Biotechnological approaches to breeding and cultivation of ornamental crop plants

Recent advances in plant biotechnology hold great potential for the ornamental horticulture industry. In addition to conventional methods, breeders can now introduce genetic variation into ornamentals by the application of recombinant DNA technology. This technology is particularly useful for effecting changes in phenotypic expression encoded by single genes such as corolla and foliage color and texture, stem length, scent, temporal regulation of flowering, vase life of cut flowers and resistance to stressful environments. In part, the commercial success of this technology will depend on developing reliable methods of transformation of ornamentals and on the stability of the introduced or altered genes. In addition, new and improved strategies of in vitro culture have been commercially implemented for the propagation and breeding of a wide variety of ornamental crops and will undoubtedly play a major role in the screening and propagation of chimeric plants developed by recombinant DNA technology.     

Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13

In this work, the binding mechanism of new Polyketide Synthase 13 (Pks13) inhibitors has been studied through molecular dynamics simulation and free energy calculations. The drug Tam1 and its analogs, belonging to the benzofuran class, were submitted to 100 ns simulations, and according to the results obtained for root mean square deviation, all the simulations converged from approximately 30 ns. For the analysis of backbone flotation, the root mean square fluctuations were plotted for the Cα atoms; analysis revealed that the greatest fluctuation occurred in the residues that are part of the protein lid domain. The binding free energy value (ΔG_bind) obtained for the Tam16 lead molecule was of ?51.43 kcal/mol. When comparing this result with the ΔG_bind values for the remaining analogs, the drug Tam16 was found to be the highest ranked: this result is in agreement with the experimental results obtained by Aggarwal and collaborators, where it was verified that the IC₅₀ for Tam16 is the smallest necessary to inhibit the Pks13 (IC₅₀ = 0.19 μM). The energy decomposition analysis suggested that the residues which most interact with inhibitors are: Ser1636, Tyr1637, Asn1640, Ala1667, Phe1670, and Tyr1674, from which the greatest energy contribution to Phe1670 was particularly notable. For the lead molecule Tam16, a hydrogen bond with the hydroxyl of the phenol not observed in the other analogs induced a more stable molecular structure. Aggarwal and colleagues reported this hydrogen bonding as being responsible for the stability of the molecule, optimizing its physic-chemical, toxicological, and pharmacokinetic properties.     

Studies on the mechanism of interaction of a bioresponsive endosomolytic polyamidoamine with interfaces. 1. Micelles as model surfaces

Polymers are appealing as pH-responsive elements of multicomponent systems designed to promote cytosolic delivery of macromolecular drugs (including proteins and genes), but so far the delivery efficiency achieved has been relatively modest. Therefore, the aim of this study was to apply several physicochemical techniques that are well established in the colloid field (surface tension measurements, small-angle neutron scattering (SANS), and electron paramagnetic resonance (EPR)) to probe the mechanism of endosomolytic polymer-surface interaction over the pH range 7.4 to 5.5 using the poly(amidoamine) (PAA) ISA23 x HCl and a series of "model" micelle surfaces. These micellar models were chosen to represent increasing complexity from simple, single surfactant sodium dodecylsulfate (SDS) micelles, surfactant mixtures containing bulky malono-bis-N-methylglucamide headgroups, or highly extended ethylene oxide headgroups. Spherical micelles composed of 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine (lyso-PC) were also used. Changes in the onset of micellization, micelle surface fluidity, and in selected cases, the overall micelle shape and size were all quantified as a function of pH in the presence and absence of ISA23 x HCl. This amphoteric PAA is negatively charged at pH 7.4 and becomes gradually more protonated on exposure to lower pH values representative of the endosomal-lysosomal pathway. As expected, the strength of polymer interaction with anionic micelles increased with a decrease in pH, while for cationic micelles the opposite was observed. Addition of bulky, nonionic surfactant headgroups led to weaker interactions. The observations from surface tension and SANS studies showed a complex pattern of interaction with both an electrostatic and hydrophobic component. Using EPR it was confirmed that ISA23 x HCl perturbed the micelle palisade layer leading to a decrease in fluidity of the interface with a lower degree of headgroup hydration, and a significant change in micelle morphology. Surprisingly, there was no interaction between ISA23 x HCl and globular micelles formed from lyso-PC (a more biologically relevant model), and this suggests that the PAA structure could be better optimized to promote rapid interaction with endosomal membranes at the physiologically relevant pH 6.5.     

Environmental Risk Assessment of Dams in Construction Phase Using a Multi-Criteria Decision-Making (MCDM) Method

This study was conducted to identify environmental and human health risks caused by Balarood Dam, in construction phrase. The first step, all risk-generating factors were identified using a Delphi Questionnaire. Afterwards, the identified criteria were prioritized once using the Analytical Hierarchy Process (AHP) method and then by the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS). Due to the complex and uncertain nature of decision-making in times of risk, it was necessary to use more than one weighting method to ensure accuracy of weights. The results from AHP and TOPSIS revealed a mismatch in priorities; therefore, an integration method was presented blending Mean-Rank, Borda, and Copeland methods. According to the TOPSIS results, factors including cut and fill, explosion, and transportation, were first to third highest-priority risk-generating factors, respectively. Considering the results from the AHP method, factors cut and fill, drilling, and explosion were identified as first to third top-priority risk-generating factors, respectively. The results obtained from the integration method suggested that cut and fill, explosion, and drilling are the most important environmental risks at construction phase. As a general conclusion, different weighting methods can lead to different results by which the fate of a decision may be changed and it is essential to control final scores by applying more than one weighting method.     

Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin

In the present study, we investigate the impact of a tightly bound water molecule on ligand binding in the S1 pocket of thrombin. The S1 pocket contains a deeply buried deprotonated aspartate residue (Asp189) that is, due to its charged state, well hydrated in the uncomplexed state. We systematically studied the importance of this water molecule by evaluating a series of ligands that contains pyridine-type P1 side chains that could potentially alter the binding properties of this water molecule. All of the pyridine derivatives retain the original hydration state albeit sometimes with a slight perturbance. In order to prevent a direct H-bond formation with Asp189, and to create a permanent positive charge on the P1 side chain that is positioned adjacent to the Asp189 carboxylate anion, we methylated the pyridine nitrogen. This methylation resulted in displacement of water but was accompanied by a loss in binding affinity. Quantum chemical calculations of the ligand solvation free energy showed that the positively charged methylpyridinium derivatives suffer a large penalty of desolvation upon binding. Consequently, they have a substantially less favorable enthalpy of binding. In addition to the ligand desolvation penalty, the hydration shell around Asp189 has to be overcome, which is achieved in nearly all pyridinium derivatives. Only for the ortho derivative is a partial population of a water next to Asp189 found. Possibly, the gain of electrostatic interactions between the charged P1 side chain and Asp189 helps to compensate for the desolvation penalty. In all uncharged pyridine derivatives, the solvation shell remains next to Asp189, partly mediating interactions between ligand and protein. In the case of the para-pyridine derivative, a strongly disordered cluster of water sites is observed between ligand and Asp189.