SDF2XYZ2SDF: how to exploit TINKER power in cheminformatics projects

An open-source tool capable of converting SD files (and virtually any other format through OpenBabel) into MMFF-typed XYZ coordinate files to be used with TINKER is described. SDF2XYZ2SDF allows including the power of TINKER molecular mechanics computations in automated cheminformatics workflows, such as conformational searches and virtual screening protocols.     

Antibacterial activity and chemical composition of the essential oil of Grammosciadium platycarpum Boiss. from Iran

The chemical composition of the essential oils obtained from two samples (GP1 and GP2) of Grammosciadium platycarpum Boiss. was analyzed by GC and GC-MS. The analysis of the oils resulted in the identification of twenty-two constituents. Linalool (79.0%-GP1, 81.8%-GP2) and limonene (10.0%, 5.8%) were found to be the major components, respectively. The in vitro antibacterial activities of these oils and their main compounds against seven Gram-positive and Gram-negative bacteria were investigated. The results exhibited that the total oils and their major components possess strong to moderate activities against all the tested bacteria except for Pseudomonas aeruginosa.     

Identification of an intracellular microdomain of the P2X7 receptor that is crucial in basolateral membrane targeting in epithelial cells

We investigated membrane targeting of the P2X₇ receptor (P2X₇R) in polarized epithelial cells using immunofluorescent confocal imaging. The wild-type receptor was targeted to the basolateral membrane, independently of adaptor protein μ1B. Deletion of the majority of the intracellular C-terminus, or the last 26 residues (P570-Y595), conferred targeting of the protein to the apical membrane. Alanine substitution in the microdomain P582-Q587 caused similar apical membrane targeting without major effect on the receptor function and surface expression. Our results show basolateral membrane targeting of the P2X₇R in epithelial cells and that the intracellular C-terminal microdomain P582-Q587 is crucial in this process.

Structured summary

MINT-8055849:Beta-catenin (uniprotkb:B6V8E6) and P2X7R (uniprotkb:Q64663) colocalize (MI:0403) by fluorescence microscopy (MI:0416)     

Insecticidal potential of natural zeolite and diatomaceous earth formulations against rice weevil (Coleoptera: Curculionidae) and red flour beetle (Coleoptera: Tenebrionidae)

Insecticidal potential of natural zeolites and diatomaceous earths originating from Serbia against Sitophilus oryzae (L.) and Tribolium castaneum (Herbst) was evaluated. Two natural zeolite formulations (NZ and NZ Modified) were applied to wheat at rates of 0.50, 0.75, and 1.0 g/kg, while two diatomaceous earth (DE) formulations (DE S-1 and DE S-2) were applied at rates of 0.25, 0.50, 0.75, and 1.0 g/kg. A bioassay was conducted under laboratory conditions: temperature of 24 +/- 1 degrees C, relative humidity in the range 50-55%, in tests with natural zeolites, and 60-65%, in tests with DEs, and in all combinations for progeny production. Mortality was assessed after 7, 14, and 21 d of insect contact with treated wheat, and the total mortality after an additional 7-d recovery on untreated broken wheat. Progeny production was also assessed after 8 wk for S. oryzae and 12 wk for T. castaneum. The highest mortality for S. oryzae and T. castaneum was found after the longest exposure period and 7 d of recovery, on wheat treated with NZ at the highest rate and DEs at rates of 0.50 -1.0 g/kg. Progeny reduction higher than 90% was achieved after 14 and 21 d of contact of both beetle pests with wheat treated with DE S-1 at 0.50-1.0 g/kg and DE S-2 at 0.75-1.0 g/kg, while the same level of reduction was achieved only for T. castaneum after its contact with the highest rate of NZ formulation. NZ Modified, applied even at the highest rate, revealed much lower insecticidal potential.     

The influence of peroxisome proliferator-activated receptor γ(1) during differentiation of mouse embryonic stem cells to neural cells

Peroxisome proliferator activated receptor γ, belongs to PPARs, which exerts various metabolic functions including differentiation process. To testify the importance of PPARγ in neural differentiation of mouse embryonic stem cells (mESCs), its expression level was assessed. Data revealed an elevation in expression level of PPARγ when neural precursors (NPs) are formed upon retinoic acid treatment. Thus, involvement of PPARγ in two stages of neural differentiation of mESCs, during and post-NPs formation was examined by application of its agonist and antagonist. Our results indicated that PPARγ inactivation via treatment with GW9662 during NPs formation, reduced expression of neural precursor and neural (neuronal and astrocytes) markers. However, PPARγ inactivation by antagonist treatment post-NPs formation stage only decreased the expression of mature astrocyte marker (Gfap) suggesting that inactivation of PPARγ by antagonist decreased astrocyte differentiation. Here, we have demonstrated the stage dependent role of PPARγ modulation on neural differentiation of mESCs by retinoic acid treatment for the first time.     

Effects of the Addition of Humic Substances on Soil Protease Activities in Andosols in the Presence of Cadmium

Cadmium extraction, sorption, and immobilization seem to be the effective mechanisms in detoxification of Cd-contaminated soil. Humic substances present in soils may play an important role both in controlling the negative effects of pollution with Cd and in stabilizing soil enzymes. In this context, we have compared the effects of humic substances on soil protease activities in the presence and absence of Cd in forest and cultivated field soil samples. The samples were taken from surface soils of Andosols in a single upland area of the Kanto district in Japan. Humic substances extracted from the two soils showed differences in elemental composition, the degree of condensation of aromatic groups, and the proportions of major functional groups. Compared with the control soil samples, those with added humic substances showed a significant increase in protease activities, even in the presence of Cd (10 and 50 mg Cd kg^?1 soil). However, the addition of Cd decreased the protease activities, protein contents, and soil pH in both soil samples at each of the two levels of humic substance fortification (+5% and +10%). Moreover, protease activities showed significant negative correlation with exchangeable Cd, but adding humic substances did not lead to a reduction in either sample. Thus, although the addition of humic substances increased and stabilized protease activities, it did not lead to a clear reversal of enzyme inhibition by Cd. The obtained results indicate that in both soil samples the humic substances used in this study did not have sufficient affinity to adsorb Cd, and the impact on enzyme activities depends on the difference in chemical characteristics of the added organic matter, as suggested by the difference in enhancement of protease activities between forest and cultivated field soil samples.