Molecular docking studies of anti-apoptotic BCL-2, BCL-XL, and MCL-1 proteins with ginsenosides from Panax ginseng

Anti-apoptotic proteins such as BCL-2, BCL-XL and MCL-1 bind with pro-apoptotic proteins to induce apoptosis mechanism. BCL-2 family proteins are key regulators of apoptosis process. Over expression of these anti-apoptotic proteins lead to several cancers by preventing apoptosis. A number of studies revealed that ginseng derivatives reduce tumor growth. Ginseng, the most valuable medicinal herb found in eastern Asia belongs to Araliaceae family. In this study, docking simulations were performed for anti-apoptotic proteins with several ginsenosides from Panax ginseng. Our finding shows ginsenosides Rf, Rg1, Rg3 and Rh2 have more binding affinity with BCL-2, BCL-XL and MCL-1 and other ginsenosides also interact with each anti-apoptotic proteins. Therefore, ginseng derivatives represent a novel class of potent inhibitors and could be used for cancer chemotherapy.     

A database of natural products and chemical entities from marine habitat

Marine compound database consists of marine natural products and chemical entities, collected from various literature sources, which are known to possess bioactivity against human diseases. The database is constructed using html code. The 12 categories of 182 compounds are provided with the source, compound name, 2-dimensional structure, bioactivity and clinical trial information. The database is freely available online and can be accessed at http://www.progenebio.in/mcdb/index.htm     

Comparison of vertebrate and invertebrate CLIC proteins: the crystal structures of Caenorhabditis elegans EXC-4 and Drosophila melanogaster DmCLIC

The crystal structures of two CLIC family members DmCLIC and EXC-4 from the invertebrates Drosophila melanogaster and Caenorhabditis elegans, respectively, have been determined. The proteins adopt a glutathione S-transferase (GST) fold. The structures are highly homologous to each other and more closely related to the known structures of the human CLIC1 and CLIC4 than to GSTs. The invertebrate CLICs show several unique features including an elongated C-terminal extension and a divalent metal binding site. The latter appears to alter the ancestral glutathione binding site, and thus, the invertebrate CLICs are unlikely to bind glutathione in the same manner as the GST proteins. Purified recombinant DmCLIC and EXC-4 both bind to lipid bilayers and can form ion channels in artificial lipid bilayers, albeit at low pH. EXC-4 differs from other CLIC proteins in that the conserved redox-active cysteine at the N-terminus of helix 1 is replaced by an aspartic acid residue. Other key distinguishing features of EXC-4 include the fact that it binds to artificial bilayers at neutral pH and this binding is not sensitive to oxidation. These differences with other CLIC family members are likely to be due to the substitution of the conserved cysteine by aspartic acid.     

Decolorization and biodegradation of Indigo carmine by a textile soil isolate Paenibacillus larvae

The potential of recently isolated bacteria Paenibacillus larvae for the effective decolorization of Indigo carmine was evaluated. The effects of operational parameters (temperature, pH, dye concentration, shaking/non shaking) were tested. Maximum extent of decolorization was observed when the medium was incorporated with 10 g/l of yeast extract and peptone. Decolorization was strongly inhibited at non-shaken conditions as well as incorporation of inorganic sources (sodium nitrite and ammonium chloride) in the medium. Maximum decolorization was observed at 30°C (100%) and 40°C (92%) at 8 h of incubation. The LC-MS and NMR analysis confirms the oxidation of Indigo carmine .The primary degradation products were found to be Isatin sulfonic acid and anthranilicacid.     

Oxidation of isoeugenol by Nocardia iowensis

Isoeugenol is a starting material for both the synthetic and biotechnological production of vanillin and vanillic acid. Nocardia iowensis DSM 45197 (formerly Nocardia species NRRL 5646) resting cells catalyze the conversion of isoeugenol to vanillic acid, vanillin, vanillyl alcohol and guaiacol. The present study used a variety of chemical, microbial and enzymatic approaches to probe the pathways used by N. iowensis in the oxidation of isoeugenol to these products. Of three possible pathways considered, initial side-chain olefin epoxidation, epoxide hydrolysis to a vicinal diol, and diol cleavage to vanillin and subsequently further oxidation to vanillic acid appears as the most likely route. Isoeugenol was not oxidized to ferulic acid, a well-known microbial transformation precursor for vanillin and vanillic acid. ¹⁸O-Labeled oxygen (one atom) and water (two oxygen atoms) were incorporated into vanillic acid during the whole-cell biotransformation reaction with isoeugenol indicating the likely involvement of oxygenase and hydrolase systems in the bioconversion reaction. Vanillin was converted to singly labeled vanillic acid in the presence of H₂¹⁸O suggesting the presence of an aldehyde oxidase. Cell extracts achieved the conversion of isoeugenol to vanillic acid and vanillin without cofactors. Partial fractionation of two enzyme activities supported the presence of isoeugenol monooxygenase and vanillin oxidase activities in N. iowensis.     

Detection of microcystin producing cyanobacteria in Spirulina dietary supplements using multiplex HRM quantitative PCR

Arthrospira species, under the name ‘Spirulina’, are used as food supplement for its protein, vitamins, and minerals which have several health benefits. Cyanobacterial toxins including microcystins can possibly contaminate these dietary supplements causing hepatotoxicity, tumour formation, and other disorders. The safe use of dietary supplements necessitates the need to assess such toxins in the algal food supplement. The methods which evaluate these dietary supplements should be highly sensitive, cost-effective, and rapid. In this study, multiplex HRM qPCR analysis was used to detect microcystin (MC)-producing cyanobacteria in Spirulina dietary supplements. The multiplex HRM qPCR detection limit was found to be 25 ag of mcyB spiked in a standard concentration of pcb (25 pg). Two distinct melt curves characteristic of pcb (Tm 82.8 ± 0.07 °C) and mcyB (Tm 77.9 ± 0.05 °C) were observed. Microcystin contamination was detected only in the fish food supplements and not in human dietary supplements of Spirulina. Liquid chromatography–high-resolution mass spectrometry analysis further confirmed the presence of the congeners of microcystin in the identified positive samples.     

<Emphasis Type="Italic">Lysobacter panacihumi</Emphasis> sp. nov., isolated from ginseng cultivated soil

A Gram-negative, non-motile, aerobic, catalase-, and oxidasepositive bacterial strain, designated DCY117^T, was isolated from ginseng cultivated soil in Gochang-gun, Republic of Korea, and was characterized taxonomically using a multifaceted approach. 16S rRNA gene sequence analysis revealed that strain DCY117^T showed highest similarity to Lysobacter ruishenii CTN-1^T (95.3%). Phylogenetic analysis revealed that closely related relatives of strain DCY117^T were L. aestuarii S2-C^T (95.1%), L. daejeonensis GH1-9^T (95.0%), and L. caeni BUT-8^T (94.9%). Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE) were the major polar lipids of strain DCY117^T. The major isoprenoid quinone was Q-8. The major cellular fatty acids of strain DCY117^T were iso-C_15:0, iso-C_16:0, and summed feature 9 (comprising iso-C_17:1ω9c and/or 10-methyl-C_16:0). Genomic DNA G + C content was 61.8 mol%. On the basis of our findings, strain DCY117^T is a novel species in the genus Lysobacter. We propose the name Lysobacter panacihumi sp. nov., and the type strain is DCY117^T (= KCTC 62019^T = JCM 32168^T).     

Optimization of quorum quenching mediated bacterial attenuation of Solanum torvum root extract by response surface modelling through Box-Behnken approach

The present study was intended to optimize the quorum sensing inhibitory action of Solanum torvum root extract against Chromobacterium violaceum. Factors such as bacterial density, frequency of administration and concentration of extract were analysed. Plant samples were collected from Thrissur District, Kerala, India. Response surface modelling of factors by Box-Behnken approach was employed for optimizing quorum quenching activity of extract. The adequacy of mathematical model was verified by ANOVA and Cook’s distance table. Results revealed that quorum quenching property of Solanum torvum root extract is highly influenced by variables studied whereas maximum activity was found during administration of 300?µg/ml extract thrice in a day. It was also understood that extract does not possess any bactericidal activity wherein it only silence its quorum sensing mediated functions. This observations can be further used in quorum quenching studies.