An advanced 3D multi-body system model for the human lumbar spine

Series : Mechanisms and machine science, ISSN 2211-0984, vol. 24A novel 3D multi-body system model of the human lumbar spine is presented, allowing the dynamic study of the all set but also to access mechanical demands, characteristics and performance under work of the individual intervertebral discs. An advanced FEM analysis was used for the most precise characterization of the disc 6DOF mechanical behavior, in order to build up a tool capable of predicting and assist in the design of disc recovery strategies – namely in the development of replace-ment materials for the degenerated disc nucleus – as well as in the analysis of variations in the me-chanical properties (disorders) at disc level or kinematic structure (e.g. interbody fusion, pedicle fixa-tion, etc.), and its influence in the overall spine dynamics and at motion segments individual level. Preliminary results of the model, at different levels of its development, are presented

Development of an unbiased statistical method for the analysis of unigenic evolution

BACKGROUND: Unigenic evolution is a powerful genetic strategy involving random mutagenesis of a single gene product to delineate functionally important domains of a protein. This method involves selection of variants of the protein which retain function, followed by statistical analysis comparing expected and observed mutation frequencies of each residue. Resultant mutability indices for each residue are averaged across a specified window of codons to identify hypomutable regions of the protein. As originally described, the effect of changes to the length of this averaging window was not fully eludicated. In addition, it was unclear when sufficient functional variants had been examined to conclude that residues conserved in all variants have important functional roles. RESULTS: We demonstrate that the length of averaging window dramatically affects identification of individual hypomutable regions and delineation of region boundaries. Accordingly, we devised a region-independent chi-square analysis that eliminates loss of information incurred during window averaging and removes the arbitrary assignment of window length. We also present a method to estimate the probability that conserved residues have not been mutated simply by chance. In addition, we describe an improved estimation of the expected mutation frequency. CONCLUSION: Overall, these methods significantly extend the analysis of unigenic evolution data over existing methods to allow comprehensive, unbiased identification of domains and possibly even individual residues that are essential for protein function

Estimating the evidence of selection and the reliability of inference in unigenic evolution

<p>Abstract</p> <p>Background</p> <p>Unigenic evolution is a large-scale mutagenesis experiment used to identify residues that are potentially important for protein function. Both currently-used methods for the analysis of unigenic evolution data analyze 'windows' of contiguous sites, a strategy that increases statistical power but incorrectly assumes that functionally-critical sites are contiguous. In addition, both methods require the questionable assumption of asymptotically-large sample size due to the presumption of approximate normality.</p> <p>Results</p> <p>We develop a novel approach, termed the Evidence of Selection (EoS), removing the assumption that functionally important sites are adjacent in sequence and and explicitly modelling the effects of limited sample-size. Precise statistical derivations show that the EoS score can be easily interpreted as an expected log-odds-ratio between two competing hypotheses, namely, the hypothetical presence or absence of functional selection for a given site. Using the EoS score, we then develop selection criteria by which functionally-important yet non-adjacent sites can be identified. An approximate power analysis is also developed to estimate the reliability of inference given the data. We validate and demonstrate the the practical utility of our method by analysis of the homing endonuclease <monospace>I-Bmol</monospace>, comparing our predictions with the results of existing methods.</p> <p>Conclusions</p> <p>Our method is able to assess both the evidence of selection at individual amino acid sites and estimate the reliability of those inferences. Experimental validation with <monospace>I-Bmol</monospace> proves its utility to identify functionally-important residues of poorly characterized proteins, demonstrating increased sensitivity over previous methods without loss of specificity. With the ability to guide the selection of precise experimental mutagenesis conditions, our method helps make unigenic analysis a more broadly applicable technique with which to probe protein function.</p> <p>Availability</p> <p>Software to compute, plot, and summarize EoS data is available as an open-source package called 'unigenic' for the 'R' programming language at <url>http://www.fernandes.org/txp/article/13/an-analytical-framework-for-unigenic-evolution</url>.</p

Characterisation of SEQ0694 (PrsA/PrtM) of Streptococcus equi as a functional peptidyl-prolyl isomerase affecting multiple secreted protein substrates

YesPeptidyl-prolyl isomerase (PPIase) lipoproteins have been shown to influence the virulence of a number of Gram-positive bacterial human and animal pathogens, most likely through facilitating the folding of cell envelope and secreted virulence factors. Here, we used a proteomic approach to demonstrate that the Streptococcus equi PPIase SEQ0694 alters the production of multiple secreted proteins, including at least two putative virulence factors (FNE and IdeE2). We demonstrate also that, despite some unusual sequence features, recombinant SEQ0694 and its central parvulin domain are functional PPIases. These data add to our knowledge of the mechanisms by which lipoprotein PPIases contribute to the virulence of streptococcal pathogens

Sildenafil Weaning After Discharge in Infants With Congenital Diaphragmatic Hernia

Sildenafil is used to treat pulmonary hypertension (PAH) in infants with congenital diaphragmatic hernia (CDH). However, data to guide sildenafil dosing and weaning are limited. This is concerning in light of a recent report describing increased risk associated with high-dose sildenafil regimens in non-CDH PAH. A retrospective cohort study of sildenafil usage, dosing, and weaning in infants with CDH was conducted at the authors' institution. The findings show that 17 % (19/122) of infants were discharged receiving sildenafil at a median dose of 8 mg/kg/day (range 2.91-5.78 mg/kg/day). The weaning rate was 0.1 mg/kg/week (range 0.01-0.5 mg/kg/week). The infants ceased therapy after a median of 343 days. At the age of 1 year, 29 % were receiving sildenafil at a dose higher than 1.5 mg/kg/day. One infant died of severe PAH. Sildenafil therapy at discharge is common in severe CDH. Variation in dosing and weaning rates highlights the need for standardized assessment and treatment of PAH after discharge to optimize the benefits and minimize the adverse effects of sildenafil