Relevant distance between two different instances of the same potential energy in protein folding

In the context of complex systems and, particularly, of protein folding, a physically meaningful distance is defined which allows to make useful statistical statements about the way in which energy differences are modified when two different instances of the same potential-energy function are used. When the two instances arise from the fact that different algorithms or different approximations are used, the distance herein defined may be used to evaluate the relative accuracy of the two methods. When the difference is due to a change in the free parameters of which the potential depends on, the distance can be used to quantify, in each region of parameter space, the robustness of the modeling to such a change and this, in turn, may be used to assess the significance of a parameters' fit. Both cases are illustrated with a practical example: the study of the Poisson-based solvation energy in the Trp-Cage protein (PDB code 1L2Y).     

Dynamic optimization of bioprocesses: efficient and robust numerical strategies

The dynamic optimization (open loop optimal control) of non-linear bioprocesses is considered in this contribution. These processes can be described by sets of non-linear differential and algebraic equations (DAEs), usually subject to constraints in the state and control variables. A review of the available solution techniques for this class of problems is presented, highlighting the numerical difficulties arising from the non-linear, constrained and often discontinuous nature of these systems. In order to surmount these difficulties, we present several alternative stochastic and hybrid techniques based on the control vector parameterization (CVP) approach. The CVP approach is a direct method which transforms the original problem into a non-linear programming (NLP) problem, which must be solved by a suitable (efficient and robust) solver. In particular, a hybrid technique uses a first global optimization phase followed by a fast second phase based on a local deterministic method, so it can handle the nonconvexity of many of these NLPs. The efficiency and robustness of these techniques is illustrated by solving several challenging case studies regarding the optimal control of fed-batch bioreactors and other bioprocesses. In order to fairly evaluate their advantages, a careful and critical comparison with several other direct approaches is provided. The results indicate that the two-phase hybrid approach presents the best compromise between robustness and efficiency.     

Improved stabilization of chemically aminated enzymes via multipoint covalent attachment on glyoxyl supports

The surface carboxylic groups of penicillin G acylase and glutaryl acylase were chemically aminated in a controlled way by reaction with ethylenediamine via the 1-ethyl-3-(dimethylamino-propyl) carbodiimide coupling method. Then, both proteins were immobilized on glyoxyl agarose. In both cases, the immobilization of the chemically modified enzymes improved the enzyme stability compared to the stability of the immobilized but non-modified enzyme (by a four-fold factor in the case of PGA and a 20-fold factor in the case of GA). The chemical modification presented a deleterious effect on soluble enzyme stability. Therefore, the improved stability should be related to a higher multipoint covalent attachment, involving both the lysine amino groups and also the new amino groups chemically introduced on the enzyme. Moreover, the lower pK(a) of the new amino groups permitted to immobilize the enzyme under milder conditions. In fact, the aminated proteins could be immobilized even at pH 9, while the non-modified enzymes could only be immobilized at pH over 10.     

PLGA:poloxamer and PLGA:poloxamine blend nanoparticles: new carriers for gene delivery

The main objective of the present work was the development of new nanoparticulate carrier systems for the delivery of plasmid DNA. These new carriers consist of a blend matrix formed by a poly(lactic-co-glycolic acid) (PLGA) copolymer and polyoxyethylene derivatives. More specifically, we have prepared nanostructures with different PLGA:poloxamer and PLGA:poloxamine compositions by an optimized emulsification-solvent diffusion technique and studied the potential of these carriers for the encapsulation and controlled release of plasmid DNA. Depending on the particle composition, the encapsulation efficiency of the model plasmid pEGFP-C1 varied between 30% and 45%. All formulations provided continuous and controlled release of the plasmid with minimal burst effect. In addition, the release rate and duration was dependent on the composition of the particle matrix. Moreover, gel electrophoresis and cell culture (MCF-7 cell line) assays allowed us to confirm that the biologically active form of the plasmid was preserved during the particle preparation process and also during its release. Cell culture experiments also indicated that the new nanoparticles do not exhibit toxic effects on these cells at concentrations up to 5 mg/mL. Altogether, these results indicate that these composite nanostructures present a promising approach for the delivery of plasmid DNA.     

Haemophilus paragallinarum secretes metalloproteases

Haemophilus paragallinarum secretes metalloproteases into different culture media lacking serum. Secreted proteins, concentrated by precipitation with 70% ammonium sulphate ((NH(4))(2)SO(4)) or methanol, displayed proteolytic activity at >100 kDa molecular mass in 10% polyacrylamide gels co-polymerized with porcine gelatin (0.1%). They were active in a broad pH range (4-9); pH 7.5 being the optimum. Protease activity was inhibited by 20 mmol EDTA/L and reactivated by calcium. The proteolytic activity was heat-stable at 40, 50, and 60 degrees C, but its activity diminished at 70 degrees C or higher. Secreted proteins partially degraded chicken immunoglobulin G (IgG) and cross-reacted with a polyclonal serum against a high molecular mass protease secreted by Actinobacillus pleuropneumoniae. Extracellular proteases could play a role in infectious coryza caused by H. paragallinarum.     

Mating system, sex ratio, and persistence of females in the gynodioecious shrub Daphne laureola L. (Thymelaeaceae)

Although in gynodioecious populations male steriles require a fecundity advantage to compensate for their gametic disadvantage, southern Spanish populations of the long-lived shrub Daphne laureola do not show any fecundity advantage over hermaphrodites in terms of seed production and early seedling establishment. By using allozyme markers, we assess the mating system of this species in five populations differing in sex ratio, and infer levels of inbreeding depression over the whole life cycle by comparing the inbreeding coefficients at the seed and adult plant stages. Extremely low outcrossing rates (0.001相似文献   

Cyclic and high molecular weight chiral binaphthoxy-phosphazene polymers carrying Br or trimethylsilyl-acetylene groups

The new chiral and functionalized cyclic binaphthoxyphosphazenes R,R,R-[N₃P₃(O₂C₂₀H₁₀Br₂)₃] (R-1), R,R,R-[N₃P₃(O₂C₂₀H₁₀(CCSiMe₃)₂)₃] (R-2), and the high molecular weight linear polymers R/S-[NP(O₂C₂₀H₁₀Br₂)]_n (R/S-3), R-[NP(O₂C₂₀H₁₀Br₂)]_n (R-3), and R-{NP[O₂C₂₀H₁₀(CCSiMe₃)₂]}_n, (R-4), with M_w on the order of 10⁶ and very high T_g, have been synthesized and characterized by IR and NMR spectroscopy. The optically active polymer (R-3) was configurationally stable below 300 °C, but at higher temperatures an atropisomerization process took place that became faster near the glass transition temperature (ca. 350 °C).     

Regulation of inflammatory response in neural cells in vitro by thiadiazolidinones derivatives through peroxisome proliferator-activated receptor gamma activation

In most neurodegenerative disorders, including multiple sclerosis, Parkinson disease, and Alzheimer disease, a massive neuronal cell death occurs as a consequence of an uncontrolled inflammatory response, where activated astrocytes and microglia and their cytotoxic agents play a crucial pathological role. Current treatments for these diseases are not effective. In the present study we investigate the effect of thiadiazolidinone derivatives, which have been recently suggested to play a role in neurodegenerative disorders. We have found that thiadiazolidinones are potent neuroprotector compounds. Thiadiazolidinones inhibited inflammatory activation of cultured brain astrocytes and microglia by diminishing lipopolysaccharide-induced interleukin 6, tumor necrosis factor alpha, inducible nitric-oxide synthase, and inducible cyclooxygenase type 2 expression. In addition, thiadiazolidinones inhibited tumor necrosis factor-alpha and nitric oxide production and, concomitantly, protected cortical neurons from cell death induced by the cell-free supernatant from activated microglia. The neuroprotective effects of thiadiazolidinones are completely inhibited by the peroxisome proliferator-activated receptor gamma antagonist GW9662. In contrast the glycogen synthase kinase 3beta inhibitor LiCl did not show any effect. These findings suggest that thiadiazolidinones potently attenuate lipopolysaccharide-induced neuroinflammation and reduces neuronal death by a mechanism dependent of peroxisome proliferator-activated receptor gamma activation.