In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila,Persephonella marina,Thermosulfidibacter takaii,and Thermus thermophilus

Carbonic anhydrases (CAs) have been identified as ideal catalysts for CO₂ sequestration. Here, we report the sequence and structural analyses as well as the molecular dynamics (MD) simulations of four γ-CAs from thermophilic bacteria. Three of these, Persephonella marina, Persephonella hydrogeniphila, and Thermosulfidibacter takaii originate from hydrothermal vents and one, Thermus thermophilus HB8, from hot springs. Protein sequences were retrieved and aligned with previously characterized γ-CAs, revealing differences in the catalytic pocket residues. Further analysis of the structures following homology modeling revealed a hydrophobic patch in the catalytic pocket, presumed important for CO₂ binding. Monitoring of proton shuttling residue His69 (P. marina γ-CA numbering) during MD simulations of P. hydrogeniphila and P. marina’s γ-CAs (γ-PhCA and γ-PmCA), showed a different behavior to that observed in the γ-CA of Escherichia coli, which periodically coordinates Zn²⁺. This work also involved the search for hotspot residues that contribute to interface stability. Some of these residues were further identified as key in protein communication via betweenness centrality metric of dynamic residue network analysis. T. takaii’s γ-CA showed marginally lower thermostability compared to the other three γ-CA proteins with an increase in conformations visited at high temperatures being observed. Hydrogen bond analysis revealed important interactions, some unique and others common in all γ-CAs, which contribute to interface formation and thermostability. The seemingly thermostable γ-CA from T. thermophilus strangely showed increased unsynchronized residue motions at 423 K. γ-PhCA and γ-PmCA were, however, preliminarily considered suitable as prospective thermostable CO₂ sequestration agents.     

Teaching robust programming

Robust programming aims to prevent abnormal termination or unexpected actions and requires code to handle bad (invalid or absurd) inputs in a way that is consistent with the developer's intent. For example, if an internal error occurs, the program might terminate gracefully rather than simply failing, providing enough information for the programmer to debug the program and avoiding giving the user additional access or information. This article focuses on teaching these principles.     

Security issues for downloaded code in mobile phones

'Software defined radio' (SDR) is a technology that will appear in future generations of mobile phones, i.e. following the third-generation mobile phone technology that is currently being defined and developed. Early versions of 'pragmatic' SDR will allow the terminal to be reconfigured at any level of its protocol stack. Ultimately, the 'pure' SDR technology will allow a mobile phone or terminal to have its air interface software configured or reconfigured by other software (or software parameters) that have been downloaded to the terminal, e.g. over the air, or from a remote server via the Internet and one's personal computer (PC). A number of security issues arise with downloaded code that implements the air interface functions, and these may not be obvious simply from looking at the way PC software is updated on-line today. This paper starts with an outline of the code that allows a mobile phone to operate over a particular air interface. This sets the baseline for a discussion of the security issues surrounding the change of this code from one that is fixed and downloaded once only, to code that is reconfigurable during the life of a product.     

Primary afferent depolarizations of sensory origin within contact-sensitive mechanoreceptive afferents of a crayfish leg

Recordings from the central branches of single identified dactyl sensory afferent (DSA) neurons in a crayfish in vitro preparation were performed to study modifications of the sensory message occurring before the first central synapse. These afferents comprised hairs and force-sensitive mechanoreceptors with phasic and phasotonic response characteristics in the terminal segment (dactyl) of the crayfish leg. More than one afferent spike size was often observed in intracellular recordings from these afferents, thus indicating the presence of electrical coupling between the central processes of DSA fibers. Additionally, in identified DSA fibers with large spike sizes, primary afferent depolarizations (PADs) of up to 15 mV were observed, which sometimes triggered antidromic spikes in the afferent. Nevertheless, PADs were clearly inhibitory, because they shunted the afferent spikes. They exhibited the following properties. First, each PAD was preceded by an afferent spike from a neighboring hair, indicating that the PADs had a sensory rather than central origin. Second, PADs could follow high frequencies of afferent discharges without failure, a property suggestive of monosynaptic connections, but because PAD latencies varied by +/-0.5 ms it is more likely that they were mediated by a disynaptic pathway. Third, although PADs were evoked in an extremely reliable manner, their amplitude varied in a quantal manner. Most unitary PADs were the result of the release of < 12 quanta, the mean quantal content lying between 4 and 5; quantal size was large, approximately 1 mV. Fourth, PADs showed facilitation in some fibers, whereas in others they became much smaller when occurring at brief intervals. We suggest that PADs may be an efficient and parsimonious way to limit sensory inflow in space and time, allowing the crayfish to identify precisely both weak and strong mechanical stimuli.     

Passive sensitization of human airways induces myogenic contractile responses in vitro

We assessed effects of passive sensitization on human bronchial smooth muscle (BSM) response to mechanical stretching in vitro. Bronchial rings were sham (control) or passively sensitized overnight by using sera from donors demonstrating sensitivity to Dermatophagoides farinae and having immunoglobulin E (IgE) concentrations of 2,600 +/- 200 U/ml. Tissues were fixed isometrically to force transducers to measure responses to electrical field stimulation (EFS) and quick stretch (QS). The myogenic response to QS was normalized to the maximal response to EFS (%EFS). The myogenic response of sensitized BSM was 47.9 +/- 10.9 %EFS to a QS of approximately 6.5% optimal length (Lo); sham-sensitized tissues had a myogenic response of 13.5 +/- 6.4 %EFS (P = 0.012 vs. passively sensitized). A QS of approximately 13% Lo in sensitized BSM caused a response of 82.8 +/- 20.9 %EFS; sham-sensitized tissues developed a response of 38.2 +/- 17.3 %EFS (P = 0.004). BSM incubated with serum from nonallergic donors did not demonstrate increased QS response (4.6 +/- 1.4 %EFS, P = not significant vs. tissue exposed to atopic sera). However, tissues incubated in sera from nonatopic donors supplemented with hapten-specific chimeric IgE (JW8) demonstrated augmented myogenic response to QS of approximately 6.5% Lo (21.9 +/- 6.2 %EFS, P = 0. 027 vs. nonatopic sera alone). We demonstrate that passive sensitization of human BSM preparations causes induction and augmentation of myogenic contractions to QS; this hyperresponsiveness corresponds to the IgE concentration in sensitizing sera.     

Growth factor receptor expression during in vitro differentiation of partially purified populations containing murine stem cells

The Word Accentuation Test assesses the accentuation of 30 infrequent Spanish words written without the accentuation mark and is an easy-to-use tool for estimating premorbid intelligence of Spanish-speaking people. Its intraobserver (0.97) and interobserver (0.93) reliabilities and its correlation with the Wechsler Adult Intelligence Scale (.837) and Raven's Progressive Matrices (.655) are high, offering a good prediction of general intelligence. It is resistant to mental deterioration; 20 demented and 40 controls matched by sex, age, and education obtained similar scores. The discrepancies between current and predicted scores in Raven's scale can diagnose mild-moderate dementia with 0.79 accuracy (sensitivity, 0.78; specificity, 0.82).