Structure-based binding between protein farnesyl transferase and PRL-PTP of malaria parasite: an interaction study of prenylation process in Plasmodium

Protein prenylation is a post-translational modification critical for many cellular processes such as DNA replication, signaling, and trafficking. It is mediated by protein farnesyltransferase by recognizing ‘CAAX’ motif on protein substrate. Plasmodium falciparum also possesses many such proteins with ‘CAAX’ motif, involved in various pathways of the parasite. The interaction studies of PfPFT with its substrate were carried out using synthetic peptides but not with full protein. Therefore, in this study, we have modeled both PfPFT and its substrate protein tyrosine phosphatase (PfPRL-PTP) followed by interaction studies using protein–protein docking and molecular dynamics simulation. Our findings provided a clear picture of interactions at atomic level between prenyltransferase and its protein substrate. We are assured that this piece of information can be extended to many other proteins of parasite containing ‘CAAX’ motif and that it may also lead to the development of anti-malarials based on the inhibition of prenylation-dependent pathways of parasite..     

Live food mediated vitamin C transfer to Dicentrarchus labrax and Clarias gariepinus

Live food enrichment techniques, using formulated diets and emulsions for improving the nutritional quality of Brachionus and Artemia , were studied as a tool for transferring ascorbic acid (AA) to fish larvae.
Artemia nauplii enriched for 24 h with an experimental emulsion containing 20% HUFA and 0%, 10% and 20% ascorbyl palmitate (AP) were administered to catfish larvae in a 20-day feeding trial. Survival was not affected by the dietary AA, but from day 7 onwards a significantly positive effect of supplemental AA on growth was demonstrated. At the end of the experiment the 20% AP group weighed 30% more than the control (0% AP), i.e. 9.5 and 6.3 mg DW, respectively. Evaluation of the physiological condition was demonstrated by salinity tests. In all three treatments larval growth was relatively low, and it still has to be verified if extra vitamin C in the diet really promotes growth. Seabass larvae fed on AP-enriched rotifers (days 4–12) and Artemia nauplii (days 13–46) showed no significant differences in production characteristics nor in stress resistance, however, for all salinity stress tests the 20% AP group performed better. AA was well incorporated into the predator larvae from the Brachionus feeding onwards.     

Solution structure of a nucleic acid photoproduct of deoxyfluorouridylyl-(3'-5')-thymidine monophosphate (d-FpT) determined by NMR and restrained molecular dynamics: structural comparison of two sequence isomer photoadducts (d-U5p5T and d-T5p5U).

Acetone-sensitized irradiation using UV-B (sun lamp, lambda max = 313 nm) of deoxyfluorouridylyl-(3'-5')-thymidine monophosphate (d-FpT, F = fluorouracil), produces two major photoproducts, the cis-syn cyclobutane-type photodimer and a defluorinated (5-5) photoadduct, d-U5p5T. Product distribution is dependent on the pH of the irradiation solution, as was the case of irradiated d-TpF. At high pH (8-10) the (5-5) photoadduct is the major photoproduct. Irradiation of d-FpT shows a much faster photodegradation rate than the sequence isomer d-TpF. Multinuclear NMR experiments establish the formation of (5-5) covalent bonding between the C5 (d-U5p-, where the fluorine had been) and the C5 (-p5T) and the C6 (-p5T) acquires an OH group. NOE interproton distances and dihedral angles derived from J coupling analysis are constrained to refine model structures of d-U5p5T in restrained molecular dynamics calculations. The resultant structures obtained show 5S-6S as the most chiralities of the C5 and C6 atoms of the thymine, which is the opposite chirality to the corresponding atoms in the sequence isomer d-T5p5U. The orientation of the C5 substituents (-p5T fragment), the CH3 and the uracil are pseudo-axial and pseudo-equatorial respectively. Glycosidic angles are in the anti regions for both the d-U5p- and -p5T residues. Averaged backbone conformations of the two photoadducts, d-U5p5T and d-T5p5U, are similar, although the overall structure of d-U5p5T appears much more flexible than that of d-T5p5U. In particular, the sugar conformations of the 5'-end residues show a remarkable difference in flexibility.     

Deciphering mechanistic implications of antimicrobial and antioxidant potentials of certain new dibutyltin(IV) formulations as possible therapeutic options based on DFT and hybrid materials paradigm

Mechanistic implications of antimicrobial and in vitro antioxidant potentials of a set of newly generated nonbridged mononuclear N,O-orthometallated and carboxylate bridged binuclear nonorthometallated dibutyltin(IV) formulations have been investigated. Some of these formulations were screened for their antibacterial and antifungal activities against Escherichia coli and Candida albicans, respectively whereas in vitro antioxidant potential was examined by Ferric reducing antioxidant power (FRAP) assay. Nonbridged mononuclear N,O-orthometallated dibutyltin(IV) formulations were generated by the reactions of Bu₂SnCl₂ with sodium salts of 2-aminophenol/substituted 2-aminophenol and flexible N-protected amino acids in 1:1:1 molar ratio in refluxing dry THF. Plausible structures of these nonbridged mononuclear N,O-orthometallated dibutyltin(IV) formulations containing flexible N-protected amino acids have been suggested on the basis of spectroscopic and mass studies of some representative formulations. Plausible structures suggested on the basis of spectroscopic studies are corroborated by density functional theory (DFT/B3LYP method) (SPARTAN-20) investigation of a representative dibutyltin(IV) complex and the ligands involved in it. The presence of two different classes of organic ligands in this complex provides an opportunity to study optimized topologies, bonding, distortions, optimized energy, and stability of the complex.     

Quantification of Phytochemicals and Metal Ions as well as the Determination of Volatile Compounds,Antioxidant, Antimicrobial and Antacid Activities of the Mimosa pudica L. Leaf: Exploration of Neglected and Under-Utilized Part

Mimosa pudica L. (MP) is well-known plant in traditional medicinal system, especially in India. Unfortunately, leaves of MP are less explored. To determine the food and nutritional value of the neglected part of Mimosa pudica L. (MP), that is MP leaves, phytochemicals and metal ions of MP were quantified by newly developed HPLC and ICPOES-based methods. The content of phytochemicals observed using HPLC analysis for chlorogenic acid, catechin, and epicatechin was 141.823 (±8.171), 666.621 (±11.432), and 293.175 (±12.743) μg/g, respectively. Using GC/MS/MS analysis, fatty acid like oleic acid were identified. In ICP-OES analysis, a significant content of Na, K, Ca, Cu, Fe, Mg, Mn, and Zn was observed. The observed TPC and TFC for MP leaf extracts was 44.327 (±1.041) mg GAE/ g of wt. and 214.217 (±4.372) mg QCE/ g of wt., respectively. The DPPH assay depicted a strong antioxidant activity of MP leaf extracts with IC₅₀ values of 0.796 (±0.081) mg/mL and a TEAC value of 0.0356 (±0.0003). A significant antacid activity (666 mg MP+400 mg CaCO₃ >400 mg CaCO₃ ≫666 mg Gelusil) of MP leaves was noticed. The methanolic extract of MP leaves demonstrated anti-microbial activity against Staphylococcus aureus (15±2mm), Pseudomonas aeruginosa (12±2mm) and Escherichia coli (10±2mm). In silico studies confirmed the in vitro results obtained for antioxidant, antiacid, and anti-microbial activities. In addition, in silico studies revealed the anti-cancerous and anti-inflammatory potential of the MP leaves. In summary, this study demonstrated the medicinal significance of MP leaves and the conversion of agro-waste or the under-utilized part of MP into pharmaceutical potent materials. Consequently, the present study highlighted that MP leaves alone have medicinal importance with good nutritional utility and possess large promise in the pharma industry along with improving bio-valorization and the environment.     

Electron-probe microanalysis of silicon in the epidermis of rice (Oryza sativa L.) internodes

Summary Electron-probe X-ray microanalysis showed that significant amounts of silicon are accumulated in the entire epidermal system of the rice internode except in the stomatal apparatuses. Thus, there is a lack of specific sites for Si deposition from levels just above the base to the tip of the rice internode. In the intercalary meristem region, 1 cm above the base of the internode, point-count data indicate more Si accumulation in the dumb-bell shaped silica cells than in the long epidermal cells. Above this region, Si is accumulated essentially in a uniform pattern in all epidermal cells. Such a pattern for Si accumulation in rice internodes markedly contrasts with that for Avena internodes and may explain, in part, why rice plants have a higher percentage Si (dry weight basis) in their shoots. The adaptive significance of this silicification pattern in rice is discussed.     

Life cycle assessment research and application in Indonesia

The International Journal of Life Cycle Assessment - This paper presents a review of the research and application of life cycle assessment (LCA) in Indonesia over the last 20 years and...