Molecular dynamics simulation and molecular docking studies of 1,4-Dihydropyridines as P-glycoprotein’s allosteric inhibitors

P-glycoprotein (P-gp) is a main factor contributing to multidrug resistance. The effect of this transporter protein on limiting the effectiveness of chemotherapy has been shown by various studies. In a previous report, we synthesized some 14-dihydropyridine (DHP) derivatives as inhibitors of human P-gp. In the present study, a computational approach has been exploited to reveal the main interactions between DHPs and P-gp. In order to do this, homology modeling was performed to obtain a model of the protein. Then, molecular dynamics simulation was used to refine the constructed model of P-gp in the presence of the lipids bilayer. Model validation was performed with several tools. Finally, molecular docking followed by MD simulation of ligand–protein complex was employed to elucidate the binding mode and the dynamical changes of protein with/without DHPs bound. The results emphasized that interaction of the residues Gln912, Ser909, Arg905, Ser474, Val472 with DHPs play a crucial role in the inhibitory of these ligands and this was in a relatively good accordance with the results reported in the experimental studies.     

Cultural and physiological characteristics of Stemphylium lycopersici causing leaf blight disease on vegetable crops

During 2011–2012, an extensive leaf spot disease caused by Stemphylium lycopersici was observed on vegetable crops including, tomato, eggplant, pepper and lettuce in major vegetable-growing regions of Malaysia. Four isolates of S. lycopersici obtained from each vegetable crop were used to determine cultural and physiological characteristics. The variations were found in colony colour (pale to light grey or light as well as the brown), texture (cottony or mycelium flat), shape (regular with concentric growth rings or irregular) and pigmentation (yellow or deep red) of the cultures. The optimum temperature for the conidial germination and mean radial growth of the isolates was 25?°C, and the radial growth of the isolates was maximal on V-8 juice agar followed by potato carrot agar. The maximum sporulation of S. lycopersici isolates was observed on V-8 juice agar media under 12/12 h light/darkness photoperiod at 25?°C.     

Interaction of lubricin with type II collagen surfaces: Adsorption,friction, and normal forces

One of the major constituents of the synovial fluid that is thought to be responsible for chondroprotection and boundary lubrication is the glycoprotein lubricin (PRG4); however, the molecular mechanisms by which lubricin carries out its critical functions still remain largely unknown. We hypothesized that the interaction of lubricin with type II collagen, the main component of the cartilage extracellular matrix, results in enhanced tribological and wear properties. In this study, we examined: (i) the molecular details by which lubricin interacts with type II collagen and how binding is related to boundary lubrication and adhesive interactions; and (ii) whether collagen structure can affect lubricin adsorption and its chondroprotective properties. We found that lubricin adsorbs strongly onto denatured, amorphous, and fibrillar collagen surfaces. Furthermore, we found large repulsive interactions between the collagen surfaces in presence of lubricin, which increased with increasing lubricin concentration. Lubricin attenuated the large friction and also the long-range adhesion between fibrillar collagen surfaces. Interestingly, lubricin adsorbed onto and mediated the frictional response between the denatured and native amorphous collagen surfaces equally and showed no preference on the supramolecular architecture of collagen. However, the coefficient of friction was lowest on fibrillar collagen in the presence of lubricin. We speculate that an important role of lubricin in mediating interactions at the cartilage surface is to attach to the cartilage surface and provide a protective coating that maintains the contacting surfaces in a sterically repulsive state.     

Functional tissue engineering: Ten more years of progress

“Functional tissue engineering” is a subset of the field of tissue engineering that was proposed by the United States National Committee on Biomechanics over a decade ago in order to place more emphasis on the roles of biomechanics and mechanobiology in tissue repair and regeneration. Over the past decade, there have been tremendous advances in this area, pointing out the critical role that biomechanical factors can play in the engineered repair of virtually all tissue and organ systems. In this special issue of the Journal of Biomechanics, we present a series of articles that address a broad array of the fundamental topics of functional tissue engineering, including: (1) measurement and modeling of the in vivo biomechanical environment and history in native and repair tissues; (2) further understanding of the biomechanical properties of native tissues across all geometric scales, in the context of repair or regeneration; (3) prioritization of specific biomechanical properties as design criteria; (4) development of biomaterials, scaffolds, and engineered tissues with prescribed biomechanical properties; (5) development of success criteria based on appropriate outcome measures; (6) investigation of the effects of mechanical factors on tissue repair in vivo; (7) investigation of the mechanisms by which physical factors may enhance tissue regeneration in vitro; and (8) development and validation of computational models of tissue growth and remodeling. These articles represent the tremendous expansion of this field in recent years, and emphasize the critical roles that biomechanics and mechanobiology play in controlling tissue repair and regeneration.     

Evaluation of entomopathogenic nematodes against the olive fruit fly, Bactrocera oleae (Diptera: Tephritidae)

Infectivity of six entomopathogenic nematode (EPNs) species against Bactrocera oleae was compared. Similar infection levels were observed when third-instar larvae were exposed to infective juveniles (IJs) on a sand-potting soil substrate. When IJs were sprayed over naturally infested fallen olives, many larvae died within treated olives as well as in the soil; Steinernema feltiae caused the highest overall mortality of 67.9%. In addition, three laboratory experiments were conducted to optimize a time period for S. feltiae field application. (1) Abundance of fly larvae inside fallen olives was estimated over the 2006–2007 season with the highest number of susceptible larvae (3 mm and larger) per 100 olives being observed during December, 2006. (2) S. feltiae efficacy against fly larvae dropped to the soil post-IJ-application was determined. B. oleae added to the substrate before and after nematode application were infected at similar levels. (3) Effect of three temperature regimes (min–max: 10–27, 6–18, and 3–12 °C) corresponding to October through December in Davis, California on S. feltiae survival and infectivity was determined. After 8 weeks, the IJs at the 3–12 °C treatment showed the highest survival rate. However, the cold temperature significantly limited S. feltiae infectivity. Our results demonstrate that B. oleae mature larvae are susceptible to EPN infection both in the soil and within infested olives. Being the most effective species, S. feltiae may have the potential to suppress overwintering populations of B. oleae. We suggest that November is the optimal time for S. feltiae field application in Northern California.     

Force generated by actomyosin contraction builds bridges between adhesive contacts

Extracellular matrices in vivo are heterogeneous structures containing gaps that cells bridge with an actomyosin network. To understand the basis of bridging, we plated cells on surfaces patterned with fibronectin (FN)‐coated stripes separated by non‐adhesive regions. Bridges developed large tensions where concave cell edges were anchored to FN by adhesion sites. Actomyosin complexes assembled near those sites (both actin and myosin filaments) and moved towards the centre of the non‐adhesive regions in a treadmilling network. Inhibition of myosin‐II (MII) or Rho‐kinase collapsed bridges, whereas extension continued over adhesive areas. Inhibition of actin polymerization (latrunculin‐A, jasplakinolide) also collapsed the actomyosin network. We suggest that MII has distinct functions at different bridge regions: (1) at the concave edges of bridges, MIIA force stimulates actin filament assembly at adhesions and (2) in the body of bridges, myosin cross‐links actin filaments and stimulates actomyosin network healing when breaks occur. Both activities ensure turnover of actin networks needed to maintain stable bridges from one adhesive region to another.     

MRI-based characterization of bone anatomy in the human knee for size matching of a medial meniscal implant

Allograft or synthetic menisci have been suggested as a means to restore contact pressures following meniscectomy. However, when the natural meniscus is severely damaged/absent, the necessary size cannot be determined according to the recipient size and there is a need to estimate it from magnetic resonance imaging (MRI) of the contralateral knee or the injured knee bones. The use of the contralateral-knee for size matching is problematic due to economic and practical reasons. Hence, there are significant advantages for a sizing algorithm based only on the candidate knee geometry. The aim of this study is to characterize midrange values and variability of knee dimensions and to develop a set of mathematical relations representing knee dimensions using a minimum of imaging-based bone measurements. Tibia, femur, and meniscus measurements were taken in 118 MRI scans and used to develop a representative parametric knee model in which all dimensions are expressed using tibia plateau width. The model was verified by comparing the predicted values to direct MRI measurements for 20 additional subjects by means of the Pearson correlation and Bland and Altman (1986, "Statistical Methods for Assessing Agreement Between Two Methods of Clinical Measurement," Lancet, 1, pp. 307-310) plot. Anatomical parameters in the male knee were significantly larger (～17%) compared with corresponding female measurements. However, most relations between tibia, femur, and meniscus measurements (43/56) were not significantly different between male and female populations (p ≥ 0.05), indicating that differences between male and female joints are generally related to scaling and not shape. Dimensions predicted by the knee model were in a good agreement with dimensions measured directly from the MRI (R(2)>0.96) and the Bland and Altman plot indicated that ～95% of data points were well within the ± 2 standard deviation lines of agreement. The model proposed in this study is advantageous in being able to describe typical knee proportions for a given tibial width and can be used to predict the dimensions of a candidate knee based on a single measurement. The anatomical/anthropometric data presented in the study can be utilized in a sizing algorithm for artificial meniscal implants or in the design of artificial meniscus prostheses.     

Nucleosome dynamics between tension-induced states

We studied the dynamical behavior of a mononucleosome under tension using a theoretical model that takes into account the nucleosomal geometry, DNA elasticity, nonspecific DNA-protein binding, and effective repulsion between the two DNA turns. Using a dynamical Monte-Carlo simulation algorithm, we demonstrate that this model shows a behavior that for an appropriate set of parameters is in quantitative agreement with data from micromanipulation experiments on individual nucleosomes. All of the parameters of the model follow from the data obtained from two types of pulling experiments, namely, constant force and constant loading rate ensembles.