A Predictive Model of Intein Insertion Site for Use in the Engineering of Molecular Switches

Inteins are intervening protein domains with self-splicing ability that can be used as molecular switches to control activity of their host protein. Successfully engineering an intein into a host protein requires identifying an insertion site that permits intein insertion and splicing while allowing for proper folding of the mature protein post-splicing. By analyzing sequence and structure based properties of native intein insertion sites we have identified four features that showed significant correlation with the location of the intein insertion sites, and therefore may be useful in predicting insertion sites in other proteins that provide native-like intein function. Three of these properties, the distance to the active site and dimer interface site, the SVM score of the splice site cassette, and the sequence conservation of the site showed statistically significant correlation and strong predictive power, with area under the curve (AUC) values of 0.79, 0.76, and 0.73 respectively, while the distance to secondary structure/loop junction showed significance but with less predictive power (AUC of 0.54). In a case study of 20 insertion sites in the XynB xylanase, two features of native insertion sites showed correlation with the splice sites and demonstrated predictive value in selecting non-native splice sites. Structural modeling of intein insertions at two sites highlighted the role that the insertion site location could play on the ability of the intein to modulate activity of the host protein. These findings can be used to enrich the selection of insertion sites capable of supporting intein splicing and hosting an intein switch

Computing with bacterial constituents, cells and populations: from bioputing to bactoputing

The relevance of biological materials and processes to computing—aliasbioputing—has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating

Hemiarthroplasty for three- and four-part displaced fractures of the proximal humerus in patients over 65 years of age

This is a prospective case series, in which the outcome of shoulder hemiarthroplasty in recent three- and four-part fractures of the proximal humerus was evaluated in patients over 65 years of age. From February 1993 to October 2002, 51 patients with 3- or 4-part fractures of the proximal humerus were entered into the study. The criteria for inclusion were age over 65 years and 3- or 4- part displaced fracture. The mean age of the patients was 73 years (range 65 to 84). The mean follow-up was 5.5 years (range 2 to 12). According to the Constant-Murley scale, the results were satisfactory or very satisfactory for 74% of the patients. Thirty nine patients (78%) experienced mild or no pain, 50% achieved active anterior elevation greater than 120 degrees, while 40% had active lateral elevation of more than 120 degrees. None of the patients experienced complete recovery of strength and full range of motion. Thirty four patients were able to resume all their daily activities. There were complications in 26% of the patients. Assessment following the Constant-Murley scale demonstrated that two thirds of the patients were pain free and regained a wide range of shoulder movement, while one third resumed their pre-fracture activities to a great extent. The majority of the patients did not recover normal strength

Clinical Outcome Study and Radiological Findings of Zweymuller Metal on Metal Total Hip Arthroplasty. A Follow-up of 6 to 15 Years

We report the clinical and radiological outcome of 99 Zweymuller metal on metal total hip arthroplasties in 84 patients followed up prospectively for a mean period of 9.5 (range, 6-15) years. There were 29 (34.5%) male and 55 (65.5%) female patients with a mean age of 62.85 years (range, 50-70 years) at the time of surgery. All patients had osteoarthritis. One acetabular component and one stem were revised due to aseptic loosening. One femoral stem was revised due to a periprosthetic fracture. HHS score improved from a preoperative mean of 62.56 points (SD 8.87) to a final postoperative follow-up mean of 93.48 (SD 7.7). Cumulative success rate for both implants at 13 years, with aseptic loosening as the end point, was 97.05%, while for both implants at 13 years, with revision for any reason as the end point, it was 91.17%. Satisfactory results were observed with the use of this prosthesis. (Hip International 2009; 19: 301-8