Ki-Hyeong Rhee

Mucilaginibacter herbaticus sp. nov., isolated from the rhizosphere of the medicinal plant Angelica sinensis.

A strictly aerobic, Gram-staining-negative, non-motile and rod-shaped bacterial strain, DR-9(T), was isolated from rhizosphere soil of the medicinal herb Angelica sinensis. Strain DR-9(T) grew at 20-40 °C, at pH 4.0-9.0 and in the presence of 0-1 % (w/v) NaCl. The major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH), MK-7 was the major isoprenoid quinone, and phosphatidylethanolamine and an unidentified aminophospholipid were the major polar lipids. A phylogenetic tree based on 16S rRNA gene sequences showed that strain DR-9(T) formed a lineage within the genus Mucilaginibacter and was closely related to Mucilaginibacter polysacchareus DRP28(T) (96.1 % sequence similarity), Mucilaginibacter myungsuensis HMD1056(T) (95.9 % sequence similarity), Mucilaginibacter ximonensis XM-003(T) (95.8 %) and Mucilaginibacter boryungensis BDR-9(T) (95.1 %). The status of strain DR-9(T) as a representative of a separate species was confirmed by DNA hybridization, with 38.6, 36.3 and 29.9 % DNA-DNA relatedness with M. polysacchareus DRP28(T), M. ximonensis XM-003(T) and M. boryungensis BDR-9(T), respectively. The genomic DNA G+C content of strain DR-9(T) was 49.8 %. These data suggest that strain DR-9(T) should be considered as a representative of a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter herbaticus sp. nov. is proposed. The type strain is DR-9(T) ( = KACC 16469(T) = NBRC 108839(T)).

In silico prediction of potential chemical reactions mediated by human enzymes

BackgroundAdministered drugs are often converted into an ineffective or activated form by enzymes in our body. Conventional in silico prediction approaches focused on therapeutically important enzymes such as CYP450. However, there are more than thousands of different cellular enzymes that potentially convert administered drug into other forms.ResultWe developed an in silico model to predict which of human enzymes including metabolic enzymes as well as CYP450 family can catalyze a given chemical compound. The prediction is based on the chemical and physical similarity between known enzyme substrates and a query chemical compound. Our in silico model was developed using multiple linear regression and the model showed high performance (AUC = 0.896) despite of the large number of enzymes. When evaluated on a test dataset, it also showed significantly high performance (AUC = 0.746). Interestingly, evaluation with literature data showed that our model can be used to predict not only enzymatic reactions but also drug conversion and enzyme inhibition.ConclusionOur model was able to predict enzymatic reactions of a query molecule with a high accuracy. This may foster to discover new metabolic routes and to accelerate the computational development of drug candidates by enabling the prediction of the potential conversion of administered drugs into active or inactive forms.

Retraction note: A hot pepper cDNA encoding ascorbate peroxidase is induced during the incompatible interaction with virus and bacteria

Retraction Note: Mol. Cells 14 (2002) 75–84 Members of the editorial board have unanimously agreed to retract the article [Mol. Cells 14 (2002) 75–84] for potential misconducts mainly concerning manipulation and repeated uses of photomicrographs of control data internally along with mislabeling and/or externally in multiple publications. As specified in the “Instructions to Authors”, Molecules and Cells (Mol. Cells) explicitly prohibits mis-representation or falsification of experimental data including duplication of previously published data. In the article, lanes 1-6 and Lanes 10–15 of EtBr gel of rRNA in Fig. 5 are mirror images of each other; a part of this image has been previously used in Fig. 4B of Mol. Cells 11 (2001) 122–127; this image has also been used in Fig. 2D of Plant Physiol. 135 (2004) 561–573; rRNA gels in Figs. 6A, 6B, and 6C are identical, and rRNA gels in Figs. 7A and 7B are identical as well.