A Practical Teaching Course in Directed Protein Evolution Using the Green Fluorescent Protein as a Model

Protein engineering is a powerful tool, which correlates protein structure with specific functions, both in applied biotechnology and in basic research. Here, we present a practical teaching course for engineering the green fluorescent protein (GFP) from Aequorea victoria by a random mutagenesis strategy using error-prone polymerase chain reaction. Screening of bacterial colonies transformed with random mutant libraries identified GFP variants with increased fluorescence yields. Mapping the three-dimensional structure of these mutants demonstrated how alterations in structural features such as the environment around the fluorophore and properties of the protein surface can influence functional properties such as the intensity of fluorescence and protein solubility.

Interpretation of negative values of the interaction parameter in the adsorption equation through the effects of surface layer heterogeneity

The problem of the negative values of the interaction parameter in the equation of Frumkin has been analyzed with respect to the adsorption of nonionic molecules on energetically homogeneous surface. For this purpose, the adsorption states of a homologue series of ethoxylated nonionic surfactants on air/water interface have been determined using four different models and literature data (surface tension isotherms). The results obtained with the Frumkin adsorption isotherm imply repulsion between the adsorbed species (corresponding to negative values of the interaction parameter), while the classical lattice theory for energetically homogeneous surface (e.g., water/air) admits attraction alone. It appears that this serious contradiction can be overcome by assuming heterogeneity in the adsorption layer, that is, effects of partial condensation (formation of aggregates) on the surface. Such a phenomenon is suggested in the Fainerman-Lucassen-Reynders-Miller (FLM) 'Aggregation model'. Despite the limitations of the latter model (e.g., monodispersity of the aggregates), we have been able to estimate the sign and the order of magnitude of Frumkin's interaction parameter and the range of the aggregation numbers of the surface species. (C) 2004 Elsevier B.V All rights reserved.

Modeling volatile organic compounds (voc`s) adsorption onto cup-stacked carbon nanotubes (cscnt) using the linear driving force model

Modeling volatile organic compounds (voc`s) adsorption onto cup-stacked carbon nanotubes (cscnt) using the linear driving force model. Volatile organic compounds (VOC`s) are an important category of air pollutants and adsorption has been employed in the treatment (or simply concentration) of these compounds. The current study used an ordinary analytical methodology to evaluate the properties of a cup-stacked nanotube (CSCNT), a stacking morphology of truncated conical graphene, with large amounts of open edges on the outer surface and empty central channels. This work used a Carbotrap bearing a cup-stacked structure (composite); for comparison, Carbotrap was used as reference (without the nanotube). The retention and saturation capacities of both adsorbents to each concentration used (1, 5, 20 and 35 ppm of toluene and phenol) were evaluated. The composite performance was greater than Carbotrap; the saturation capacities for the composite was 67% higher than Carbotrap (average values). The Langmuir isotherm model was used to fit equilibrium data for both adsorbents, and a linear driving force model (LDF) was used to quantify intraparticle adsorption kinetics. LDF was suitable to describe the curves.

Ferromagnetism, paramagnetism, and a Curie-Weiss metal in an electron-doped Hubbard model on a triangular lattice

Motivated by the unconventional properties and rich phase diagram of NaxCoO2 we consider the electronic and magnetic properties of a two-dimensional Hubbard model on an isotropic triangular lattice doped with electrons away from half-filling. Dynamical mean-field theory (DMFT) calculations predict that for negative intersite hopping amplitudes (t < 0) and an on-site Coulomb repulsion, U, comparable to the bandwidth, the system displays properties typical of a weakly correlated metal. In contrast, for t > 0 a large enhancement of the effective mass, itinerant ferromagnetism, and a metallic phase with a Curie-Weiss magnetic susceptibility are found in a broad electron doping range. The different behavior encountered is a consequence of the larger noninteracting density of states (DOS) at the Fermi level for t > 0 than for t < 0, which effectively enhances the mass and the scattering amplitude of the quasiparticles. The shape of the DOS is crucial for the occurrence of ferromagnetism as for t > 0 the energy cost of polarizing the system is much smaller than for t < 0. Our observation of Nagaoka ferromagnetism is consistent with the A-type antiferromagnetism (i.e., ferromagnetic layers stacked antiferromagnetically) observed in neutron scattering experiments on NaxCoO2. The transport and magnetic properties measured in NaxCoO2 are consistent with DMFT predictions of a metal close to the Mott insulator and we discuss the role of Na ordering in driving the system towards the Mott transition. We propose that the Curie-Weiss metal phase observed in NaxCoO2 is a consequence of the crossover from a bad metal with incoherent quasiparticles at temperatures T > T-* and Fermi liquid behavior with enhanced parameters below T-*, where T-* is a low energy coherence scale induced by strong local Coulomb electron correlations. Our analysis also shows that the one band Hubbard model on a triangular lattice is not enough to describe the unusual properties of NaxCoO2 and is used to identify the simplest relevant model that captures the essential physics in NaxCoO2. We propose a model which allows for the Na ordering phenomena observed in the system which, we propose, drives the system close to the Mott insulating phase even at large dopings.

Satellite observation and climate system model simulation of the St. Lawrence Island polynya

The St. Lawrence Island polynya (SLIP) is a commonly occurring winter phenomenon in the Bering Sea, in which dense saline water produced during new ice formation is thought to flow northward through the Bering Strait to help maintain the Arctic Ocean halocline. Winter darkness and inclement weather conditions have made continuous in situ and remote observation of this polynya difficult. However, imagery acquired from the European Space Agency ERS-1 Synthetic Aperture Radar (SAR) has allowed observation of the St. Lawrence Island polynya using both the imagery and derived ice displacement products. With the development of ARCSyM, a high resolution regional model of the Arctic atmosphere/sea ice system, simulation of the SLIP in a climate model is now possible. Intercomparisons between remotely sensed products and simulations can lead to additional insight into the SLIP formation process. Low resolution SAR, SSM/I and AVHRR infrared imagery for the St. Lawrence Island region are compared with the results of a model simulation for the period of 24-27 February 1992. The imagery illustrates a polynya event (polynya opening). With the northerly winds strong and consistent over several days, the coupled model captures the SLIP event with moderate accuracy. However, the introduction of a stability dependent atmosphere-ice drag coefficient, which allows feedbacks between atmospheric stability, open water, and air-ice drag, produces a more accurate simulation of the SLIP in comparison to satellite imagery. Model experiments show that the polynya event is forced primarily by changes in atmospheric circulation followed by persistent favorable conditions: ocean surface currents are found to have a small but positive impact on the simulation which is enhanced when wind forcing is weak or variable.

The uncharged surface features surrounding the active site of Escherichia coli DsbA are conserved and are implicated in peptide binding

DsbA is a protein-folding catalyst from the periplasm of Escherichia coli that interacts with newly translocated polypeptide substrate and catalyzes the formation of disulfide bonds in these secreted proteins. The precise nature of the interaction between DsbA and unfolded substrate is not known. Here, we give a detailed analysis of the DsbA crystal structure, now refined to 1.7 Angstrom, and present a proposal for its interaction with peptide. The crystal structure of DsbA implies flexibility between the thioredoxin and helical domains that may be an important feature for the disulfide transfer reaction. A hinge point for domain motion is identified-the typo IV beta-turn Phe 63-Met 64-Gly 65-Gly 66, which connects the two domains. Three unique features on the active site surface of the DsbA molecule-a groove, hydrophobic pocket, and hydrophobic patch-form an extensive uncharged surface surrounding the active-sits disulfide. Residues that contribute to these surface features are shown to be generally conserved in eight DsbA homologues. Furthermore, the residues immediately surrounding the active-site disulfide are uncharged in all nine DsbA proteins. A model for DsbA-peptide interaction has been derived from the structure of a human thioredoxin:peptide complex. This shows that peptide could interact with DsbA in a manner similar to that with thioredoxin. The active-site disulfide and all three surrounding uncharged surface features of DsbA could, in principle, participate in the binding or stabilization of peptide.

Preliminary findings from a new animal model for Peyronie`s disease involving extracorporeal shock waves

To develop an experimental model in rabbits to analyse the efficiency of extracorporeal shock wave therapy (ESWT) for Peyronie`s disease. We used 15 adult male rabbits divided into three equal groups. In group 1 (no penile ESWT) rabbits had three sessions of ESWT with 2000 shocks each (15 kV), but a rubber mat was placed between the shock head and rabbit to protect the penis; the rabbits were killed at 7 days after the last session of ESWT. In group 2 the rabbits had three sessions of ESWT using the same parameters, and were killed immediately after the last session to analyse the penis. In group 3 the rabbits had three sessions of ESWT as before but were killed at 7 days after the last session, and the penile tissue analysed macroscopically and histologically. The results showed clearly that the model was efficient, creating a similar situation to that when applying ESWT in the human penis. All of the rabbits in groups 2 and 3 had haematomas and diffuse petechiae after ESWT, and only four had urethral and penile bleeding. Almost all macroscopic changes disappeared after 48 h and only one rabbit in group 3 after 7 days had a haematoma on the dorsal penile surface. The histology (assessed using haematoxylin and eosin staining) of the cavernous body of the penis showed: unchanged histology in group 1; in group 2 there was a dilated and congested vascular space in the cavernous body, with interstitial extensive bleeding in the dermis; and in group 3 there was an increase in interstitial fibrous tissue in the cavernous septum, with deposition of collagen fibres and thickening of the tunica albuginea. The present model was efficient in producing tissue injury in the normal penis when treated with ESWT, suggesting that this promising model should be considered for use future studies of Peyronie`s disease.

Effects of changing blood viscosity and heart rate on vena contracta width as evaluated by color Doppler flow mapping. An in vitro study with a pulsatile flow model

Background: There is only limited knowledge on how the quantification of valvular regurgitation by color Doppler is affected by changing blood viscosity. This study was designed to evaluate the effect of changing blood viscosity on the vena contracta width using an in vitro model of valvular insufficiency capable of providing ample variation in the rate and stroke volume. Methods: We constructed a pulsatile flow model filled with human blood at varying hematocrit (15%, 35%, and 55%) and corresponding blood viscosity (blood/water viscosity: 2.6, 4.8, 9.1) levels in which jets were driven through a known orifice (7 mm(2)) into a 110 mL compliant receiving chamber (compliance: 2.2 mL/mmHg) by a pulsatile pump. In addition, we used variable pump stroke volumes (5, 7.5, and 10 mL) and rates (40, 60, and 80 ppm). Vena contracta region was imaged using a 3.5 MHz transducer. Pressure and volume in the flow model were kept constant during each experimental condition, as well as ultrasound settings. Results: Blood viscosity variation in the experimental range did not induce significant changes in vena contracta dimensions. Also, vena contracta width did not change from normal to low hematocrit and viscosity levels. A very modest increase only in vena contracta dimension was observed at very high level of blood viscosity when hematocrit was set to 55% . Pump rate, in the evaluated range, did not influence vena contracta width. These results in controlled experimental settings suggest that the vena contracta is an accurate quantitative method for quantifying valvular regurgitation even when this condition is associated with anemia, a frequent finding in patients with valvular heart disease.

Surface electromyographic assessment of patients with long lasting temporomandibular joint disorder pain

The normalized electromyographic characteristics of masticatory muscles in patients with temporomandibular joint disorders (TMD) and healthy controls were compared. Thirty TMD patients (15 men, 15 women, mean age 23 years) with long lasting pain (more than 6 months), and 20 control subjects matched for sex and age were examined. All patients had arthrogenous TMD according to the Research Diagnostic Criteria for TMD (RDC/TMD). Surface electromyography of masseter and temporal muscles was performed during maximum teeth clenching either on cotton rolls or in intercuspal position. Standardized EMG indices and the median power frequency were obtained, and compared between the two groups and sexes using ANOVAs. During clenching, the TMD patients had larger asymmetry in their temporalis muscles, larger temporalis activity relative to masseter, and reduced mean power frequencies than the control subjects (p < 0.05, ANOVA). In both groups, the mean power frequencies of the temporalis muscles were larger than those of the masseter muscles (p < 0.001). No sex related differences, and no sex x group interactions were found. In conclusion, young adult patients with long lasting TMD have an increased and more asymmetric standardized activity of their temporalis anterior muscle, and reduced mean power frequencies, relative to healthy controls. (C) 2011 Elsevier Ltd. All rights reserved.

Plasminogen Acquisition and Activation at the Surface of Leptospira Species Lead to Fibronectin Degradation

Pathogenic Leptospira species are the etiological agents of leptospirosis, a widespread disease of human and veterinary concern. In this study, we report that Leptospira species are capable of binding plasminogen (PLG) in vitro. The binding to the leptospiral surface was demonstrated by indirect immunofluorescence confocal microscopy with living bacteria. The PLG binding to the bacteria seems to occur via lysine residues because the ligation is inhibited by addition of the lysine analog 6-aminocaproic acid. Exogenously provided urokinase-type PLG activator (uPA) converts surface-bound PLG into enzymatically active plasmin, as evaluated by the reaction with the chromogenic plasmin substrate D-Val-Leu-Lys 4-nitroanilide dihydrochloridein. The PLG activation system on the surface of Leptospira is PLG dose dependent and does not cause injury to the organism, as cellular growth in culture was not impaired. The generation of active plasmin within Leptospira was observed with several nonvirulent high-passage strains and with the nonpathogenic saprophytic organism Leptospira biflexa. Statistically significant higher activation of plasmin was detected with a low-passage infectious strain of Leptospira. Plasmin-coated virulent Leptospira interrogans bacteria were capable of degrading purified extracellular matrix fibronectin. The breakdown of fibronectin was not observed with untreated bacteria. Our data provide for the first time in vitro evidence for the generation of active plasmin on the surface of Leptospira, a step that may contribute to leptospiral invasiveness.

Caries Resistance of Lased Human Root Surface with 10.6 mu m CO(2) Laser-Thermal, Morphological, and Microhardness Analysis

Although the cariostatic effects of CO(2) laser on enamel have been shown, its effects on root surface demineralization remains uncertain. The objectives of this in vitro research was to establish safe parameters for a pulsed 10.6 mu m CO(2) laser and to evaluate its effect on morphological features of the root surface, as well as on the reduction of root demineralization. Ninety-five human root surfaces were randomly divided into five groups: G1-No treatment (control); G2-2.5 J/cm(2); G3-4.0 J/cm(2); G4-5.0 J/cm(2); and G5-6.0 J/cm(2). Intrapulpal temperature was evaluated during root surface irradiation by a thermocouple and morphological changes were evaluated by SEM. After the surface treatment, the specimens were submitted to a 7-day pH-cycling model. Subsequently, the cross-sectional Knoop microhardness values were measured. For all irradiated groups, intrapulpal temperature changes were less than 1.5 degrees C. Scanning electron microscopy images indicated that fluences as low as 4.0 J/cm(2) were sufficient to induce morphological changes in the root surface. Additionally, for fluences reaching or exceeding 4.0 J/cm(2), laser-induced inhibitory effects on root surface demineralization were observed. It was concluded that laser energy density in the range of 4.0 to 6.0 J/cm(2) could be applied to a dental root to reduce demineralization of this surface without compromising pulp vitality.

High concentration of residual aluminum oxide on titanium surface inhibits extracellular matrix mineralization

In the present study we characterized titanium (Ti) surfaces submitted to different treatments and evaluated the response of osteoblasts derived from human alveolar bone to these surfaces. Five different surfaces were evaluated: ground (G), ground and chemical etched (G1-HF for 60 s), sand blasted (SB-Al2O3 particles 65 pm), sand blasted and chemical etched (SLA1-HF for 60 s and SLA2-HF for 13 s). Surface morphology was evaluated under SEM and roughness parameters by contact scanning instrument. The presence of Al2O3 was detected by EDS and the amount calculated by digital analyses. Osteoblasts, were cultured on these surfaces and it was evaluated: cell adhesion, proliferation, and viability, alkaline phosphatase activity, total protein content, and matrix mineralization formation. Physical and chemical treatments produced very different surface morphologies. Al2O3 residues were detected on SB and SLA2 surfaces. Only matrix mineralization formation was affected by different surface treatments, being increased on rough surface (SLA1) and reduced on surface with high amount of Al2O3 residues (SB). On the basis of these findings, it is possible to conclude that high concentration of residual Al2O3 negatively interfere with the process of matrix mineralization formation in contact with Ti implant surfaces. (C) 2008 Wiley Periodicals, Inc. J Biomed Mater Res 87A: 588-597, 2008

Temperature variation at the external root surface during 980-nm diode laser irradiation in the root canal

Objective: To assess the temperature variation in the cervical, middle and apical thirds of root external wall, caused by 980-nm diode laser irradiation with different parameters. Methods: The roots of 90 canines, had their canals instrumented and were randomly distributed into 3 groups (n = 30) according to the laser potency (1.5 W, 3.0 W and 5.0 W). Each group was subdivided into 3 (n = 10) according to the frequency (CM, 100 Hz and 1000 Hz), and each subgroup divided into 2 (n = S): dried canal or filled with distilled water. The maximum temperature values were collected by 3 thermocouples located at each third of the root external wall and recorded by digital thermometers. Results: The groups irradiated in the continuous mode (CM) presented the highest values (11.82 +/- 5.78), regardless of the canals were dry or not, which were statistically different (p < 0.01) from those obtained with 100 Hz (6.22 +/- 3.64) and 1000 Hz (6.00 +/- 3.36), which presented no statistical difference between them (p > 0.01). The groups irradiated with 5.0 W presented the greatest temperature variation (12.15 +/- 5.14), followed by 3.0 W (7.88 +/- 3.92) and 1.5 W (4.02 +/- 2.16), differing between them (p < 0.01). The cervical third of the root presented the highest temperature rises (9.68 +/- 5.80), followed by the middle (7.66 +/- 4.87) and apical (6.70 +/- 4.23), with statistical difference among them (p < 0.01). After 30 s from the end of irradiation, all the specimens presented temperature variation lower than 10 degrees C. Conclusions: Application of 980-nm diode laser in the root, at 1.5 W in all operating modes, and 3.0 W, in the pulsed mode, for 20 s, can safely be used in endodontic treatment, irrespective of the presence of humidity. (C) 2008 Elsevier Ltd. All rights reserved.

Effects of Ethanol on the Surface and Bulk Properties of a Microwave-Processed PMMA Denture Base Resin

Purpose: This study evaluated the effect of different concentrations of ethanol on hardness, roughness, flexural strength, and color stability of a denture base material using a microwave-processed acrylic resin as a model system. Materials and Methods: Sixty circular (14 x 4 mm) and 60 rectangular microwave-polymerized acrylic resin specimens (65 x 10 x 3 mm(3)) were employed in this study. The sample was divided into six groups according to the ethanol concentrations used in the immersion solution, as follows: 0% (water), 4.5%, 10%, 19%, 42%, and 100%. The specimens remained immersed for 30 days at 37 degrees C. The hardness test was performed by a hardness tester equipped with a Vickers diamond penetrator, and a surface roughness tester was used to measure the surface roughness of the specimens. Flexural strength testing was carried out on a universal testing machine. Color alterations (Delta E) were measured by a portable spectrophotometer after 12 and 30 days. Variables were analyzed by ANOVA/Tukey`s test (alpha = 0.05). Results: For the range of ethanol-water solutions for immersion (water only, 4.5%, 10%, 19.5%, 42%, and 100%), the following results were obtained for hardness (13.9 +/- 2.0, 12.1 +/- 0.7, 12.9 +/- 0.9, 11.2 +/- 1.5, 5.7 +/- 0.3, 2.7 +/- 0.5 VHN), roughness (0.13 +/- 0.01, 0.15 +/- 0.07, 0.13 +/- 0.05, 0.13 +/- 0.02, 0.23 +/- 0.05, 0.41 +/- 0.19 mu m), flexural strength (90 +/- 12, 103 +/- 18, 107 +/- 16, 90 +/- 25, 86 +/- 22, 8 +/- 2 MPa), and color (0.8 +/- 0.6, 0.8 +/- 0.3, 0.7 +/- 0.4, 0.9 +/- 0.3, 1.3 +/- 0.3, 3.9 +/- 1.5 Delta E) after 30 days. Conclusions: The findings of this study showed that the ethanol concentrations of tested drinks affect the physical properties of the investigated acrylic resin. An obvious plasticizing effect was found, which could lead to a lower in vivo durability associated with alcohol consumption.

The expression of plasminogen activator system in a rat model of periodontal wound healing

Background: The plasminogen activator system has been proposed to play a role in proteolytic degradation of extracellular matrices in tissue remodeling, including wound healing. The aim of this study was to elucidate the presence of components of the plasminogen activator system during different stages of periodontal wound healing. Methods: Periodontal wounds were created around the molars of adult rats and healing was followed for 28 days. Immunohistochemical analyses of the healing tissues and an analysis of the periodontal wound healing fluid by ELISA were carried out for the detection of tissue-type plasminogen activator (t-PA), urokinase-type plasminogen activator (u-PA), and 2 plasminogen activator inhibitors (PAI-1 and PAI-2). Results: During the early stages (days 1 to 3) of periodontal wound healing, PAI-1 and PAI-2 were found to be closely associated with the deposition of a fibrin clot in the gingival sulcus. These components were strongly associated with the infiltrating inflammatory cells around the fibrin clot. During days 3 to 7, u-PA, PAI-1, and PAI-2 were associated with cells (particularly monocytes/macrophages, fibroblasts, and endothelial cells) in the newly formed granulation tissue. During days 7 to 14, a new attachment apparatus was formed during which PAI-1, PAI-2, and u-PA were localized in both periodontal ligament fibroblasts (PDL) and epithelial cells at sites where these cells were attaching to the root surface. In the periodontal wound healing fluid, the concentration for t-PA increased and peaked during the first week. PAI-2 had a similar expression to t-PA, but at a lower level over the entire wound-healing period. Conclusions: These findings indicate that the plasminogen activator system is involved in the entire process of periodontal wound healing, in particular with the formation of fibrin matrix on the root surface and its replacement by granulation tissue, as well as the subsequent formation of the attachment of soft tissue to the root surface during the later stages of wound repair.