A Phylogenetic and Morphological Evolution Study of <i>Ribes</i> L. in China Using RAD-Seq

Ribes L. belongs to the Grossulariaceae family and has important edible, medicinal, ornamental, and landscaping values. Taxonomic classification within this genus is difficult due to its large variety of species, wide distribution, large morphological variations, and presence of two complex taxonomic groups with bisexual or unisexual flowers. Our study aims to clarify the phylogenetic relationships of Ribes L. taxa in China, and further, to provide a reference for a revised global classification of it. The phylogenetic analysis of 52 Ribes L. samples from 30 species was constructed based on restriction site-associated DNA sequencing and single nucleotide polymorphisms. Afterward, two important taxonomic characters were selected for ancestral state reconstruction over the molecular phylogeny. The results showed that the 52 samples could be divided into six branches, i.e., six subgenera, which caused some controversy regarding the morphological classification of Ribes L. in China. The molecular phylogeny supported the separation of subg. Coreosma from subg. Ribesia and subg. Hemibotrya from subg. Berisia and validated the rationale for recognizing subg. Grossularia as an independent subgenus, the rationality of which was further verified by the reconstruction of ancestor traits. Gene flow among Ribes L. was identified and further confirmed our results

In Vitro Antifungal Activity of Dihydrochelerythrine and Proteomic Analysis in Ustilaginoidea virens

Dihydrochelerythrine (DHCHE) is an isoquinoline compound, which has distinct antifungal activity and can induce apoptosis. The antifungal activity of DHCHE against five rice pathogenic fungi was studied in vitro. At the concentration of 7.5 mg/L, DHCHE exhibited the highest efficacy among tested compounds in inhibiting mycelium growth, with an inhibition rate of 68.8% in Ustilaginoidea virens, which was approximately 2.4 times of that of validamycin (28.7%). After exposure to DHCHE, transmission electron micrographs revealed spores showed incomplete organelles, malformed cell walls and nuclear membranes, as well as irregular lipid spheres. Reactive oxygen species accumulation in treated spores was markedly higher than that in control spores. DHCHE induced cell damage increased in a dose-dependent manner, as indicated by the decrease in mitochondrial membrane potential and initiation of apoptosis. The differences of expression levels of Fip1, ACP1, PMS2 and COX13 that are important for oxidative phosphorylation and mismatch repair pathway were significant, which may be some of the reasons for the induction of apoptosis in DHCHE-treated U. virens. The protein levels of Fip1, ACP1, PMS2 and COX13 agreed with protein fold change ratio from parallel reaction monitoring Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathway of differentially expressed proteins were further analyzed. These findings will help to elucidate the mechanisms associated with antifungal and pro-apoptotic effects of DHCHE on U. virens, thereby aiding the potential development of novel pesticides

Putrescine Promotes Betulin Accumulation in Suspension Cell Cultures of Betula platyphylla by Regulating NO and NH4+ Production

Putrescine (Put) can enhance secondary metabolite production, but its intrinsic regulatory mechanism remains unclear. In this study, Put treatment promoted betulin production and gene expression of lupeol synthase (LUS), one of betulin synthetic enzymes. The maximum betulin content and gene expression level of LUS was 4.25 mg&middot;g&minus;1 DW and 8.25 at 12 h after 1 mmol&middot;L&minus;1 Put treatment, approximately two- and four-times that in the control, respectively. Put treatment increased the content of nitric oxide (NO) and its biosynthetic enzyme activity of nitrate reductase (NR) and NO synthase (NOS). Pretreatment of the birch suspension cells with NO-specific scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline- 1-oxyl-3-oxide (cPTIO), NR inhibitor sodium azide (NaN3), and NOS inhibitor NG-nitro-L-Arg methyl ester (L-NAME) decreased Put-triggered NO generation and blocked Put-induced betulin production. Put treatment improved the content of NH4+ and its assimilation enzyme activity of glutamate synthase and glutamate dehydrogenase. NH4+ supplementation also promoted NO and betulin production. Thus, the above data indicated that Put-induced NO was essential for betulin production. NO derived from NR, NOS, and NH4+ mediated betulin production in birch suspension cell cultures under Put treatment

Bowmanella pacifica sp nov., isolated from a pyrene-degrading consortium

A taxonomic study was carried out on a strain, designated W3-3A(T), which was isolated from a pyrene-degrading consortium, enriched from sediment of the Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain W3-3A(T) belonged to the genus Bowmanella, with the highest sequence similarity (99.0%) with Bowmanella denitrificans BD1(T), whereas sequence similarities with other species were less than 93%. The nucleotide sequence similarity of both gyrB and rpoD genes of strain W3-3A(T) and B. denitrificans BD1(T) was 81.1%. However, the protein sequence similarities of the gyrB and rpoD genes of strain W3-3A(T) and B. denitrificans BD1(T) were 96.1% and 91.0%, respectively. Phylogenetic trees based on these housekeeping genes showed that strain W3-3A(T) and B. denitrificans BD1(T) formed a distinct lineage in the Gammaproteobacteria. The DNA-DNA hybridization value between strain W3-3A(T) and B. denitrificans BD1(T) was 43%. Strain W3-3A(T) could also be differentiated from B. denitrificans BD1(T) based on the repetitive extragenic palindromic DNA-PCR fingerprint. The G+C content of the chromosomal DNA of strain W3-3A(T) was 49 mol%. The combined genotypic and phenotypic data showed that strain W3-3A(T) represents a novel species of the genus Bowmanella, for which the name Bowmanella pacifica sp. nov. is proposed, with the type strain W3-3A(T) (=CGMCC 1.7086(T)=LMG 24568(T)=MCCC 1A01018(T)).National Natural Science Foundation of China [40376041]; National Infrastructure of Natural Resources for Science and Technology Program of China [2005DKA21209]; COMRA program [DYXCM115-02-2-05]; National Basic Research Program of China [2004CB719601, 2006CB708200

Oceanicola pacificus sp nov., isolated from a deep-sea pyrene-degrading consortium

A taxonomic study was carried out on a Gram-negative, rod-shaped, non-motile, halophilic bacterium, designated strain W11-2B(T), which was isolated from a pyrene-degrading consortium that was enriched from sediment from the Pacific Ocean. Growth was observed at salinities of 0.5-10% and at temperatures of 10-41 degrees C. Strain W11-2B(T) was unable to degrade Tween 80 or gelatin. 16S rRNA gene sequence comparisons showed that strain W11-2B(T) was related most closely to Oceanicola nanhaiensis SS011B1-20(T) (95.8% similarity) and Oceanicola batsensis HTCC2597(T) (95.7%); levels of 16S rRNA gene sequence similarity between strain W11-2B(T) and the type strains of other species tested were below 95.2%. The dominant fatty acids of strain W11-2B(T) were C-18:1 omega 7c (32.1% of the total), C-19:0 cyclo (20.9%), C-18:1 omega 7c 11-methyl (119.5%), C-18:0 (7.3%), C-17:0 (6.6%) and C-16:0 (3.8%). The G+C content of the chromosomal DNA was 64.6 mol%. The above data were in good agreement with those of members of the genus Oceanicola. Based on morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain W11-2B(T) is considered to represent a novel species of the genus Oceanicola, for which the name Oceanicola pacificus sp. nov. is proposed. The type strain is W11-2B(T) (=CCTCC AB 208224(T) =LMG 24619(T)=MCCC 1A01034(T)).National Infrastructure of Natural Resources for Science and Technology Program of China [2005DKA21209]; COMRA program [DYXM115-02-2-05]; National Basic Research Program of China [2004CB719601, 2006CB708200

Studies on the Regioselective Nucleophilic Aromatic Substitution (S_NAr) Reaction of 2‑Substituted 3,5-Dichloropyrazines

Differences in regioselectivity were observed during the S_NAr reaction of amines with unsymmetrical 3,5-dichloropyrazines. This study revealed that when the 2-position of the pyrazine was occupied with an electron-withdrawing group (EWG), nucleophilic attack occurred preferentially at the 5-position. When the 2-position was substituted with an electron-donating group (EDG), nucleophilic attack occurred preferentially at the 3-position. These results are reported along with a computational rationale for the experimental observations based on the Fukui index at the reacting centers