Processivity and specificity of histone acetylation by the male-specific lethal complex

Acetylation of lysine 16 of histone H4 (H4K16ac) stands out among the histone modifications, because it decompacts the chromatin fiber. The metazoan acetyltransferase MOF (KAT8) regulates transcription through H4K16 acetylation. Antibody-based studies had yielded inconclusive results about the selectivity of MOF to acetylate the H4 N-terminus. We used targeted mass spectrometry to examine the activity of MOF in the male-specific lethal core (4-MSL) complex on nucleosome array substrates. This complex is part of the Dosage Compensation Complex (DCC) that activates X-chromosomal genes in male Drosophila. During short reaction times, MOF acetylated H4K16 efficiently and with excellent selectivity. Upon longer incubation, the enzyme progressively acetylated lysines 12, 8 and 5, leading to a mixture of oligo-acetylated H4. Mathematical modeling suggests that MOF recognizes and acetylates H4K16 with high selectivity, but remains substrate-bound and continues to acetylate more N-terminal H4 lysines in a processive manner. The 4-MSL complex lacks non-coding roX RNA, a critical component of the DCC. Remarkably, addition of RNA to the reaction non-specifically suppressed H4 oligo-acetylation in favor of specific H4K16 acetylation. Because RNA destabilizes the MSL-nucleosome interaction in vitro we speculate that RNA accelerates enzyme-substrate turn-over in vivo, thus limiting the processivity of MOF, thereby increasing specific H4K16 acetylation.

pyPESTO: a modular and scalable tool for parameter estimation for dynamic models

SUMMARY

Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. pyPESTO is a modular framework for systematic parameter estimation, with scalable algorithms for optimization and uncertainty quantification. While tailored to ordinary differential equation problems, pyPESTO is broadly applicable to black-box parameter estimation problems. Besides own implementations, it provides a unified interface to various popular simulation and inference methods.

AVAILABILITY AND IMPLEMENTATION

pyPESTO is implemented in Python, open-source under a 3-Clause BSD license. Code and documentation are available on GitHub (https://github.com/icb-dcm/pypesto).

Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks

Dynamical models in the form of systems of ordinary differential equations have become a standard tool in systems biology. Many parameters of such models are usually unknown and have to be inferred from experimental data. Gradient-based optimization has proven to be effective for parameter estimation. However, computing gradients becomes increasingly costly for larger models, which are required for capturing the complex interactions of multiple biochemical pathways. Adjoint sensitivity analysis has been pivotal for working with such large models, but methods tailored for steady-state data are currently not available. We propose a new adjoint method for computing gradients, which is applicable if the experimental data include steady-state measurements. The method is based on a reformulation of the backward integration problem to a system of linear algebraic equations. The evaluation of the proposed method using real-world problems shows a speedup of total simulation time by a factor of up to 4.4. Our results demonstrate that the proposed approach can achieve a substantial improvement in computation time, in particular for large-scale models, where computational efficiency is critical.

A protocol for dynamic model calibration

Ordinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models typically have many unknown and nonmeasurable parameters, which have to be determined by fitting the model to experimental data. In order to perform this task, known as parameter estimation or model calibration, the modeller faces challenges such as poor parameter identifiability, lack of sufficiently informative experimental data and the existence of local minima in the objective function landscape. These issues tend to worsen with larger model sizes, increasing the computational complexity and the number of unknown parameters. An incorrectly calibrated model is problematic because it may result in inaccurate predictions and misleading conclusions. For nonexpert users, there are a large number of potential pitfalls. Here, we provide a protocol that guides the user through all the steps involved in the calibration of dynamic models. We illustrate the methodology with two models and provide all the code required to reproduce the results and perform the same analysis on new models. Our protocol provides practitioners and researchers in biological modelling with a one-stop guide that is at the same time compact and sufficiently comprehensive to cover all aspects of the problem.

Mini-batch optimization enables training of ODE models on large-scale datasets

Quantitative dynamic models are widely used to study cellular signal processing. A critical step in modelling is the estimation of unknown model parameters from experimental data. As model sizes and datasets are steadily growing, established parameter optimization approaches for mechanistic models become computationally extremely challenging. Mini-batch optimization methods, as employed in deep learning, have better scaling properties. In this work, we adapt, apply, and benchmark mini-batch optimization for ordinary differential equation (ODE) models, thereby establishing a direct link between dynamic modelling and machine learning. On our main application example, a large-scale model of cancer signaling, we benchmark mini-batch optimization against established methods, achieving better optimization results and reducing computation by more than an order of magnitude. We expect that our work will serve as a first step towards mini-batch optimization tailored to ODE models and enable modelling of even larger and more complex systems than what is currently possible.

AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models

Summary

Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However, for large and comprehensive models, the computational cost of simulating or calibrating can be limiting. AMICI is a modular toolbox implemented in C++/Python/MATLAB that provides efficient simulation and sensitivity analysis routines tailored for scalable, gradient-based parameter estimation and uncertainty quantification.

Availabilityand implementation

AMICI is published under the permissive BSD-3-Clause license with source code publicly available on https://github.com/AMICI-dev/AMICI. Citeable releases are archived on Zenodo.

Supplementary information

Supplementary data are available at Bioinformatics online.

PEtab-Interoperable specification of parameter estimation problems in systems biology

Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been-so far-no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies.

The effect of including increased arterial stiffness in the upper body when modelling Coarctation of the Aorta

Coarctation of the Aorta is a congenital narrowing of the aorta and diagnosis can be difficult. Treatments result in idiopathic sequelae including hypertension. Untreated patients are known to develop increased arterial stiffness in the upper body, which worsens with time. We present results from simulations with a one-dimensional mathematical model, about the effect of stiffness, stenting, surgery and coarctation severity on blood pressure, Pulsatility and Resistivity Index. One conclusion is that increased stiffness may explain both hypertension in treated patients and why diagnosis can be difficult.

The effects of tapering and artery wall stiffness on treatments for Coarctation of the Aorta

Coarctation of the Aorta is a congenital narrowing of the aorta. Two commonly used treatments are resection and end-to-end anastomosis, and stent placements. We simulate blood flow through one-dimensional models of aortas. Different artery stiffnesses, due to treatments, are included in our model, and used to compare blood flow properties in the treated aortas. We expand our previously published model to include the natural tapering of aortas. We look at change in aorta wall radius, blood pressure and blood flow velocity, and find that, of the two treatments, the resection and end-to-end anastomosis treatment more closely matches healthy aortas.

Efficacy of systemic therapies for moderate-to-severe psoriasis: a systematic review and meta-analysis of long-term treatment

BACKGROUND

Despite the chronicity of psoriasis, most systematic reviews focus on short-term treatment.

METHODS

The systematic search strategy and results from the German Psoriasis Guidelines were adapted. To update the data a literature search in Medline, Embase and the Cochrane Library was conducted. The proportion of participants achieving ≥75% decrease in Psoriasis Area and Severity Index (PASI) as well as Dermatology Life Quality Index (DLQI) reduction at different time points were assessed. Trials were summarized with respect to time periods and study designs. Suitable trials were included in a meta-analysis. Particular attention was paid to statistical approaches of handling dropouts.

RESULTS

A total of 33 articles including 27 trials totaling 6575 patients with active treatment were included in the systematic review. Seven randomized controlled trials were eligible for the meta-analysis. Over a 24 week treatment period infliximab [risk difference (RD) 78%, 95% confidence interval (CI) 72-83%] and ustekinumab 90 mg every 12 weeks (RD 77%, 95% CI 71-83%) were the most efficacious treatments. Adalimumab (RD: 60%, 95% CI 45-74%) showed results within the range of different etanercept dosages (etanercept 50 mg once weekly: RD 62%, 95% CI, 52-72%), (etanercept 25 mg twice weekly: RD 45%, 95% CI 34-56%), (etanercept 50 mg twice weekly: RD 56%, 95% CI 49-62%) and (etanercept 50 mg twice weekly until week 12, then 25 mg twice weekly: RD 50%, 95% CI 42-57%). After 24 weeks a decrease in efficacy for inflximab, adalimumab and etanercept was observed.

CONCLUSIONS

More sufficient data is required to draw reliable conclusions in extended long-term treatment and head-to-head comparisons are necessary.

European S3-guidelines on the systemic treatment of psoriasis vulgaris

Of the 131 studies on monotherapy or combination therapy assessed, 56 studies on the different forms of phototherapy fulfilled the criteria for inclusion in the guidelines. Approximately three-quarters of all patients treated with phototherapy attained at least a PASI 75 response after 4 to 6 weeks, and clearance was frequently achieved (levels of evidence 2 and 3). Phototherapy represents a safe and very effective treatment option for moderate to severe forms of psoriasis vulgaris. The onset of clinical effects occurs within 2 weeks. Of the unwanted side effects, UV erythema from overexposure is by far the most common and is observed frequently. With repeated or long-term use, the consequences of high, cumulative UV doses (such as premature aging of the skin) must be taken into consideration. In addition, carcinogenic risk is associated with oral PUVA and is probable for local PUVA and UVB. The practicability of the therapy is limited by spatial, financial, human, and time constraints on the part of the physician, as well as by the amount of time required by the patient. From the perspective of the cost-bearing institution, phototherapy has a good cost-benefit ratio. However, the potentially significant costs for, and time required of, the patient must be considered.

A preliminary study on neonatal septicaemia in a tertiary referral hospital paediatric unit

OBJECTIVE

To estimate the incidence of neonatal septicaemia, and to identify risk factors, clinical presentations and causal organisms.

DESIGN

A cross-sectional study.

SETTING

Neonatal Care Unit, University Paediatric Unit, Colombo North Teaching Hospital.

SUBJECTS

Neonates admitted from January to December 1996 with clinical evidence of septicaemia.

METHOD

Gestational age, birth weight and mode of delivery were evaluated as risk factors for septicaemia. Although diagnosis of septicaemia was made on clinical grounds, blood cultures were performed in all babies. Data was analysed by using Epi Info version 6.

RESULTS

98 babies had septicaemia. Incidence of septicaemia was 24.4 per 1000 live births and case fatality rate was 11.2%. Incidence was significantly higher in preterm babies, babies with low birth weight (LBW) and those born following instrumental delivery. 21.4% developed septicaemia on the first day of life, 74.5% between 2 and 7 days and 4.1% after the first week. Common presenting features were fever 61.2%, jaundice 52%, lethargy 37.8% refusal of feeds 25.5%, coffee grounds vomiting 22.4%, and fits 12.2%. Common bacteria identified were Klebsiella 26.5%, Staphylococcus aureus 15.3%, coliform bacilli 9.2% and spore forming bacilli 9.2%. Common sensitive antibiotics were amikacin 88.9%, amoxycillin + clavulanic acid 83%, ceftriaxone 78.1% and netilmicin 63.9%.

CONCLUSIONS

Septicaemia is an important cause of morbidity, particularly in preterm babies, in babies with LBW and those with instrumentation at birth. The high incidence of late onset septicaemia together with the findings of Klebsiella and Staphylococcus aureus as common and resistant pathogens for septicaemia indicate that the majority were nosocomial infections.