Reverse Engineering of Biochemical Reaction Networks Using Co-evolution with Eng-Genes

A major challenge when attempting to model biochemical reaction networks within the cell is that the dimensionality can become huge, where a large number of molecular species can be involved even in relatively small networks. This investigation attempts to infer models of these networks using a co-evolutionary algorithm that reverse engineers differential equation models of the target system from time-series data. The algorithm not only estimates the system parameters, but also the symbolic structure of the network. To reduce the problem of dimensionality, the algorithm uses a partitioning method while integrating candidate models in order to decouple system equations. In addition, the conventional evolutionary algorithm has been modified and extended to include a technique called ‘eng-genes’, where candidate models are built up from fundamental mathematical terms derived from knowledge about the target system a priori. This technique essentially focuses the search on more biologically plausible models. The approach is demonstrated on several example reaction networks. The results show that the eng-genes method of limiting the term pool using a priori knowledge improves the convergence of the reverse engineering process compared with the conventional method, resulting in more accurate and transparent models.     

CXCR1 and CXCR2 haplotypes synergistically modulate cystic fibrosis lung disease

Cystic fibrosis (CF) lung disease severity is largely independent on the CF transmembrane conductance regulator (CFTR) genotype, indicating the contribution of genetic modifiers. The chemokine receptors CXCR1 and CXCR2 have been found to play essential roles in the pathogenesis of CF lung disease. Here, we determine whether genetic variation of CXCR1 and CXCR2 influences CF lung disease severity. Genomic DNA of CF patients in Germany (n = 442) was analysed for common variations in CXCR1 and CXCR2 using a single-nucleotide polymorphism (SNP) tagging approach. Associations of CXCR1 and CXCR2 SNPs and haplotypes with CF lung disease severity, CXCR1 and CXCR2 expression, and neutrophil effector functions were assessed. Four SNPs in CXCR1 and three in CXCR2 strongly correlated with age-adjusted lung function in CF patients. SNPs comprising haplotypes CXCR1_Ha and CXCR2_Ha were in high linkage disequilibrium and patients heterozygous for the CXCR1-2 haplotype cluster (CXCR1-2_Ha) had lower lung function compared with patients with homozygous wild-type alleles (forced expiratory volume in 1 s ≤ 70% predicted, OR 7.24; p = 2.30 × 10(-5)). CF patients carrying CXCR1-2_Ha showed decreased CXCR1 combined with increased CXCR2 mRNA and protein expression, and displayed disturbed antibacterial effector functions. CXCR1 and CXCR2 genotypes modulate lung function and antibacterial host defence in CF lung disease.     

Biomechanical performance of different cable and wire cerclage configurations

Purpose

Cerclage technology is regaining interest due to the increasing number of periprosthetic fractures. Different wiring techniques have been formerly proposed and have hibernated over years. Hereby, they are compared to current cerclage technology.

Methods

Seven groups (n = 6) of different cable cerclage (Ø1.7 mm, crimp closure) configurations (one single cerclage looped once around the shells, one single cerclage looped twice, two cerclages each looped once) and solid wire cerclages (Ø1.5 mm, twist closure) (same configurations as cable cerclages, and two braided wires, twisted around each other looped once) fixed two cortical half shells of human femoral shaft mounted on a testing jig. Sinusoidal cyclic loading with constantly increasing force (0.1 N/cycle) was applied starting at 50 N peak load. Cerclage pretension (P), load leading to onset of plastic deformation (D) and load at total failure (T) were identified. Statistical differences between the groups were detected by univariate ANOVA.

Results

Double looped cables (P442N ± 129; D1334N ± 319; T2734N ± 330) performed significantly better (p < 0.05) than single looped cables (P292N ± 56; D646N ± 108; T1622N ± 171) and were comparable to two single cables (P392N ± 154; D1191N ± 334; T2675N ± 361). Double looped wires (P335N ± 49; D752N ± 119; T1359N ± 80) were significantly better (p < 0.05) than single looped wires (P181N ± 16; D343N ± 33; T606N ± 109) and performed similarly to single looped cables. Braided wires (P119N ± 26; D225N ± 55; T919N ± 197) exhibited early loss of pretension and plastic deformation.

Conclusion

Double looped cerclages provided a better fixation stability compared to a single looped cerclage. Double looped wires were comparable to a single looped cable. The use of braided wires could not be recommended mechanically.     

Fatigue performance of angle-stable tibial nail interlocking screws

Purpose

Tibial nail interlocking screw failure often occurs during delayed fracture consolidation or at early weight bearing of nailed unstable fractures, in general when high implant stress could not be reduced by other means. Is there a biomechanical improvement in long-term performance of angle stable locking screws compared to conventional locking screws for distal locking of intramedullary tibial nails?

Methods

Surrogate bones of human tibiae were cut in the distal third and distal locking of the 10 mm intramedullary tibial nail was performed with either two angle stable locking screws or two conventional locking screws in the mediolateral plane. Six specimens per group were mechanically tested under quasi-static and cyclic axial loading with constantly increasing force.

Results

Angle stable locking screw constructs exhibited significantly higher stiffness values (7,809 N/mm ± 647, mean ± SD) than conventional locking screw constructs (6,614 N/mm ± 859, p = 0.025). Angle stable locking screw constructs provided a longer fatigue life, expressed in a significantly higher number of cycles to failure (187,200 ± 18,100) compared to conventional locking screw constructs (128,700 ± 7,000, p = 0.004).

Conclusion

Fatigue performance of locking screws can be ameliorated by the use of angle stable locking screws, being especially important if the nail acts as load carrier and an improved stability during fracture healing is needed.     

Non-linear dynamics of heart rate variability during incremental cycling exercise

Within the last years complex models of cardiovascular regulation and exercise fatigue have implemented heart rate variability (HRV) as a measure of autonomic nervous system. Using detrended fluctuation analysis (DFA) to assess heart rate correlation properties, the present study examines the influence of exercise intensity on total variability and complexity in non-linear dynamics of HRV. Sixteen cyclists performed a graded exercise test on a bicycle ergometer. HRV time domain measures and fractal correlation properties were analyzed using short-term scaling exponent alpha1 of DFA. Amplitude and complexity of HRV parameters decreased significantly. DFA-alpha1 increased from rest to low exercise intensity and showed an almost linear decrease from higher intensities until exhaustion. These findings support a qualitative change in self-organized heart rate regulation from a complex autonomic control at rest and low intensities towards a breakdown of the interaction in control mechanisms with non-autonomic heart rate control dominating at high intensities.