Bypass of complex co-directional replication-transcription collisions by replisome skipping.

Collisions between the replisome and RNA polymerases [RNAP(s)] are the main obstacle to DNA replication. These collisions can occur either head-on or co-directionally with respect to the direction of translocation of both complexes. Whereas head-on collisions require additional factors to be resolved, co-directional collisions are thought to be overcome by the replisome itself using the mRNA transcript as a primer. We show that mRNA takeover is utilized primarily after collisions with single RNAP complexes with short transcripts. Bypass of more complex transcription complexes requires the synthesis of a new primer downstream of the RNAP for the replisome to resume leading-strand synthesis. In both cases, bypass proceeds with displacement of the RNAP. Rep, Mfd, UvrD and RNase H can process the RNAP block and facilitate replisome bypass by promoting the formation of continuous leading strands. Bypass of co-directional RNAP(s) and/or R-loops is determined largely by the length of the obstacle that the replisome needs to traverse: R-loops are about equally as potent obstacles as RNAP arrays if they occupy the same length of the DNA template.

Replisome bypass of transcription complexes and R-loops.

The vast majority of the genome is transcribed by RNA polymerases. G+C-rich regions of the chromosomes and negative superhelicity can promote the invasion of the DNA by RNA to form R-loops, which have been shown to block DNA replication and promote genome instability. However, it is unclear whether the R-loops themselves are sufficient to cause this instability or if additional factors are required. We have investigated replisome collisions with transcription complexes and R-loops using a reconstituted bacterial DNA replication system. RNA polymerase transcription complexes co-directionally oriented with the replication fork were transient blockages, whereas those oriented head-on were severe, stable blockages. On the other hand, replisomes easily bypassed R-loops on either template strand. Replication encounters with R-loops on the leading-strand template (co-directional) resulted in gaps in the nascent leading strand, whereas lagging-strand template R-loops (head-on) had little impact on replication fork progression. We conclude that whereas R-loops alone can act as transient replication blocks, most genome-destabilizing replication fork stalling likely occurs because of proteins bound to the R-loops.

Single-molecule live cell imaging of Rep reveals the dynamic interplay between an accessory replicative helicase and the replisome.

DNA replication must cope with nucleoprotein barriers that impair efficient replisome translocation. Biochemical and genetic studies indicate accessory helicases play essential roles in replication in the presence of nucleoprotein barriers, but how they operate inside the cell is unclear. With high-speed single-molecule microscopy we observed genomically-encoded fluorescent constructs of the accessory helicase Rep and core replisome protein DnaQ in live Escherichia coli cells. We demonstrate that Rep colocalizes with 70% of replication forks, with a hexameric stoichiometry, indicating maximal occupancy of the single DnaB hexamer. Rep associates dynamically with the replisome with an average dwell time of 6.5 ms dependent on ATP hydrolysis, indicating rapid binding then translocation away from the fork. We also imaged PriC replication restart factor and observe Rep-replisome association is also dependent on PriC. Our findings suggest two Rep-replisome populations in vivo: one continually associating with DnaB then translocating away to aid nucleoprotein barrier removal ahead of the fork, another assisting PriC-dependent reloading of DnaB if replisome progression fails. These findings reveal how a single helicase at the replisome provides two independent ways of underpinning replication of protein-bound DNA, a problem all organisms face as they replicate their genomes.

The 2B subdomain of Rep helicase links translocation along DNA with protein displacement.

Helicases catalyse DNA and RNA strand separation. Proteins bound to the nucleic acid must also be displaced in order to unwind DNA. This is exemplified by accessory helicases that clear protein barriers from DNA ahead of advancing replication forks. How helicases catalyse DNA unwinding is increasingly well understood but how protein displacement is achieved is unclear. Escherichia coli Rep accessory replicative helicase lacking one of its four subdomains, 2B, has been shown to be hyperactivated for DNA unwinding in vitro but we show here that RepΔ2B is, in contrast, deficient in displacing proteins from DNA. This defect correlates with an inability to promote replication of protein-bound DNA in vitro and lack of accessory helicase function in vivo. Defective protein displacement is manifested on double-stranded and single-stranded DNA. Thus binding and distortion of duplex DNA by the 2B subdomain ahead of the helicase is not the missing function responsible for this deficiency. These data demonstrate that protein displacement from DNA is not simply achieved by helicase translocation alone. They also imply that helicases may have evolved different specific features to optimise DNA unwinding and protein displacement, both of which are now recognised as key functions in all aspects of nucleic acid metabolism.

Digital Analysis of Nasal Airflow Facilitating Decision Support in Rhinosurgery.

Successful functional surgery on the nasal framework requires reliable and comprehensive diagnosis. In this regard, the authors introduce a new methodology: Digital Analysis of Nasal Airflow (diANA). It is based on computational fluid dynamics, a statistical shape model of the healthy nasal cavity and rhinologic expertise. diANA necessitates an anonymized tomographic dataset of the paranasal sinuses including the complete nasal cavity and, when available, clinical information. The principle of diANA is to compare the morphology and the respective airflow of an individual nose with those of a reference. This enables morphometric aberrations and consecutive flow field anomalies to localize and quantify within a patient's nasal cavity. Finally, an elaborated expert opinion with instructive visualizations is provided. Using diANA might support surgeons in decision-making, avoiding unnecessary surgery, gaining more precision, and target-orientation for indicated operations.

The Healthy Nasal Cavity-Characteristics of Morphology and Related Airflow Based on a Statistical Shape Model Viewed from a Surgeon's Perspective.

Functional surgery on the nasal framework requires referential criteria to objectively assess nasal breathing for indication and follow-up. This motivated us to generate a mean geometry of the nasal cavity based on a statistical shape model. In this study, the authors could demonstrate that the introduced nasal cavity's mean geometry features characteristics of the inner shape and airflow, which are commonly observed in symptom-free subjects. Therefore, the mean geometry might serve as a reference-like model when one considers qualitative aspects. However, to facilitate quantitative considerations and statistical inference, further research is necessary. Additionally, the authors were able to obtain details about the importance of the isthmus nasi and the inferior turbinate for the intranasal airstream.

Use of streptavidin bound to biotinylated DNA structures as model substrates for analysis of nucleoprotein complex disruption by helicases.

Helicases are a subfamily of translocases that couple the directional translocation along a nucleic acid lattice to the separation of nucleic acid duplexes using the energy derived from nucleoside triphosphate hydrolysis. These enzymes perform essential functions in all aspects of nucleic acid metabolism by unwinding and remodelling DNA or RNA in DNA replication, repair, recombination, transcription and translation. Most classical biochemical studies assay the ability of these enzymes to separate naked nucleic acids. However, many different types of proteins form non-covalent interactions with nucleic acids in vivo and so the true substrates of helicases are protein-nucleic acid complexes rather than naked DNA and RNA. Studies over the last decade have revealed that bound proteins can have substantial inhibitory effects on the ability of helicases to unwind nucleic acids. Any analysis of helicase mechanisms in vitro must therefore consider helicase function within the context of nucleoprotein substrates rather than just DNA or RNA. Here we discuss how to analyse the impact of bound proteins on the ability of helicases to unwind DNA substrates in vitro.

Generation of synthetic aortic valve stenosis geometries for in silico trials.

In silico trials are a promising way to increase the efficiency of the development, and the time to market of cardiovascular implantable devices. The development of transcatheter aortic valve implantation (TAVI) devices, could benefit from in silico trials to overcome frequently occurring complications such as paravalvular leakage and conduction problems. To be able to perform in silico TAVI trials virtual cohorts of TAVI patients are required. In a virtual cohort, individual patients are represented by computer models that usually require patient-specific aortic valve geometries. This study aimed to develop a virtual cohort generator that generates anatomically plausible, synthetic aortic valve stenosis geometries for in silico TAVI trials and allows for the selection of specific anatomical features that influence the occurrence of complications. To build the generator, a combination of non-parametrical statistical shape modeling and sampling from a copula distribution was used. The developed virtual cohort generator successfully generated synthetic aortic valve stenosis geometries that are comparable with a real cohort, and therefore, are considered as being anatomically plausible. Furthermore, we were able to select specific anatomical features with a sensitivity of around 90%. The virtual cohort generator has the potential to be used by TAVI manufacturers to test their devices. Future work will involve including calcifications to the synthetic geometries, and applying high-fidelity fluid-structure-interaction models to perform in silico trials.

Population-based reference values for 4D flow MRI derived aortic blood flow parameters.

Objective. This study assesses age-related differences of thoracic aorta blood flow profiles and provides age- and sex-specific reference values using 4D flow cardiovascular magnetic resonance (CMR) data.Approach. 126 volunteers (age 20-80 years, female 51%) underwent 4D flow CMR and 12 perpendicular analysis planes in the thoracic aorta were specified. For these planes the following parameters were evaluated: body surface area-adjusted aortic area (A'), normalized flow displacement (NFD), the degree of wall parallelism (WPD), the minimal relative cross-sectional area through which 80% of the volume flow passes (A80) and the angle between flow direction and centerline (α).Main results. Age-related differences in blood flow parameters were seen in the ascending aorta with higher values for NFD and angle and lower values for WPD and A80 in older subjects. All parameters describing blood flow patterns correlated with the cross-sectional area in the ascending aorta. No relevant sex-differences regarding blood flow profiles were found.Significance. These age- and sex-specific reference values for quantitative parameters describing blood flow within the aorta might help to study the clinical relevance of flow profiles in the future.

Impact of turbulence modeling on the simulation of blood flow in aortic coarctation.

Numerical simulations of pulsatile blood flow in an aortic coarctation require the use of turbulence modeling. This paper considers three models from the class of large eddy simulation (LES) models (Smagorinsky, Vreman, σ -model) and one model from the class of variational multiscale models (residual-based) within a finite element framework. The influence of these models on the estimation of clinically relevant biomarkers used to assess the degree of severity of the pathological condition (pressure difference, secondary flow degree, normalized flow displacement, wall shear stress) is investigated in detail. The simulations show that most methods are consistent in terms of severity indicators such as pressure difference and stenotic velocity. Moreover, using second-order velocity finite elements, different turbulence models might lead to considerably different results concerning other clinically relevant quantities such as wall shear stresses. These differences may be attributed to differences in numerical dissipation introduced by the turbulence models.

CT-based comparison of porcine, ovine, and human pulmonary arterial morphometry.

To facilitate pre-clinical animal and in-silico clinical trials for implantable pulmonary artery pressure sensors, understanding the respective species pulmonary arteries (PA) anatomy is important. Thus, morphological parameters describing PA of pigs and sheep, which are common animal models, were compared with humans. Retrospective computed tomography data of 41 domestic pigs (82.6 ± 18.8 kg), 14 sheep (49.1 ± 6.9 kg), and 49 patients (76.8 ± 18.2 kg) were used for reconstruction of the subject-specific PA anatomy. 3D surface geometries including main, left, and right PA as well as LPA and RPA side branches were manually reconstructed. Then, specific geometric parameters (length, diameters, taper, bifurcation angle, curvature, and cross-section enlargement) affecting device implantation and post-interventional device effect and efficacy were automatically calculated. For both animal models, significant differences to the human anatomy for most geometric parameters were found, even though the respective parameters' distributions also featured relevant overlap. Out of the two animal models, sheep seem to be better suitable for a preclinical study when considering only PA morphology. Reconstructed geometries are provided as open data for future studies. These findings support planning of preclinical studies and will help to evaluate the results of animal trials.

In-silico enhanced animal study of pulmonary artery pressure sensors: assessing hemodynamics using computational fluid dynamics.

To assess whether in-silico models can be used to predict the risk of thrombus formation in pulmonary artery pressure sensors (PAPS), a chronic animal study using pigs was conducted. Computed tomography (CT) data was acquired before and immediately after implantation, as well as one and three months after the implantation. Devices were implanted into 10 pigs, each one in the left and right pulmonary artery (PA), to reduce the required number of animal experiments. The implantation procedure aimed at facilitating optimal and non-optimal positioning of the devices to increase chances of thrombus formation. Eight devices were positioned non-optimally. Three devices were positioned in the main PA instead of the left and right PA. Pre-interventional PA geometries were reconstructed from the respective CT images, and the devices were virtually implanted at the exact sites and orientations indicated by the follow-up CT after one month. Transient intra-arterial hemodynamics were calculated using computational fluid dynamics. Volume flow rates were modelled specifically matching the animals body weights. Wall shear stresses (WSS) and oscillatory shear indices (OSI) before and after device implantation were compared. Simulations revealed no relevant changes in any investigated hemodynamic parameters due to device implantation. Even in cases, where devices were implanted in a non-optimal manner, no marked differences in hemodynamic parameters compared to devices implanted in an optimal position were found. Before implantation time and surface-averaged WSS was 2.35±0.47 Pa, whereas OSI was 0.08±0.17, respectively. Areas affected by low WSS magnitudes were 2.5±2.7 cm2, whereas the areas affected by high OSI were 18.1±6.3 cm2. After device implantation, WSS and OSI were 2.45±0.49 Pa and 0.08±0.16, respectively. Surface areas affected by low WSS and high OSI were 2.9±2.7 cm2, and 18.4±6.1 cm2, respectively. This in-silico study indicates that no clinically relevant differences in intra-arterial hemodynamics are occurring after device implantation, even at non-optimal positioning of the sensor. Simultaneously, no embolic events were observed, suggesting that the risk for thrombus formation after device implantation is low and independent of the sensor position.

Comparison of rhinomanometric and computational fluid dynamic assessment of nasal resistance with respect to measurement accuracy.

PURPOSE: Computational fluid dynamics (CFD)-based calculation of intranasal airflow became an important method in rhinologic research. Current evidence shows weak to moderate correlation as well as a systematic underprediction of nasal resistance by numerical simulations. In this study, we investigate whether these differences can be explained by measurement uncertainties caused by rhinomanometric devices and procedures. Furthermore, preliminary findings regarding the impact of tissue movements are reported. METHODS: A retrospective sample of 17 patients, who reported impaired nasal breathing and for which rhinomanometric (RMM) measurements using two different devices as well as computed tomography scans were available, was investigated in this study. Three patients also exhibited a marked collapse of the nasal valve. Agreement between both rhinomanometric measurements as well as between rhinomanometry and CFD-based calculations was assessed using linear correlation and Bland-Altman analyses. These analyses were performed for the volume flow rates measured at trans-nasal pressure differences of 75 and 150 Pa during inspiration and expiration. RESULTS: The correlation between volume flow rates measured using both RMM devices was good (R2 > 0.72 for all breathing states), and no relevant differences in measured flow rates was observed (21.6 ml/s and 14.8 ml/s for 75 and 150 Pa, respectively). In contrast, correlation between RMM and CFD was poor (R2 < 0.5) and CFD systematically overpredicted RMM-based flow rate measurements (231.8 ml/s and 328.3 ml/s). No differences between patients with and without nasal valve collapse nor between inspiration and expiration were observed. CONCLUSION: Biases introduced during RMM measurements, by either the chosen device, the operator or other aspects as for example the nasal cycle, are not strong enough to explain the gross differences commonly reported between RMM- and CFD-based measurement of nasal resistance. Additionally, tissue movement during breathing is most likely also no sufficient explanation for these differences.

Geometric uncertainty in intracranial aneurysm rupture status discrimination: a two-site retrospective study.

OBJECTIVES: Assessing the risk associated with unruptured intracranial aneurysms (IAs) is essential in clinical decision making. Several geometric risk parameters have been proposed for this purpose. However, performance of these parameters has been inconsistent. This study evaluates the performance and robustness of geometric risk parameters on two datasets and compare it to the uncertainty inherent in assessing these parameters and quantifies interparameter correlations. METHODS: Two datasets containing 244 ruptured and unruptured IA geometries from 178 patients were retrospectively analysed. IAs were stratified by anatomical region, based on the PHASES score locations. 37 geometric risk parameters representing four groups (size, neck, non-dimensional, and curvature parameters) were assessed. Analysis included standardised absolute group differences (SADs) between ruptured and unruptured IAs, ratios of SAD to median relative uncertainty (MRU) associated with the parameters, and interparameter correlation. RESULTS: The ratio of SAD to MRU was lower for higher dimensional size parameters (ie, areas and volumes) than for one-dimensional size parameters. Non-dimensional size parameters performed comparatively well with regard to SAD and MRU. SAD was higher in the posterior anatomical region. Correlation of parameters was strongest within parameter (sub)groups and between size and curvature parameters, while anatomical region did not strongly affect correlation patterns. CONCLUSION: Non-dimensional parameters and few parameters from other groups were comparatively robust, suggesting that they might generalise better to other datasets. The data on discriminative performance and interparameter correlations presented in this study may aid in developing and choosing robust geometric parameters for use in rupture risk models.

3D modeling and printing for complex biventricular repair of double outlet right ventricle.

Background: Double outlet right ventricle (DORV) describes a group of congenital heart defects where pulmonary artery and aorta originate completely or predominantly from the right ventricle. The individual anatomy of DORV patients varies widely with multiple subtypes classified. Although the majority of morphologies is suitable for biventricular repair (BVR), complex DORV anatomy can render univentricular palliation (UVP) the only option. Thus, patient-specific decision-making is critical for optimal surgical treatment planning. The evolution of image processing and rapid prototyping techniques facilitate the generation of detailed virtual and physical 3D models of the patient-specific anatomy which can support this important decision process within the Heart Team. Materilas and methods: The individual cardiovascular anatomy of nine patients with complex DORV, in whom surgical decision-making was not straightforward, was reconstructed from either computed tomography or magnetic resonance imaging data. 3D reconstructions were used to characterize the morphologic details of DORV, such as size and location of the ventricular septal defect (VSD), atrioventricular valve size, ventricular volumes, relationship between the great arteries and their spatial relation to the VSD, outflow tract obstructions, coronary artery anatomy, etc. Additionally, physical models were generated. Virtual and physical models were used in the preoperative assessment to determine surgical treatment strategy, either BVR vs. UVP. Results: Median age at operation was 13.2 months (IQR: 9.6-24.0). The DORV transposition subtype was present in six patients, three patients had a DORV-ventricular septal defect subtype. Patient-specific reconstruction was feasible for all patients despite heterogeneous image quality. Complex BVR was feasible in 5/9 patients (55%). Reasons for unsuitability for BVR were AV valve chordae interfering with potential intraventricular baffle creation, ventricular hypoplasia and non-committed VSD morphology. Evaluation in particular of qualitative data from 3D models was considered to support comprehension of complex anatomy. Conclusion: Image-based 3D reconstruction of patient-specific intracardiac anatomy provides valuable additional information supporting decision-making processes and surgical planning in complex cardiac malformations. Further prospective studies are required to fully appreciate the benefits of 3D technology.

Virtual treatment planning in three patients with univentricular physiology using computational fluid dynamics-Pitfalls and strategies.

Background: Uneven hepatic venous blood flow distribution (HFD) to the pulmonary arteries is hypothesized to be responsible for the development of intrapulmonary arteriovenous malformations (PAVM) in patients with univentricular physiology. Thus, achieving uniform distribution of hepatic blood flow is considered favorable. However, no established method for the prediction of the post-interventional hemodynamics currently exists. Computational fluid dynamics (CFD) offers the possibility to quantify HFD in patient-specific anatomies before and after virtual treatment. In this study, we evaluated the potential benefit of CFD-assisted treatment planning. Materials and methods: Three patients with total cavopulmonary connection (TCPC) and PAVM underwent cardiovascular magnetic resonance imaging (CMR) and computed tomography imaging (CT). Based on this imaging data, the patient-specific anatomy was reconstructed. These patients were considered for surgery or catheter-based intervention aiming at hepatic blood flow re-routing. CFD simulations were then performed for the untreated state as well as for different surgical and interventional treatment options. These treatment options were applied as suggested by treating cardiologists and congenital heart surgeons with longstanding experience in interventional and surgical treatment of patients with univentricular physiology. HFD was quantified for all simulations to identify the most viable treatment decision regarding redistribution of hepatic blood flow. Results: For all three patients, the complex TCPC anatomy could be reconstructed. However, due to the presence of metallic stent implants, hybrid models generated from CT as well as CMR data were required. Numerical simulation of pre-interventional HFD agreed well with angiographic assessment and physiologic considerations. One treatment option resulting in improvement of HFD was identified for each patient. In one patient follow-up data after treatment was available. Here, the virtual treatment simulation and the CMR flow measurements differed by 15%. Conclusion: The combination of modern computational methods as well as imaging methods for assessment of patient-specific anatomy and flow might allow to optimize patient-specific therapy planning in patients with pronounced hepatic flow mismatch and PAVM. In this study, we demonstrate that these methods can also be applied in patients with complex univentricular physiology and extensive prior interventions. However, in those cases, hybrid approaches utilizing information of different image modalities may be required.

Computed Tomography-Based Assessment of Transvalvular Pressure Gradient in Aortic Stenosis.

Background: In patients with aortic stenosis, computed tomography (CT) provides important information about cardiovascular anatomy for treatment planning but is limited in determining relevant hemodynamic parameters such as the transvalvular pressure gradient (TPG). Purpose: In the present study, we aimed to validate a reduced-order model method for assessing TPG in aortic stenosis using CT data. Methods: TPGCT was calculated using a reduced-order model requiring the patient-specific peak-systolic aortic flow rate (Q) and the aortic valve area (AVA). AVA was determined by segmentation of the aortic valve leaflets, whereas Q was quantified based on volumetric assessment of the left ventricle. For validation, invasively measured TPGcatheter was calculated from pressure measurements in the left ventricle and the ascending aorta. Altogether, 84 data sets of patients with aortic stenosis were used to compare TPGCT against TPGcatheter. Results: TPGcatheter and TPGCT were 50.6 ± 28.0 and 48.0 ± 26 mmHg, respectively (p = 0.56). A Bland-Altman analysis revealed good agreement between both methods with a mean difference in TPG of 2.6 mmHg and a standard deviation of 19.3 mmHg. Both methods showed good correlation with r = 0.72 (p < 0.001). Conclusions: The presented CT-based method allows assessment of TPG in patients with aortic stenosis, extending the current capabilities of cardiac CT for diagnosis and treatment planning.