Selection of effective antisense oligodeoxynucleotides with a green fluorescent protein-based assay. Discovery of selective and potent inhibitors of glutathione S-transferase Mu expression.

Antisense oligodeoxynucleotides (AS-ODNs) are frequently used for the down-regulation of protein expression. Because the majority of potential antisense sequences lacks effectiveness, fast screening methods for the selection of effective AS-ODNs are needed. We describe a new cellular screening assay for the evaluation of the potency and specificity of new antisense sequences. Fusion constructs of the gene of interest and the gene encoding the enhanced green fluorescent protein (EGFP) are cotransfected with AS-ODNs to COS-7 cells. Subsequently, cells are analysed for expression of the EGFP fusion protein by flow cytometry. With the assay, we tested the effectiveness of a set of 15 phosphorothioate ODNs against rat glutathione S-transferase Mu1 (GSTM1) and/or Mu2 (GSTM2). We found several AS-ODNs that demonstrated potent, sequence-specific, and concentration-dependent inhibition of fusion protein expression. At 0.5 microm, AS-6 and AS-8 inhibited EGFP-GSTM1 expression by 95 +/- 4% and 81 +/- 6%, respectively. AS-5 and AS-10 were selective for GSTM2 (82 +/- 4% and 85 +/- 0.4% decrease, respectively). AS-2 and AS-3, targeted at homologous regions in GSTM1 and GSTM2, inhibited both isoforms (77-95% decrease). Other AS-ODNs were not effective or displayed non-target-specific inhibition of protein expression. The observed decrease in EGFP expression was accompanied by a decrease in GSTM enzyme activity. As isoform-selective, chemical inhibitors of GSTM and GSTM knock-out mice are presently unavailable, the selected AS-ODNs constitute important tools for the study of the role of GSTM in detoxification of xenobiotics and protection against chemical-induced carcinogenesis.     

Genetic transformation of the commercial barley (Hordeum vulgare L.) cultivar Conlon by particle bombardment of callus

Commercial barley cultivars are difficult to transform because of the lack of an efficient regeneration system. By modifying certain components in the standard culture medium, we have developed a reproducible and more efficient regeneration system. Herbicide-resistant transgenic plants from barley (Hordeum vulgare L. cv. Conlon) were obtained using this medium. Embryo-derived callus was bombarded with pAHC25, which contains the screenable marker gus (#-glucuronidase) and the selectable marker bar (bialaphos resistance gene), both driven by the maize ubiquitin promoter (Ubi1) and followed by the nos terminator. Following bombardment, callus was transferred to callus-induction medium supplemented with 5 mg/l bialaphos for selection. Resistant calli were subsequently transferred to maintenance medium containing 5 mg/l bialaphos for further selection and finally transferred to regeneration medium with 5 mg/l bialaphos. Green shoots that developed on the regeneration medium were transferred to rooting medium containing 3 mg/l bialaphos. Eighty-five transgenic plants were obtained from 13 independent transformation events. Progeny tests showed Mendelian inheritance for the transgenes. This is the first report of the production of large numbers of transgenic plants from a commercial cultivar adapted to Midwestern US barley production.     

Probing the structure of Leishmania donovani chagasi DHFR-TS: comparative protein modeling and protein–ligand interaction studies

Dihydrofolate reductase (DHFR) has been used successfully as a drug target in the area of anti-bacterial, anti-cancer and anti-malarial therapy. It also acts as a drug target for Leishmaniasis. Inhibition of DHFR leads to cell death through lack of thymine (nucleotide metabolism). Although the crystal structures of Leishmania major and Trypanosoma cruzi DHFR-thymidylate synthase (TS) have been resolved, to date there is no three-dimensional (3D)-structural information on DHFR-TS of Leishmania donovani chagasi, which causes visceral leishmaniasis. Our aim in this study was to model the 3D structure of L. donovani chagasi DHFR-TS, and to investigate the structural requirements for its inhibition. In this paper we describe a highly refined homology model of L. donovani chagasi DHFR-TS based on available crystallographic structures by using the Homology module of Insight II. Structural refinement and minimization of the generated L. donovani chagasi DHFR-TS model employed the Discover 3 module of Insight II and molecular dynamic simulations. The model was further validated through use of the PROCHECK, Verify_3D, PROSA, PSQS and ERRAT programs, which confirm that the model is reliable. Superimposition of the model structure with the templates L. major A chain, L. major B chain And T. cruzi A chain showed root mean square deviations of 0.69 Å, 0.71 Å and 1.11 Å, respectively. Docking analysis of the L. donovani chagasi DHFR-TS model with methotrexate enabled us to identify specific residues, viz. Val156, Val30, Lys95, Lys75 and Arg97, within the L. donovani chagasi DHFR-TS binding pocket, that play an important role in ligand or substrate binding. Docking studies clearly indicated that these five residues are important determinants for binding as they have strong hydrogen bonding interactions with the ligand.     

Fragment-based virtual screening approach and molecular dynamics simulation studies for identification of BACE1 inhibitor leads

Traditional structure-based virtual screening method to identify drug-like small molecules for BACE1 is so far unsuccessful. Location of BACE1, poor Blood Brain Barrier permeability and P-glycoprotein (Pgp) susceptibility of the inhibitors make it even more difficult. Fragment-based drug design method is suitable for efficient optimization of initial hit molecules for target like BACE1. We have developed a fragment-based virtual screening approach to identify/optimize the fragment molecules as a starting point. This method combines the shape, electrostatic, and pharmacophoric features of known fragment molecules, bound to protein conjugate crystal structure, and aims to identify both chemically and energetically feasible small fragment ligands that bind to BACE1 active site. The two top-ranked fragment hits were subjected for a 53 ns MD simulation. Principle component analysis and free energy landscape analysis reveal that the new ligands show the characteristic features of established BACE1 inhibitors. The potent method employed in this study may serve for the development of potential lead molecules for BACE1-directed Alzheimer’s disease therapeutics.     

Inhibitory effects of the essential oils α-longipinene and linalool on biofilm formation and hyphal growth of Candida albicans

Candida albicans is one of the most common fungal pathogens, and causes systemic and invasive infections in humans. C. albicans biofilms are composed of yeast and hyphal and pseudohyphal elements, and the transition of yeast to the hyphal stage could be a virulence factor. In this study, diverse essential oils were initially investigated for anti-biofilm activity against C. albicans strains, and cascarilla bark oil and helichrysum oil and their components α-longipinene (a major constituent of both) and linalool were found to markedly inhibit biofilm formation without affecting planktonic cell growth. Moreover, α-longipinene and linalool were found to synergistically reduce biofilm formation. Notably, treatments with cascarilla bark oil, helichrysum oil, α-longipinene, or linalool clearly inhibited hyphal formation, and this appeared to be largely responsible for their anti-biofilm effect. Furthermore, the two essential oils, α-longipinene and linalool, reduced C. albicans virulence in Caenorhabditis elegans.     

Treatment of carrots with spent green tea extract reduces the soft rot of Pectobacterium spp.

In the present study the antibacterial activity of spent green tea (SGT) was evaluated against Pectobacterium spp. causing soft rot incidence. Gas chromatography and mass spectroscopy (GC-MS) analysis reveal the presence of caffeine in the SGT extracts. Time kill assay revealed that SGT was able to kill Pectobacterium spp. at 18 h at 10 × MIC and at 24 h at 1 × MIC concentration. SGT led to the significant decrease in pectin lyase (PL), polygalcturonase (PG) and pectin methyl esterase activity in carrots challenge inoculated with Pectobacterium spp. SGT treated carrots recorded low degree of maceration, and relative electrolyte leakage (REL) values and also maintained high β carotene content, phenolic content and total antioxidant percentage. Based on the results of this study it could be concluded that SGT was able to offer protection to carrot against soft rot causing Pectobacterium spp. under post-harvest storage conditions.     

Uptake and Translocation of Tri- and Hexa-Valent Chromium and Their Effects on Black Gram (Vigna mungo L. Hepper cv. Co4) Roots

An equal concentration (100 μM) of Cr(III)- and Cr(VI)-induced changes in activities of antioxidative enzymes and metabolites of ascorbate-glutathione cycle was studied in 7-d-old black gram (Vigna mungo L Hepper cv. Co4) seedlings for 5-d after infliction of Cr stress. Seeds were germinated and grown in the presence or absence of Cr under controlled environmental conditions. Uptake and translocation of Cr rate was relatively higher during first 12 h of treatment with both speciation of Cr, Cr(III)- and Cr(VI)-treated black gram roots retained 15 times more Cr than the shoots. Significantly increased lipid peroxidation was observed in the form of accumulation of malondialdehyde (MDA) and production of hydrogen peroxide (H₂O₂) molecule and superoxide (O₂ ) radical after 6 h of infliction with Cr(VI) and after 12 h in Cr(III)-treated black gram roots. Superoxide dismutase (SOD) and ascorbate peroxidase (APX) activities were significantly increased under Cr(VI)-treatment after 12 and 6 h, respectively. However, catalase (CAT) and monodehydroascorbate reductase (MDHAR) activities were not significantly increased under Cr(Ill)-treatment. There was a steep increase of 2.71 μmol g^-1 FW in ascorbic acid (AA) content was observed between 6 and 24 h of Cr(VI)-treatment. Oxidized glutathione (GSSG) content was steadily increased through the course of Cr(III)- and Cr(VI)-treatments, where as reduced glutathione (GSH) level was decreased after 24 h of treatment. GSH/GSSG ratio was rapidly decreased in treatment with Cr(III) than the Cr(VI). There was significant increase of 99 nmol g^-1 FW in non-protein thiol (NPT) content was recorded between 6 and 24 h of Cr(VI)-treatment. The present results showed differential response to AA and H₂O₂ signaling by Cr(III) and Cr(VI), AA in combination with APX was more effective in mitigating oxidative stress as against the role of GSH as an antioxidant.