The genome of black raspberry (Rubus occidentalis)

Black raspberry (Rubus occidentalis) is an important specialty fruit crop in the US Pacific Northwest that can hybridize with the globally commercialized red raspberry (R. idaeus). Here we report a 243 Mb draft genome of black raspberry that will serve as a useful reference for the Rosaceae and Rubus fruit crops (raspberry, blackberry, and their hybrids). The black raspberry genome is largely collinear to the diploid woodland strawberry (Fragaria vesca) with a conserved karyotype and few notable structural rearrangements. Centromeric satellite repeats are widely dispersed across the black raspberry genome, in contrast to the tight association with the centromere observed in most plants. Among the 28 005 predicted protein‐coding genes, we identified 290 very recent small‐scale gene duplicates enriched for sugar metabolism, fruit development, and anthocyanin related genes which may be related to key agronomic traits during black raspberry domestication. This contrasts patterns of recent duplications in the wild woodland strawberry F. vesca, which show no patterns of enrichment, suggesting gene duplications contributed to domestication traits. Expression profiles from a fruit ripening series and roots exposed to Verticillium dahliae shed insight into fruit development and disease response, respectively. The resources presented here will expedite the development of improved black and red raspberry, blackberry and other Rubus cultivars.     

Differential alkaloid profile in <Emphasis Type="Italic">Uncaria tomentosa</Emphasis> micropropagated plantlets and root cultures

The alkaloids of Uncaria tomentosa micropropagated plantlets and root cultures were isolated and identified by NMR and mass spectrometry. Plantlets yielded pteropodine (1), isopteropodine (2), mitraphylline (3), isomitraphylline (4), uncarine F (5), speciophylline (6), rhynchophylline (7) and isorhynchophylline (8). In plantlets growing under continuous light, tetracyclic alkaloids 7 and 8 decreased from 20 ± 1.8 at 2 months to 2.2 ± 0.33 mg/g dry wt at 6 months, while the pentacyclic alkaloids 1–4 increased from 7.7 ± 1.4 to 15 ± 0.05 mg/g dry wt, supporting their biogenetic conversion. Micropropagated plantlets produced four times more alkaloids (27.6 ± 3.1 mg/g dry wt) than greenhouse plants. Plantlet roots yielded 3, 4, 8 and the glucoindole alkaloids 3α-dihydrocadambine (9) and dolichantoside (10), the last one not previously found in Uncaria.     

Phenolic compounds and their anti-oxidative properties and protein kinase inhibition from the Chinese mangrove plant Laguncularia racemosa

Phenolic compounds, named integracin D (1), (7′R, 8′S, 8S)-8-hydroxyisoguaiacin (3), (2R, 3R) pinobanksin-3-caffeoylate (5) and threo-8S-7-methoxysyringylglycerol (6), respectively, were isolated from the Chinese mangrove plant Laguncularia racemosa (L) Gaertn. f. (Combretaceae), together with 23 known phenolic metabolites. Their structures were elucidated on the basis of extensive spectroscopic analyses including that of IR, UV, MS, CD, 1D and 2D NMR spectra as well as by comparison with literature data. Compound 5 showed significant anti-oxidative activity in the DPPH and TEAC free-radical-scavenging assays, while several of the phenolic compounds were tested for protein kinase inhibitory activity in an assay involving 24 different human tumor related protein kinases. Compounds 5, 7, and 23 showed potential inhibition with IC₅₀ values between 2.2 and 3.6 μg/mL toward individual kinases. The ellagic acid derivatives were tested for insecticidal activity.     

Chemical constituents from Tsoongiodendron odorum Chun

The present study reports the isolation of sixteen lignans (1–16), an aporphine alkaloid (17), two phenolic amides (18 and 19), and a germacrane sesquiterpene lactone (20) from T. odorum. Except for compound 20, the other isolated constituents are firstly reported from T. odorum. And in this study, three polylignans (11–13) and six norlignans (5–7, 14–16) are reported for the first time from the Magnoliaceae family, which may support the opinion to establish Tsoongiodendron as a monotypic genus from a chemotaxonomical point of view.     

Genetic control of the reactions of raspberry to black raspberry necrosis, raspberry leaf mottle and raspberry leaf spot viruses

Black raspberry necrosis virus (BRNV) induces a severe apical necrosis in black raspberry (Rubus occidentalis) but fails to induce diagnostic symptoms in red raspberry. However, BRNV infection of F₁, F₂ and F₃ hybrids from the cross black raspberry × red raspberry induced mosaic symptoms of varying intensity but no typical apical necrosis. In a survey of 28 red raspberry cultivars, a few developed severe angular chlorotic leaf spots when infected with raspberry leaf mottle virus and a few others did so when infected with raspberry leaf spot virus. These reactions were determined by single dominant genes designated Lm and Ls respectively. The value of the different host reactions for controlling the effects and spread of these viruses is discussed.     

Novel phenolic and diterpenoid compounds isolated from the fruit spikes of Prunella vulgaris L. and their anti-inflammatory activities

Two novel phenolic compounds, prunellanate A (1) and prunellanate B (2), together with a diterpenoid compound, prunelladiterpenol A (3), were successfully isolated from the fruit spikes of Prunella vulgaris L. (Figure 1). Their structures were determined after extensive spectroscopic analyses including IR NMR, HR-ESI-MS empirical electronic circular dichroism (ECD), and X-ray diffraction. The biological activities of these new compounds on NO production in LPS (Lipopolysaccharide)-simulated RAW264.7 cells were evaluated. Compounds 1 and 3 showed significant anti-inflammatory activities revealing IC₅₀ values of 6.77 and 8.61 μM, respectively (aminoguanidine as positive control, IC₅₀ 20.33 ± 1.08 μM).     

Osteogenic activity of diphenyl ether-type cyclic diarylheptanoids derived from Acer nikoense

Osteogenic activity of six diarylheptanoids, acerogenin A (1), (R)-acerogenin B (2), aceroside I (3), aceroside B₁ (4), aceroside III (5) and (−)-centrolobol (6) and two phenolic compounds; (+)-rhododendrol (7) and (+)-cathechin (8), isolated from the stem bark of Acer nikoense (Nikko maple) was evaluated using alkaline phosphatase (ALP) activity as a marker for early osteoblast differentiation. We found that the diphenyl ether-type cyclic diarylheptanoids 1-5 promoted ALP activity in mouse preosteoblastic MC3T3-E1 cells without affecting cell proliferation, but linear-type diarylheptanoid 6 and phenolic compounds 7 and 8 did not. Diphenyl ether-type cyclic diarylheptanoids 1-4 also increased protein production of osteocalcin, a late stage maker for osteoblast differentiation, and induced osteoblastic mineralization. Structure-activity relationships of these compounds demonstrated that the stimulative efficacy of aglycones was higher than that of its glycosides. Taken together, diphenyl ether-type cyclic diarylheptanoids promote early- and late-stage osteoblastogenesis, which may open the possibility for the development of novel osteogenic agents.     

Adventitious shoot regeneration from leaf explants of tissue cultured and greenhouse-grown raspberry

Adventitious shoot regeneration was observed using leaf-petiole explants from shoot-proliferating cultures of Comet red raspberry (Rubus idaeus L.). A maximum regeneration rate of 70% (3.7 shoots/explant) was obtained using 4.5–9.1 M (1–2 mg l^–1) N-phenyl-N-1,2,3-thiadiazol-5-ylurea (thidiazuron or TDZ) with 2.5–4.9 M (0.5–1 mg l^–1) 1H-indole-3-butanoic acid (IBA) or 2.3 M (0.5 mg l^–1) TDZ with 4.9 M (1 mg l^–1) IBA in modified Murashige-Skoog medium. TDZ was more effective than N-(phenylmethyl)-1H-purin-6-amine (BA) at promoting regeneration in combinations tested with IBA (maximum 50% regeneration rate; 1.8 shoots/explant). Variation in the agar concentration or incubation temperature, orientation or scoring of the leaf-petiole explants and use of separate leaf or petiole explants had no effect on shoot regeneration. Incubation in the dark for 1, 2 or 3 weeks prior to growth in the light did not influence the percent regeneration rate but depressed the number of adventitious shoots. Explant source, from micropropagated shoots or greenhouse-grown plants, had an effect on shoot regeneration that was genotype dependent. Only 8 of 22 (36%) raspberry cultivars were capable of regeneration from leaf explants derived from greenhouse-grown plants.     

Novel Macrocyclic Monoterpene Glycosides from Bioactive Extract of Parkinsonia aculeata L

Five novel macrocyclic monoterpene O-glycosides, parkinsenes A–E (1–5), and eleven known phenolic metabolites including three 3-O-glycosylflavonols (6–8), five C-glycosylflavones (9–13), p-hydroxybenzoic acid (14), esculetin (15), and diosmetin (16) were isolated from the leaves and small twigs of Parkinsonia aculeata L. (Fabaceae). Their structures were established by chemical and spectroscopic analyses (UV, ESI–MS, and 1D/2D NMR). The investigated 80 % aqueous methanol extract (AME) showed significant analgesic, antipyretic, anti-inflammatory, hepatoprotective, hypoglycemic, hypocholesterolemic, and antioxidant activities in a dose-dependent manner using two different doses 250 and 500 mg/kg b. wt.     

Phenolic compounds and rare polyhydroxylated triterpenoid saponins from Eryngium yuccifolium

Phytochemical investigation on the whole plant of Eryngium yuccifolium resulted in the isolation and identification of three phenolic compounds (1-3) and 12 polyhydroxylated triterpenoid saponins, named eryngiosides A-L (4-15), together with four known compounds kaempferol-3-O-(2,6-di-O-trans-p-coumaroyl)-β-d-glucopyranoside (16), caffeic acid (17), 21β-angeloyloxy-3β-[β-d-glucopyranosyl-(1→2)]-[β-d-xylopyranosyl-(1→3)]-β-d-glucuronopyranosyloxyolean-12-ene-15α,16α,22α,28-tetrol (18), and saniculasaponin III (19). This study reports the isolation of these compounds and their structural elucidation by extensive spectroscopic analyses and chemical degradation.     

Aporphine alkaloids and cytotoxic lignans from the roots of Illigera luzonensis

Six aporphine alkaloids, (+)-(S)-N-butyrylcaaverine (1), (+)-(S)-N-propionylcaaverine (2), (+)-(S)-N-acetylcaaverine (3), (+)-(6aR,7R)-N-butyrylnorushinsunine (4), (+)-(6aR,7R,E)-N-(but-2-enoyl)norushinsunine (5), and N-formyldehydrocaaverine (6) were isolated from the roots of Illigera luzonensis, together with 16 known compounds. Their structures were determined through spectroscopic and MS analyses. Among the isolates, (−)-deoxypodophyllotoxin (13) was the most cytotoxic, with IC₅₀ values of 0.0057, 0.0067, 0.00004, and 0.0035 μg/mL, respectively, against DLD-1, CCRF-CEM, HL-60, and IMR-32 cell lines. In addition, (−)-yatein (12) exhibited cytotoxic effects, with IC₅₀ values of 0.81, 0.20, and 0.59 μg/mL, respectively, against DLD-1, CCRF-CEM, and HL-60 cell lines.     

Tyrosinase activity of Greyia flanaganii (Bolus) constituents

Hyper-pigmentation of the skin is a common problem that is prevalent in middle aged and elderly people. It is caused by over production of melanin. Tyrosinase is known to be the key enzyme in melanin production. Ethanolic extract of Greyia flanaganii leaves showed significant (P < 0.05) antityrosinase activity exhibiting the IC₅₀ of 32.62 μg/ml. The total extract was further investigated for its toxicity and effect on melanin production by melanocytes cells, and showed significant inhibition (P < 0.05) (20%) of melanin production at 6.25 μg/ml and low levels of cytotoxicity (IC₅₀ < 400 μg/ml). The amount of antioxidants necessary to decrease the initial DPPH absorbance by 50% (EC₅₀) by the total ethanolic extract was found to be 22.01 μg/ml. The effect of G. flanaganii against acne causing bacteria, Propionibacterium acnes, was investigated using microdilution assay. The MIC of the extract of G. flanaganii was found to be 250 μg/ml. Bioassay-guided fractionation led to the isolation of (3S)-4-hydroxyphenethyl 3-hydroxy-5-phenylpentanoate (1), 2′,4′,6′-trihydroxydihydrochalcone (2), 2′,6′,4-trihydroxy-4′-methoxydihydrochalcone (3), 2′,6′-dihydroxy-4′-methoxydihydrochalcone (4), 5,7-dihydroxyflavanone [(2S)-pinocembrin] (5), 2′,6′-dihydroxy-4′,4-dimethoxy dihydrochalcone (6) and (2R,3R)-3,5,7-trihydroxy-3-O-acetylflavanone (7). The isolated compounds were tested for their antioxidant, cytotoxicity, tyrosinase inhibition and antibacterial activities. Compound 2 exhibited significant (P < 0.05) antityrosinase activity exhibiting the IC₅₀ of 69.15 μM. The isolated compounds showed low toxicity of the cells with reduction of melanin content of the cells. All compounds tested showed good radical scavenging activity. These data indicates that G. flanaganii extract and its isolated phenolic constituents could be possible skin lightening agents.     

New class of acetylcholinesterase inhibitors from the stem bark of Knema laurina and their structural insights

Bioassay-guided extraction of the stem bark of Knema laurina showed the acetylcholinesterase (AChE) inhibitory activity of DCM and hexane fractions. Further repeated column chromatography of hexane and DCM fractions resulted in the isolation and purification of five alkenyl phenol and salicylic acid derivatives. New compounds, (+)-2-hydroxy-6-(10′-hydroxypentadec-8′(E)-enyl)benzoic acid (1) and 3-pentadec-10′(Z)-enylphenol (2), along with known 3-heptadec-10′(Z)-enylphenol (3), 2-hydroxy-6-(pentadec-10′(Z)-enyl)benzoic acid (4), and 2-hydroxy-6-(10′(Z)-heptadecenyl)benzoic acid (5) were isolated from the stem bark of this plant. Compounds (1-5) were tested for their acetylcholinesterase inhibitory activity. The structures of these compounds were elucidated by the 1D and 2D NMR spectroscopy, mass spectrometry and chemical derivatizations. Compound 5 showed strong acetylcholinesterase inhibitory activity with IC₅₀ of 0.573 ± 0.0260 μM. Docking studies of compound 5 indicated that the phenolic compound with an elongated side chain could possibly penetrate deep into the active site of the enzyme and arrange itself through π-π interaction, H-bonding, and hydrophobic contacts with some critical residues along the complex geometry of the active gorge.     

Effect of metal coordination and intra-molecular H-bond on the acidity of phenolic proton in a set of structurally characterized octahedral Ni(II) complexes of l-histidine derivative

Four different mononuclear octahedral Ni(II) complexes with protonated and deprotonated form of the same ligand have been synthesized by controlling reaction conditions and structurally characterized. The complexes are [Ni(HL^l-his)(benzoate)(MeOH)] (1), [Ni(HL^l-his)(SCN)(MeOH)] (2), [Ni(HL^l-his)₂] (3) and [Ni(L^l-his)(imidazole)₂] (4) where H₂L^l-his is (S)-2-(2-hydroxybenzylamino)-3-(1H-imidazol-4-yl)-propionic acid. The ligand behaves as a monobasic tetradentate ligand in 1 and 2, monobasic tridentate ligand in 3 and dibasic tetradentate ligand in 4. Ni(II) coordinated phenolic proton of the ligand in the complexes 1-2 shows strong intra-molecular H-bonding with benzoate in 1 and lattice water in 2, whereas 3 shows intermolecular H-bonding between uncoordinated phenols with neighbouring carboxylate. The pH titration of the complexes revealed that metal coordination and H-bond in complexes 1 and 2 considerably lowers the acidity of ligand phenol (pK_a 6.8 and 7.0 respectively) compared to phenol (pK_a 10). The complex 4 does not show any proton loss due to the absence of phenolic proton. All the complexes show extensive H-bonded network in the crystals including narrow (7.8 × 5.2 Å) water filled one dimensional channel in 2.     

Prenylated acetophenones from Melicope obscura and Melicope obtusifolia ssp. obtusifolia var. arborea and their distribution in Rutaceae

Four prenylated acetophenones 2,6-dihydroxy-4-geranyloxyacetophenone (1), 4-geranyloxy-2,6,β-trihydroxyacetophenone (2), 2,6-dihydroxy-4-geranyloxy-3-prenylacetophenone (3), and 4-geranyloxy-3-prenyl-2,6,β-trihydroxyacetophenone (4) have for the first time been isolated from Melicope obscura (1 and 2) and Melicope obtusifolia ssp. obtusifolia var. arborea (3 and 4). The distribution of prenylated acetophenones in Rutaceae is reviewed and the results, including the new records, indicate that prenylated acetophenones are valuable as chemotaxonomic markers for the subfamily Rutoideae, tribe Xanthoxyleae sensu Engler.     

Structure–activity relationship of dihydroxy-4-methylcoumarins as powerful antioxidants: Correlation between experimental & theoretical data and synergistic effect

The chain-breaking antioxidant activities of eight coumarins [7-hydroxy-4-methylcoumarin (1), 5,7-dihydroxy-4-methylcoumarin (2), 6,7-dihydroxy-4-methylcoumarin (3), 6,7-dihydroxycoumarin (4), 7,8-dihydroxy-4-methylcoumarin (5), ethyl 2-(7,8-dihydroxy-4-methylcoumar-3-yl)-acetate (6), 7,8-diacetoxy-4-methylcoumarin (7) and ethyl 2-(7,8-diacetoxy-4-methylcoumar-3-yl)-acetate (8)] during bulk lipid autoxidation at 37 °C and 80 °C in concentrations of 0.01–1.0 mM and their radical scavenging activities at 25 °C using TLC–DPPH test have been studied and compared. It has been found that the o-dihydroxycoumarins 3–6 demonstrated excellent activity as antioxidants and radical scavengers, much better than the m-dihydroxy analogue 2 and the monohydroxycoumarin 1. The substitution at the C-3 position did not have any effect either on the chain-breaking antioxidant activity or on the radical scavenging activity of the 7,8-dihydroxy- and 7,8-diacetoxy-4-methylcoumarins 6 and 8. The comparison with DL-α-tocopherol (TOH), caffeic acid (CA) and p-coumaric acid (p-CumA) showed that antioxidant efficiency decreases in the following sequence:     

Cytotoxic terpenoids from the stem bark of Taxus wallichiana

Chemical study of the stem bark of Taxus wallichiana Zucc. afforded the isolation of two new cyclopenta[b]naphthalene terpenoids, wallichianones A (1) and B (2) and 13 taxane diterpenoids, baccatin III (3), 10-deacetylbaccatin III (4), baccatin IV (5), 1-dehydroxybaccatin IV (6), 1-deoxybaccatin VI (7), taxol (8), 10-deacetyltaxol (9), 7-epi-10-deacetyltaxol (10), taxol-7-xyloside (11), 7-xylosyl-10-deacetyltaxol C (12), cephalomannine (13), 10-deacetylcaphalomannine (14), and 7-epi-10-deacetylcephalomannine (15). Their structures were identified by comprehensive analyses of the spectroscopic methods, including NMR and mass spectra. The absolute configurations of 1 and 2 were clarified by time-dependent density functional theory (TD-DFT) electronic circular dichroism (ECD) spectroscopic analyses. Compounds 3 and 7–15 showed cytotoxicity against all five human cancer cell lines, including lung (SK-LU-1), liver (HepG2), breast (MCF7), skin (SK-Mel-2), and prostate (LNCaP), with IC₅₀ values ranging from 1.4 ± 0.2 to 88.1 ± 5.8 μM. Compounds 9–11, 14, and 15 were additionally cytotoxic against human embryonic kidney (HEK-293A) cell line (IC₅₀ = 14.5 ± 1.0–48.4 ± 1.0 μM), however, 13 was noncytotoxic toward this cell line. The positive control, ellipticine showed cytotoxicity against all the cell lines, with IC₅₀ values in a range of 1.5 ± 0.1–2.0 ± 0.3 μM. Preliminary analysis of the structural and cytotoxicity relationship of compounds 3–15 suggested that the phenylalanine substituent at C-13 may contribute an important role for the cytotoxicity of the taxane diterpenoids.     

Chemical constituents of Asarum geophilum and their hepatoprotective effects

One new chalcone glycoside, chalcononaringenin 2′,4-di-O-β-glucopyranoside (1), one new alkaloid, asageoside (2), and sixteen known flavonoids and aurone glycosides, (3-18) were isolated from a methanol extract of the aerial parts of Asarum geophilum Hemsl. Their structures were elucidated by spectroscopic methods, including 1D- and 2D NMR experiments as well as MS analysis and comparison of their NMR data with those reported in the literature. In addition, the hepatoprotective effects of all compounds were also evaluated in HepG2 cells at concentrations of 100, 20.0, 4.0, and 0.8 μg/mL. Quercetin, an antioxidant that showed hepatoprotective effect, was used as the positive control. Compounds 11 and 16 showed significant hepatocellular protective activity with IC₅₀ values of 13.4 ± 1.2 and 73.6 ± 9.1 μg/mL, respectively.