-inflammatory cytokines in CSE-induced mCMECs by using ELISA and RT-PCR. In addition, the NF-κB activity in CSE-induced mCMECs were investigated by using nuclear/cytosol fractionation and western blot analysis. RESULTS: In vitro treatment with CSE increased the transport of fluorescent markers and decreased TEER levels in mCMECs, respectively, which were attenuated by CD200Fc (10 and 100µg/ml) pretreatment. The CSE-induced up-regulation of pro-inflammatory cytokines such as Cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS), platelet endothelial cell adhesion molecule-1 (PECAM-1), vascular cell adhesion molecule-1 (ICAM-1), Prostaglandin E2 (PGE2), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and IL-8 in mCMECs was also abrogated by CD200Fc (10 and 100µg/ml) pretreatment. CD200Fc also inhibited CSE-induced nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation in mCMECs, such as inhibition of its DNA binding activity, phosphorylated expression, and translocation to nucleus. CONCLUSION: Thus, CD200Fc exert anti-inflammatory effect and protect VEB function in CSE-induced mCMECs. The vasoprotective effects of CD200Fc may be specifically beneficial in pathophysiological conditions associated with smoking related cardiovascular diseases.

Applications of fluorescent polymer superquenching to high throughput screening assays for protein kinases.

Protein kinases are involved in the regulation of cellular metabolism, growth, differentiation, and proliferation. Aberrations in their function can lead to diseases such as cancer and inflammation. Protein kinases are therefore possible targets for drug therapies. To address the need for high throughput screening of potential inhibitors, QTL has developed a homogeneous and robust kinase assay for use in multiwell plate format. The QTL Lightspeed fluorescence superquenching-based kinase assays do not require specialized equipment, nor do they involve the use of radioactive hazardous materials or antibodies. QTL Lightspeed kinase assays directly measure the enzymatic activity of the target and do not involve secondary (detector) enzyme. In this article, we compare QTL Lightspeed protein kinase assays using Protein Kinase A, Protein Kinase Balpha/Akt1, and ribosomal S6 kinase-2 as examples with other commercially available kinase kits. Our data show that QTL Lightspeed kinase assays offer significant advantages over the current commercial kits in terms of both sensitivity and performance. The QTL Lightspeed kinase assay also offers a kinetic assay mode where the substrate phosphorylation can be monitored in real-time.

Delivery of selective agents via time-delayed release tablets improves recovery of Listeria monocytogenes injured by acid and nitrite.

Listeria selective enrichment media are designed to enhance the isolation of the organism and increase the chances of detection. Drawbacks include the requirements for prolonged sample incubation (48 to 72 h) and manual addition of selective agents, which may be a source of contamination. Modified Listeria recovery broth (mLRB) is a proprietary enrichment medium formulated to facilitate the recovery of injured cells; its selective agents are incorporated into a format that allows delayed release until 6 h of incubation. We evaluated the change in cell populations over time for acid- and nitrite-injured Listeria monocytogenes in mLRB with the selective agents added manually at 0 h (mLRBS0) and 6 h (mLRBS6). Recovery of injured cells in mLRB plus time-delayed tablets (mLRBTD) was also compared with that in enrichment media recommended by the U.S. Department of Agriculture (University of Vermont broth), the U.S. Food and Drug Administration (buffered Listeria enrichment broth), and the International Organization for Standardization (demi-Fraser broth). Nitrite- or acid-injured Listeria at approximately 10 CFU/ml were inoculated into each broth medium, and Listeria populations were enumerated at various times from 12 to 48 h of incubation at 37°C. Analysis of variance revealed that acid-injured Listeria populations in mLRBS6 at 24 h were significantly higher (P < 0.05) than those in mLRBS0; however, the differences in populations on these two media were not significant for nitrite-injured cells. Cell populations of four strains of Listeria inoculated into mLRBTD were significantly higher at 24 h than when those strains were enriched in buffered Listeria enrichment broth, demi-Fraser broth, and University of Vermont broth. Comparison between artificially contaminated milk and meat samples with a four-strain cocktail of Listeria resulted in cell populations that were significantly higher (P < 0.05) at 24 h on mLRBTD for contaminated meat than on mLRB for contaminated milk. Delivery of selective agents via time-delayed release tablets into mLRB maximizes recovery of acid- and nitrite-injured Listeria and saves analyst time during food sample analysis.

Dimeric 1,3-propanediaminetetraacetato lanthanides as the precursors of catalysts for the oxidative coupling of methane.

From neutral solutions, dimeric 1,3-propanediaminetetraacetato lanthanides (NH4)2[Ln2(1,3-pdta)2(H2O)4]·8H2O [Ln = La, 1; Ce, 2] and K2[Ln2(1,3-pdta)2(H2O)4]·11H2O [Ln = La, 3; Ce, 4] (1,3-H4pdta = 1,3-propanediaminetetraacetic acid, C11H18N2O8) were isolated in high yields. The reaction of excess strontium nitrate with 1 resulted in the formation of a two dimensional coordination polymer [La2(1,3-pdta)2(H2O)4]n·[Sr2(H2O)6]n·[La2(1,3-pdta)2(H2O)2]n·18nH2O (5) at 70 °C. Complexes 1-4 show a similar central molecular structure. The lanthanide ions are coordinated by two nitrogen atoms, four carboxy oxygen atoms from one 1,3-pdta ligand, two from the neighboring 1,3-pdta ligand forming a four-membered ring and two water molecules. Complex 5 has two kinds of dimeric lanthanum unit and extends into a 2D coordination polymer through strontium ions and bridged oxygen atoms, and forms a fourteen membered ring linked by oxygen atoms from carboxy groups of pdta. Complexes 1-4 are soluble in water. The (13)C{(1)H} NMR experiments for complex 1 were tested in solution. Thermal products from 1 and 5 show good catalytic activities towards the oxidative coupling reaction of methane (OCM). The conversion of methane and selectivity to C2 reached 29.7% and 51.7% at 750 °C for the product of 5. From TGA, XRD and SEM analyses, the thermal products from 1 and 5 are rod- and poly-shaped, which are assigned as lanthanum oxocarbonate and a mixture of La2O3, SrCO3 and La2O2CO3 for 1 and 5, respectively. The precursor method is favorable for the formation of regular shaped mixed oxides.

In situ Raman and pulse reaction study on the partial oxidation of methane to synthesis gas over a Pt/Al2O3 catalyst.

Catalytic partial oxidation of methane (POM) to synthesis gas (syngas) over Pt/Al(2)O(3) was investigated by in situ microprobe Raman and pulse reaction methods with attention focused on the mechanism of syngas formation in the oxidation zone (i.e., the catalyst zone in which O(2) was still available in the reaction feed). It was found that the amount of platinum oxide in the catalyst under POM conditions was below the detection level of Raman spectroscopy. Raman bands of carbon species that originated from methane dissociation were detected at the entrance of the catalyst bed under working conditions. The results of the pulse reaction study on POM as well as steam and CO(2) reforming of methane at 700 °C with a contact time of less than 1 ms over the catalyst suggest that pyrolysis of methane on reduced platinum sites followed by coupling of two surface hydrogen atoms to H(2) and partial oxidation of surface carbon species to CO are the major reactions responsible for syngas formation in the oxidation zone. Under the experimental conditions, steam and CO(2) reforming of methane play only a minor role in syngas formation in the same reaction zone. The contribution of the last two reactions increases with increasing contact time.

pH- and mol-ratio dependent formation of zinc(II) coordination polymers with iminodiacetic acid: synthesis, spectroscpic, crystal structure and thermal studies.

Three novel zinc coordination polymers (NH(4))(n)[Zn(Hida)Cl(2)](n) (1), [Zn(ida)(H(2)O)(2)](n) (2), [Zn(Hida)(2)](n)·4nH(2)O (3) (H(2)ida = iminodiacetic acid) and a monomeric complex [Zn(ida)(phen)(H(2)O)]·2H(2)O (4) (phen=1,10-phenanthroline) have been synthesized and characterized by X-ray diffraction methods. 1 and 2 form one-dimensional (1-D) chain structures, whereas 3 exhibits a three-dimensional (3-D) diamondoid framework with an open channel. The mononuclear complex 4 is extended into a 3-D supramolecular architecture through hydrogen bonds and π-π stacking. Interestingly, cyclic nonplanar tetrameric water clusters are observed that encapsulated in the 3-D lattice of 4. Based on (1)H and (13)C NMR observations, there is obvious coordination of complex 2 in solution, while 1 and 3 decompose into free iminodiacetate ligand. Monomer [Zn(ida)(H(2)O)(3)] (5) is considered as a possible discrete species from 2. These coordination polymers can serve as good molecular precursors for zinc oxide.

Metal ion-mediated polymer superquenching for highly sensitive detection of kinase and phosphatase activities.

An assay technology for high-throughput screening of kinase and phosphatase activities is introduced. The format is based upon superquenching of fluorescent-conjugated polymers by dye-labeled kinase/phosphatase peptide substrates. The sensor platform is composed of highly fluorescent-conjugated polyelectrolytes colocated with the phosphate coordinating metal ion gallium on microspheres. Phosphorylated peptide substrates containing a quencher bind specifically to the metal ions by means of phosphate groups, resulting in quench of polymer fluorescence. The modulation of fluorescence signal is proportional to kinase or phosphatase activity and is monitored as a turn-off or turn-on signal, respectively. The assay is homogeneous and simple and can be run either as an endpoint measurement or in a kinetic mode. The assay meets the sensitivity required for high-throughput screening of kinase or phosphatase inhibitors and is a valuable tool for drug discovery. A modified version of the assay allows for the detection of protein phosphorylation.

Fluorescent-conjugated polymer superquenching facilitates highly sensitive detection of proteases.

Sensor formats have been developed for detecting the activity of proteolytic enzymes based on fluorescent conjugated polymer superquenching. These sensors employ a reactive peptide sequence within a tether linking a quencher to a biotin. The peptide binds to sensors containing colocated biotin-binding protein and fluorescent polymer by means of biotin-biotin binding protein interactions, resulting in a strong quenching of polymer fluorescence. Enzyme-mediated cleavage of the peptide results in a reversal of the fluorescence quenching. These assays for protease activity are simple, sensitive, fast, and have the specificity required for screening chemical libraries for novel protease inhibitors in a high-throughput screening assay environment. These assays have been demonstrated for enterokinase, caspase-3/7, and beta-secretase.