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.     

Regression of severe atherosclerotic plaque in patients with mild elevation of LDL cholesterol

BACKGROUND: Intensive risk factor reduction in patients with dyslipidemias and coronary atherosclerosis has been shown to result in alterations in coronary artery morphology and reduced clinical events. However, the impact of such interventions in populations with relatively normal levels of low-density lipoproteins (LDL) is unclear. METHODS: To test the hypothesis that intensive risk factor reduction results in angiographic regression in patients with only mildly elevated levels of LDL, 14 patients with angiographically proven coronary atherosclerosis were entered into the University of California Davis Coronary Artery Disease Regression Program and intensively treated with pharmacologic and nonpharmacologic interventions for 2 years. Quantitative angiography was performed prior to and after 2 years of therapy to determine changes in coronary artery diameter. RESULTS: As a result of this program, dietary fat intake was reduced by 58% and LDL fell from 120 +/- 7 mg/dL to 104 +/- 6 mg/dL (p = 0.05). The average diameter of the measured arterial locations (including all 53 stenoses and 292 nondiscrete regions) on study entry was 2.74 +/- 0.05 mm. After 24 months, there was a net increase in arterial diameter (regression) of +0.05 +/- 0.04 mm to 2.81 +/- 0.05 mm (p = 0.01). While there was no significant change in the average diameter of discrete stenoses, all 8 lesions > or = 50% initial diameter narrowing regressed, with a mean diameter change of + 0.2 mm. Conversely, only 1 of 8 mild lesions < or = 20% regressed, while 4 progressed. Intermediate lesions (20% to 50%, n = 37) had balanced progression and regression. CONCLUSIONS: When examined as a continuous variable, there was a significant linear correlation between initial lesion severity (% stenosis) and the extent of regression (mm). Therefore, risk factor reduction (dietary therapy, exercise, psycho-social counseling, and lipid lowering therapy) in patients with only mild dyslipidemia results in angiographic regression of more severe lesions (> 50% initial stenosis), but does not prevent progression of mild lesions (< 20%). These findings demonstrate that intensive risk factor reduction in patients with only mild elevation of lipids beneficially influences the morphology of the most severe lesions.     

Treatment and prognosis of secondary glaucoma in Fuchs' heterochromic iridocyclitis

After reviewing the records of 111 patients with Fuchs' heterochromic iridocyclitis, we studied the therapy and prognosis of secondary glaucoma in 30 of these 111 patients (27%) who had glaucoma or could be considered glaucoma suspects. Maximal medical therapy was unsuccessful in 22 of the 30 patients (73%). Surgical intervention (mostly trabeculectomies, half with 5-fluorouracil) successfully controlled intraocular pressure (< or = 21 mm Hg with or without medication) in 13 of the 18 operated-on patients (72%) after a mean follow-up of 26 months. All successfully operated-on patients retained a visual acuity of 20/80 or better. We had favorable results, possibly because of modern surgical techniques (use of 5-fluorouracil, sodium hyaluronate) or earlier surgical intervention, or both.     

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.     

A PMLRARalpha transgene initiates murine acute promyelocytic leukemia

The malignant cells of acute promyelocytic leukemia (APL) contain a reciprocal chromosomal translocation that fuses the promyelocytic leukemia gene (PML) with the retinoic acid receptor alpha gene (RAR alpha). To test the hypothesis that the chimera PMLRAR alpha plays a role in leukemogenesis, we expressed a PMLRAR alpha cDNA in myeloid cells of transgenic mice. PMLRAR alpha transgenic mice exhibited impaired neutrophil maturation early in life, which progressed at a low frequency over the course of several months to overt APL. Both the preleukemic state and the leukemia could be transplanted to nontransgenic mice, and the transplanted preleukemia could progress to APL. The APL recapitulated features of the human disease, including a response to retinoic acid. Retinoic acid caused the leukemic cells to differentiate in vitro and in vivo, eliciting remissions of both the preleukemic state and APL in mice. Our results demonstrate that PMLRAR alpha impairs neutrophil differentiation and initiates the development of APL. The transgenic mice described here provide an apparently accurate model for human APL that includes clear evidence of tumor progression. The model should be useful for exploring the molecular pathogenesis of APL and the mechanisms of the therapeutic response to retinoic acid, as well as for preclinical studies of therapeutic regimens.     

DMD-specific FISH probes are diagnostically useful in the detection of female carriers of DMD gene deletions

The challenge of Duchenne muscular dystrophy (DMD) carrier identification resides in the ability to identify the presence of a mutant gene over the background contributed by the normal allele. Current diagnosis of carrier status when a deletion has been identified in a proband is based on an analysis of a gene dosage. We present a diagnostic strategy that uses fluorescence in situ hybridization (FISH) to detect female carriers with major deletions in the dystrophin gene. We screened a human X-chromosome-derived genomic library with a full-length dystrophin cDNA and isolated 15 dystrophin-specific cosmids that contain DMD gene exons. Six cosmids were further tested as FISH probes in control individuals and subsequently applied on chromosomes from eight males with DMD and known deletions and on samples from three female carriers. As expected, X chromosomes in normal females displayed four signals, two for the DMD-specific probe and two for the X-chromosome centromeric probe. Hybridization on chromosomal spreads from carriers of deletions revealed only one signal from the DMD-specific probe and two from the control centromeric probe. Males carrying deletions showed no DMD-specific signal for the deleted exons tested. Our data indicate that FISH could represent an alternative method for the detection of female carriers with DMD gene deletions.