A bacteriophage reagent for Salmonella: molecular studies on Felix 01

Felix 01 (F01) is a bacteriophage originally isolated by Felix and Callow which lyses almost all Salmonella strains and has been widely used as a diagnostic test for this genus. Molecular information about this phage is entirely lacking. In the present study, the DNA of the phage was found to be a double-stranded linear molecule of about 80 kb. 11.5 kb has been sequenced and in this region A + T content is 60%. There are relatively few restriction endonuclease cleavage sites in the native genome and clones show this is due to their absence rather than modification. A restriction map of the genome has been constructed. The ends of the molecule cannot be ligated although they contain 5' phosphates. At least 60% of the genome must encode proteins. In the sequenced portion, many open reading frames exist and these are tightly packed together. These have been examined for homology to published proteins but only 1 to 17 shows similarity to known proteins. F01 is therefore the prototype of a new phage family. On the basis of restriction sites, codon usage and the distribution of nonsense codons in the unused reading frames, a strong case can be made for natural selection that reacts to mRNA structure and function.     

Investigation of the inhibitory effect of silica on the degradation of 1,1,1-trichloroethane by granular iron

Although iron-based permeable reactive barriers are gaining importance for treating groundwater contaminants, little is currently known about the effect of cosolutes on barrier longevity. Because of their corrosion inhibiting properties, dissolved silica species are of particular concern. This research investigates the effect of silica on the reduction of 1,1,1-trichloroethane by granular iron as a function of added silica concentration, pH, and duration of iron exposure to dissolved silica. Batch studies reveal that, at pH 8.5 and above, added silica concentrations as low as 0.17 mM cause a 30% reduction in the reactivity of iron. At higher silica concentrations, reactivity decreases by 65-75%. The inhibitory effect is greater at higher pH: 0.83 mM silica has no apparent adverse effect at pH 7.5, but leads to a 46% decrease in reaction rate at pH 8 and 90% at pH 9. This corresponds to observed trends in silica adsorption onto iron, which is low at pH 7.3 but increases at higher pH. Extending the duration of iron exposure to silica solutions also leads to a more pronounced inhibitory effect. This is in good agreement with the increase in silica coverage on the iron surface as revealed by X-ray photoelectron spectroscopy.     

On Boundary Condition Capturing for Multiphase Interfaces

This review paper begins with an overview of the boundary condition capturing approach to solving problems with interfaces. Although the authors’ original motivation was to extend the ghost fluid method from compressible to incompressible flow, the elliptic nature of incompressible flow quickly quenched the idea that ghost cells could be defined and used in the usual manner. Instead the boundary conditions had to be implicitly captured by the matrix formulation itself, leading to the novel approach. We first review the work on the variable coefficient Poisson equation, noting that the simplicity of the method allowed for an elegant convergence proof. Simplicity and robustness also allowed for a quick extension to three-dimensional two-phase incompressible flows including the effects of viscosity and surface tension, which is discussed subsequently. The method has enjoyed popularity in both computational physics and computer graphics, and we show some comparisons with the traditional delta function approach for the visual simulation of bubbles. Finally, we discuss extensions to problems where the velocity is discontinuous as well, as is the case for premixed flames, and show an example of multiple interacting liquids that includes all of the aforementioned phenomena.     

Social learning of an artificial fruit task in capuchin monkeys (Cebus apella).

Social learning in 11 human-raised capuchin monkeys (Cebus apella) was investigated using an artificial fruit that was designed as an analogue of natural foraging problems faced by primates. Each subject observed a human model open each of 3 principal components on the fruit in 1 of 2 alternative ways ("morphs"). The capuchin monkeys reproduced, to differing extents, the alternative techniques used for opening 1 component of the task (poking vs. pulling while twisting out a pair of smooth plastic bolts) but not the other 2. From the subjects' actions on the bolt latch, independent coders could recognize which morph they had witnessed, and they observed a degree of matching to the demonstrator's act consistent with simple imitation or object movement reenactment (A learns from watching B how an object, or parts of an object, move). Thus, these capuchins were capable of more complex social learning than has been recently ascribed to monkeys. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Nonadiabatic vibronic dynamics as a tool. From surface nanochemistry to coherently driven molecular machines

Resonances are ubiquitous in molecular heterojunctions and in scanning tunneling microscopy (STM) experiments. In the former environment, resonance tunneling is essential for favorable wire-length-dependence of the conductance and is often the mechanism underlying conductance enhancement through application of a gate voltage. In the latter environment, resonance tunneling has served to develop a powerful vibrational spectroscopy. Resonance conductance is often strongly nonadiabatic; in the course of the tunneling event, electron energy is channelled into vibrational modes and triggers molecular dynamics. The qualitative physics underlying current-driven, resonance-mediated dynamics in molecular electronics is very simple, and is familiar from related phenomena such as gas phase electron-molecule scattering and photochemistry on conducting surfaces. Equilibrium displacement between the initial and resonant states translates into vibronic coupling in the language of the Marcus theory of electron transfer; it produces a nonstationary superposition in the nuclear subspace that evolves during the resonance lifetime. Upon relaxation the system is internally excited and interesting dynamics is likely to ensue. While the underlying physics is very general, the single-molecule STM and molecular heterojunction environments open unique and exciting opportunities. The former introduces the possibility of determining resonance lifetimes through fit of experimental voltage dependencies to a quantum mechanical theory. The latter introduces the possibility of developing coherently driven molecular machines, a new form of nanolithography, and a new means of manipulating the conductivity of molecular-scale devices. We briefly review the theory of current-driven dynamics in molecular-scale devices, discuss the results of ongoing research on surface nanochemistry and molecular machines, and sketch a variety of potential applications.     

Affective and cardiovascular effects of experimentally-induced social status.

Objective: Observational research suggests subordinate social status is associated with negative mental and physical health outcomes. However, observational studies have limitations, including confounding of social status with other factors, limited ability to infer causality, and difficulty of obtaining detailed affective and physiologic data. This study used experimental methods to test the hypothesis that subordinate social status per se causes psychological distress and cardiovascular arousal. Design: Forty-four women were randomly assigned to an induced subordinate or dominant status condition. Social status was manipulated using a procedure derived from status construction theory. Main Outcome Measures: Affective responses were assessed via self-report. Cardiovascular responses were assessed by measures of systolic and diastolic blood pressures obtained with an automated blood pressure machine. Results: Participants in the subordinate condition perceived themselves as lower in status; the reverse was true for dominant condition participants. Compared with induced dominant status, induced subordinate status produced increased negative affect and systolic blood pressure over the course of the study. Conclusion: Findings suggest social status can be experimentally manipulated and short-term induction of subordinate status can have adverse effects on affect and stress-related physiological systems. Results have implications for understanding how socioeconomic status "gets under the skin" to influence health. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The computer as a zone of proximal development: Internalizing reading-related metacognitions from a Reading Partner.

We hypothesized that computer tools that provide models, opportunity for higher level thinking, and metacognitivelike guidance (e.g., "Can I conjure up an image of the story?") can serve in a learner's zone of proximal development (L. S. Vygotsky, 1978); they can develop competencies through internalization. A computerized Reading Partner presented four reading principles and metacognitivelike questions during the reading of 11 texts over three reading sessions. It was compared with one version that presented the texts with factual and inferential questions and a control version that presented only the texts. Seventh graders using the Reading Partner (n?=?25) reported the expenditure of more mental effort in the process, showed far better metacognitive reconstruction, and improved significantly more in their later reading comprehension and in the quality of their written essays than did the subjects in the other groups. Improvements in reading and writing were statistically accounted for by subjects' ability for metacognitive reconstruction. The study reinforces previous findings pertaining to the role of metacognitions in reading and shows that well-designed computer tools can cultivate competence. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Role of temperature and Suwannee River natural organic matter on inactivation kinetics of rotavirus and bacteriophage MS2 by solar irradiation

Although the sunlight-mediated inactivation of viruses has been recognized as an important process that controls surface water quality, the mechanisms of virus inactivation by sunlight are not yet clearly understood. We investigated the synergistic role of temperature and Suwannee River natural organic matter (SRNOM), an exogenous sensitizer, for sunlight-mediated inactivation of porcine rotavirus and MS2 bacteriophage. Upon irradiation by a full spectrum of simulated sunlight in the absence of SRNOM and in the temperature range of 14-42 °C, high inactivation rate constants, k(obs), of MS2 (k(obs) ≤ 3.8 h(-1) or 1-log(10) over 0.6 h) and rotavirus (k(obs) ≤ 11.8 h(-1) or ～1-log(10) over 0.2 h) were measured. A weak temperature (14-42 °C) dependence of k(obs) values was observed for both viruses irradiated by the full sunlight spectrum. Under the same irradiation condition, the presence of SRNOM reduced the inactivation of both viruses due to attenuation of lower wavelengths of the simulated sunlight. For rotavirus and MS2 solutions irradiated by only UVA and visible light in the absence of SRNOM, inactivation kinetics were slow (k(obs) < 0.3 h(-1) or <1-log(10) unit reduction over 7 h) and temperature-independent for the range considered. Conversely, under UVA and visible light irradiation and in the presence of SRNOM, temperature-dependent inactivation of MS2 was observed. For rotavirus, the SRNOM-mediated exogenous inactivation was only important at temperatures >33 °C, with low rotavirus k(obs) values (k(obs) ≈ 0.2 h(-1); 1-log(10) unit reduction over 12 h) for the temperature range of 14-33 °C. These k(obs) values increased to 0.5 h(-1) at 43 °C and 1.5 h(-1) (1-log(10) reduction over 1.6 h) at 50 °C. While SRNOM-mediated exogenous inactivation of MS2 was triggered by singlet oxygen, the presence of hydrogen peroxide was important for rotavirus inactivation in the 40-50 °C range.     

Low-Frequency Ultrasound Effects on Intracellular Barriers in Nonviral Gene Delivery Processes

Gene therapy, the expression in cells of genetic material with therapeutic activity, has emerged as a promising approach for the treatment or prevention of human diseases. At the present time, major somatic gene-transfer approaches employ either viral or nonviral vectors. Nonviral vectors are less efficient at introducing and maintaining foreign gene expression, but have the profound advantage of being nonpathogenic and nonimmunogenic. In this study, we aimed to develop an efficient nonviral gene delivery system in which low-frequency ultrasound (LFUS) was applied to enhance gene expression of polyplexes formed with poly(2-dimethylaminoethyl methacrylate) and plasmid encoding for green fluorescent protein. Ultrasound (US), and in particular LFUS, can cause temporary membrane permeabilization and thereby enhance drug and gene entrance into viable cells. We evaluated possible additional favorable effects of LFUS on the polyplex transfection process, such as overcoming intracellular barriers. We found that pDMAEMA protected the plasmid DNA from ultrasonic degradation. Atomic force microscopy analysis also confirmed that the LFUS did not change the polyplexes’ morphology. We also attained an insight into the structure of polyplexes during LFUS exposure and found that LFUS induced a temporary partial detachment between the polymer chains and the plasmid. In addition, LFUS application on ovarian carcinoma cells transfected with the polyplexes induced a 27% enhancement in transfection efficiency. Based on these results, we propose that LFUS enhances the decomplexation of the polyplexes, and therefore, can be used to optimize transfection efficiency.     

A preliminary coupled MT-GA model for the prediction of highway runoff quality

Pollutants accumulated on road pavement during dry periods are washed off the surface with runoff water during rainfall events, presenting a potentially hazardous non-point source of pollution. Estimation of pollutant loads in these runoff waters is required for developing mitigation and management strategies, yet the numerous factors involved and their complex interconnected influences make straightforward assessment impossible. Data-driven models (DDMs) have lately been used in water and environmental research and have shown very good prediction ability. The proposed methodology of a coupled MT-GA (model tree-genetic algorithm) model provides an effective, accurate and easily calibrated predictive model for EMC (event mean concentration) of highway runoff pollutants. The models were trained and verified using a comprehensive data set of runoff events monitored in various highways in California, USA. EMCs of Cr, Pb, Zn, TOC and TSS were modeled, using different combinations of explanatory variables. The models' prediction ability in terms of correlation between predicted and actual values of both training and verification data was mostly higher than previously reported values. Sensitivity analysis was performed to examine the relative significance of each explanatory variable and the models' response to changes in input values.