Regulatory control and the costs and benefits of biochemical noise

Experiments in recent years have vividly demonstrated that gene expression can be highly stochastic. How protein concentration fluctuations affect the growth rate of a population of cells, is, however, a wide open question. We present a mathematical model that makes it possible to quantify the effect of protein concentration fluctuations on the growth rate of a population of genetically identical cells. The model predicts that the population's growth rate depends on how the growth rate of a single cell varies with protein concentration, the variance of the protein concentration fluctuations, and the correlation time of these fluctuations. The model also predicts that when the average concentration of a protein is close to the value that maximizes the growth rate, fluctuations in its concentration always reduce the growth rate. However, when the average protein concentration deviates sufficiently from the optimal level, fluctuations can enhance the growth rate of the population, even when the growth rate of a cell depends linearly on the protein concentration. The model also shows that the ensemble or population average of a quantity, such as the average protein expression level or its variance, is in general not equal to its time average as obtained from tracing a single cell and its descendants. We apply our model to perform a cost-benefit analysis of gene regulatory control. Our analysis predicts that the optimal expression level of a gene regulatory protein is determined by the trade-off between the cost of synthesizing the regulatory protein and the benefit of minimizing the fluctuations in the expression of its target gene. We discuss possible experiments that could test our predictions.Comment: Revised manuscript;35 pages, 4 figures, REVTeX4; to appear in PLoS Computational Biolog

Impact of early applied upper limb stimulation: The EXPLICIT-stroke programme design

Main claims of the literature are that functional recovery of the paretic upper limb is mainly defined within the first month post stroke and that rehabilitation services should preferably be applied intensively and in a task-oriented way within this particular time window. EXplaining PLastICITy after stroke (acronym EXPLICIT-stroke) aims to explore the underlying mechanisms of post stroke upper limb recovery. Two randomized single blinded trials form the core of the programme, investigating the effects of early modified Constraint-Induced Movement Therapy (modified CIMT) and EMG-triggered Neuro-Muscular Stimulation (EMG-NMS) in patients with respectively a favourable or poor probability for recovery of dexterity.BioMechanical EngineeringMechanical, Maritime and Materials Engineerin

Predictors of adverse events after endovascular abdominal aortic aneurysm repair: A meta-analysis of case reports

Introduction: Endovascular abdominal aortic aneurysm repair is a life-saving intervention. Nevertheless, complications have a major impact. We review the evidence from case reports for risk factors of complications after endovascular abdominal aortic aneurysm repair. Case presentation: We selected case reports from PubMed reporting original data on adverse events after endovascular abdominal aortic aneurysm repair. Extracted risk factors were: age, sex, aneurysm diameter, comorbidities, re-interventions, at least one follow-up visit being missed or refusal of a re-intervention by the patient. Extracted outcomes were: death, rupture and (non-)device-related complications. In total 113 relevant articles were selected. These reported on 173 patients. A fatal outcome was reported in 15% (N = 26) of which 50% came after an aneurysm rupture (N = 13). Non-fatal aneurysm rupture occurred in 15% (N = 25). Endoleaks were reported in 52% of the patients (N = 90). In half of the patients with a rupture no prior endoleak was discovered during follow-up. In 83% of the patients one or more re-interventions were performed (N = 143). Mortality was higher among women (risk ratio 2.9; 95% confidence interval 1.4 to 6.0), while the presence of comorbidities was strongly associated with both ruptures (risk ratio 1.6; 95% confidence interval 0.9 to 2.9) and mortality (risk ratio 2.1; 95% confidence interval 1.0 to 4.7). Missing one or more follow-up visits (≥1) or refusal of a re-intervention by the patient was strongly related to both ruptures (risk ratio 4.7; 95% confidence interval 3.1 to 7.0) and mortality (risk ratio 3.8; 95% confidence interval 1.7 to 8.3). Conclusion: Female gender, the presence of comorbidities and at least one follow-up visit being missed or refusal of a re-intervention by the patient appear to increase the risk for mortality after endovascular abdominal aortic aneurysm repair. Larger aneurysm diameter, higher age and multimorbidity at the time of surgery appear to increase the risk for rupture and other complications after endovascular abdominal aortic aneurysm repair. These risk factors deserve further attention in future studies

On Schubert's Problem of Characteristics

The Schubert varieties on a flag manifold G/P give rise to a cell decomposition on G/P whose Kronecker duals, known as the Schubert classes on G/P, form an additive base of the integral cohomology of G/P. The Schubert's problem of characteristics asks to express a monomial in the Schubert classes as a linear combination in the Schubert basis. We present a unified formula expressing the characteristics of a flag manifold G/P as polynomials in the Cartan numbers of the group G. As application we develop a direct approach to our recent works on the Schubert presentation of the cohomology rings of flag manifolds G/P.Comment: 27page

A putative genomic island, PGI-1, in Ralstonia solanacearum biovar 2 revealed by subtractive hybridization

Ralstonia solanacearum biovar 2, a key bacterial pathogen of potato, has recently established in temperate climate waters. On the basis of isolates obtained from diseased (potato) plants, its genome has been assumed to be virtually clonal, but information on environmental isolates has been lacking. Based on differences in pulsed-field gel electrophoresis patterns, we compared the genomes of two biovar 2 strains with different life histories. Thus, genomic DNA of the novel environmental strain KZR-5 (The Netherlands) was compared to that of reference potato strain 715 (Bangladesh) by suppressive subtractive hybridization. Various strain-specific sequences were found, all being homologous to those found in the genome of reference potato strain 1609. Approximately 20% of these were related to genes involved in recombinational processes. We found a deletion of a 17.6-Kb region, denoted as a putative genomic island PGI-1, in environmental strain KZR-5. The deleted region was, at both extremes, flanked by a composite of two insertion sequence (IS) elements, identified as ISRso2 and ISRso3. The PGI-1 region contained open reading frames that putatively encoded a (p)ppGpp synthetase, a transporter protein, a transcriptional regulator, a cellobiohydrolase, a site-specific integrase/recombinase, a phage-related protein and seven hypothetical proteins. As yet, no phenotype could be assigned to the loss of PGI-1. The ecological behavior of strain KZR-5 was compared to that of reference strain 715. Strain KZR-5 showed enhanced tolerance to 4°C as compared to the reference strain, but was not affected in its virulence on tomato

Dutch home-based pre-reading intervention with children at familial risk of dyslexia

Children (5 and 6 years old, n = 30) at familial risk of dyslexia received a home-based intervention that focused on phoneme awareness and letter knowledge in the year prior to formal reading instruction. The children were compared to a no-training at-risk control group (n = 27), which was selected a year earlier. After training, we found a small effect on a composite score of phoneme awareness (d = 0.29) and a large effect on receptive letter knowledge (d = 0.88). In first grade, however, this did not result in beneficial effects for the experimental group in word reading and spelling. Results are compared to three former intervention studies in The Netherlands and comparable studies from Denmark and Australia