Coarse-Grained Simulation of mRNA-Loaded Lipid Nanoparticle Self-Assembly.

Ionizable lipid-containing lipid nanoparticles (LNPs) have enabled the delivery of RNA for a range of therapeutic applications. In order to optimize safe, targeted, and effective LNP-based RNA delivery platforms, an understanding of the role of composition and pH in their structural properties and self-assembly is crucial, yet there have been few computational studies of such phenomena. Here we present a coarse-grained model of ionizable lipid and mRNA-containing LNPs. Our model allows access to the large length- and time-scales necessary for LNP self-assembly and is mapped and parametrized with reference to all-atom structures and simulations of the corresponding components at compositions typical of LNPs used for mRNA delivery. Our simulations reveal insights into the dynamics of self-assembly of such mRNA-encapsulating LNPs, as well as the subsequent pH change-driven LNP morphology and release of mRNA.

Pediatric Trauma Care Standardization: A Statewide Survey of Trauma Providers and Program Managers.

INTRODUCTION: Rural-urban disparities in pediatric trauma outcomes are well documented. However, few studies examine how differences in setting and resources impact rural providers' approach to trauma. We sought to understand the provider experience in managing injured children across our state and assess the potential for standardization of care. METHODS: A statewide cross-sectional survey was distributed to trauma providers and program managers through the American College of Surgeons, the Oregon Medical Board lists, and the State Trauma Advisory Board. Topics included pediatric management processes, challenges, and transfer or admission procedures. Rural-urban commuting codes were used to categorize responses. RESULTS: Of the 350 individuals who sent the survey, 68 responded (response rate 19%), representing 67% of trauma-verified hospitals and 72% of Oregon counties. Fifty-six respondents (82%) care for injured children, with 58% practicing rurally and 22% at critical access hospitals. Rural providers experienced lower trauma volumes (<1 patient/month, 63% versus 0%, P < 0.001), more difficulties obtaining pediatric-appropriate material resources (44% versus 30%), and challenges caring for infants/toddlers (25% versus 17%). Despite 77% of rural providers stating that <10% of patients had multisystem injuries, they described using full-body CT often (41% versus 10%, P = 0.007). Transfer interruptions were common (93%), with 44% having cancelled a transfer. The majority supported admission/transfer (85%) and imaging (82%) protocols. CONCLUSIONS: Rural providers experience lower pediatric trauma volumes, greater material-resource issues, and discomfort with traumatically injured small children. Lack of care standardization may lead to reliance on full-body CT, and potentially complex/avoidable transfers. Adoption of standardized protocols could facilitate a state-wide collaborative approach to pediatric trauma management.

LLAMA: a robust and scalable machine learning pipeline for analysis of large scale 4D microscopy data: analysis of cell ruffles and filopodia.

BACKGROUND: With recent advances in microscopy, recordings of cell behaviour can result in terabyte-size datasets. The lattice light sheet microscope (LLSM) images cells at high speed and high 3D resolution, accumulating data at 100 frames/second over hours, presenting a major challenge for interrogating these datasets. The surfaces of vertebrate cells can rapidly deform to create projections that interact with the microenvironment. Such surface projections include spike-like filopodia and wave-like ruffles on the surface of macrophages as they engage in immune surveillance. LLSM imaging has provided new insights into the complex surface behaviours of immune cells, including revealing new types of ruffles. However, full use of these data requires systematic and quantitative analysis of thousands of projections over hundreds of time steps, and an effective system for analysis of individual structures at this scale requires efficient and robust methods with minimal user intervention. RESULTS: We present LLAMA, a platform to enable systematic analysis of terabyte-scale 4D microscopy datasets. We use a machine learning method for semantic segmentation, followed by a robust and configurable object separation and tracking algorithm, generating detailed object level statistics. Our system is designed to run on high-performance computing to achieve high throughput, with outputs suitable for visualisation and statistical analysis. Advanced visualisation is a key element of LLAMA: we provide a specialised tool which supports interactive quality control, optimisation, and output visualisation processes to complement the processing pipeline. LLAMA is demonstrated in an analysis of macrophage surface projections, in which it is used to i) discriminate ruffles induced by lipopolysaccharide (LPS) and macrophage colony stimulating factor (CSF-1) and ii) determine the autonomy of ruffle morphologies. CONCLUSIONS: LLAMA provides an effective open source tool for running a cell microscopy analysis pipeline based on semantic segmentation, object analysis and tracking. Detailed numerical and visual outputs enable effective statistical analysis, identifying distinct patterns of increased activity under the two interventions considered in our example analysis. Our system provides the capacity to screen large datasets for specific structural configurations. LLAMA identified distinct features of LPS and CSF-1 induced ruffles and it identified a continuity of behaviour between tent pole ruffling, wave-like ruffling and filopodia deployment.

Minimizing Variance in Gastroschisis Management Leads to Earlier Full Feeds in Delayed Closure.

BACKGROUND: Limited guidance exists regarding appropriate timing for feed initiation and advancement in gastroschisis. We hypothesized that implementation of a gastroschisis management protocol would allow for standardization of antibiotic and nutritional treatment for these patients. METHODS: We conducted a retrospective comparison of patients with simple gastroschisis at two pediatric hospitals before and after initiation of our gastroschisis care protocol. Complicated gastroschisis and early mortality were excluded. The control group extended from January 2012 to January 2014 and the protocol group from July 2014 to July 2016. Variables of interest included time to feed initiation, time to goal feeds, length of stay, and National Surgical Quality Improvement Program-defined complications. We performed a subgroup analysis for primary versus delayed gastroschisis closure. Statistical analyses, including F-tests for variance, were conducted in Prism. RESULTS: Forty-seven patients with simple gastroschisis were included (control = 22, protocol = 25). Protocol compliance was 76% with no increase in complication rates. There was no difference in length of stay or time from initiation to full feeds overall between the control and protocol groups. However, neonates who underwent delayed closure reached full feeds significantly earlier, averaging 9 d versus 15 d previously (P = 0.04). CONCLUSIONS: For infants undergoing delayed closure, the time to full feeds in this group now appears to match that of patients undergoing primary closure, indicating that delayed closure should not be a reason for slower advancement. Additional studies are needed to assess the impact of earlier full enteral nutrition on rare complications and rates of necrotizing enterocolitis.

Failure of primary closure predicts prolonged length of stay in gastroschisis patients.

PURPOSE: Current literature regarding outcomes of gastroschisis closure methods do not highlight differences in patients who successfully undergo primary closure with those who fail and require silo placement. We hypothesize that failure of primary closure has significant effects on clinical outcomes such as length of stay and time to enteral feeding. METHODS: We conducted a retrospective review between 2009 and 2018 of gastroschisis patients at a tertiary pediatric referral hospital. We compared patients successfully undergoing primary closure to patients who failed an initial primary closure attempt. Bivariate and multivariate linear regression models were used to assess the association of closure method on clinical outcomes. RESULTS: Sixty-eight neonates were included for analysis, with 44 patients who underwent primary closure and 24 who failed primary closure. On multivariate regression analysis, primary closure patients had shorter estimated time to starting and to full enteral feeds and decreased LOS as compared to those who failed primary closure. Two patients (4.44%) had complications related to primary closure. CONCLUSION: Patients able to undergo primary closure for gastroschisis were more likely to have a shorter length of stay, shorter time to enteral feeds, and use much fewer medical resources. Initial primary closure is a safe method for most patients.

Self-organisation after embryonic kidney dissociation is driven via selective adhesion of ureteric epithelial cells.

Human pluripotent stem cells, after directed differentiation in vitro, can spontaneously generate complex tissues via self-organisation of the component cells. Self-organisation can also reform embryonic organ structure after tissue disruption. It has previously been demonstrated that dissociated embryonic kidneys can recreate component epithelial and mesenchymal relationships sufficient to allow continued kidney morphogenesis. Here, we investigate the timing and underlying mechanisms driving self-organisation after dissociation of the embryonic kidney using time-lapse imaging, high-resolution confocal analyses and mathematical modelling. Organotypic self-organisation sufficient for nephron initiation was observed within a 24 h period. This involved cell movement, with structure emerging after the clustering of ureteric epithelial cells, a process consistent with models of random cell movement with preferential cell adhesion. Ureteric epithelialisation rapidly followed the formation of ureteric cell clusters with the reformation of nephron-forming niches representing a later event. Disruption of P-cadherin interactions was seen to impair this ureteric epithelial cell clustering without affecting epithelial maturation. This understanding could facilitate improved regulation of patterning within organoids and facilitate kidney engineering approaches guided by cell-cell self-organisation.

Branching morphogenesis in the developing kidney is governed by rules that pattern the ureteric tree.

Metanephric kidney development is orchestrated by the iterative branching morphogenesis of the ureteric bud. We describe an underlying patterning associated with the ramification of this structure and show that this pattern is conserved between developing kidneys, in different parts of the organ and across developmental time. This regularity is associated with a highly reproducible branching asymmetry that is consistent with locally operative growth mechanisms. We then develop a class of tip state models to represent elaboration of the ureteric tree and describe rules for 'half-delay' branching morphogenesis that describe almost perfectly the patterning of this structure. Spatial analysis suggests that the observed asymmetry may arise from mutual suppression of bifurcation, but not extension, between the growing ureteric tips, and demonstrates that disruption of patterning occurs in mouse mutants in which the distribution of tips on the surface of the kidney is altered. These findings demonstrate that kidney development occurs by way of a highly conserved reiterative pattern of asymmetric bifurcation that is governed by intrinsic and locally operative mechanisms.

Routine Chest Radiographs in Children After Image-Guided Central Lines Offer Little Diagnostic Value.

BACKGROUND: The aim of this study was to investigate the utility of postoperative chest radiograph (CXR) after image-guided central venous line (CVL) placement in children. METHODS: A retrospective review was conducted of all tunneled CVLs placed at two pediatric institutions from 2010 to 2017. A subgroup analysis comparing a clinically driven approach to postoperative imaging against routine imaging was performed. RESULTS: During the study period, 1080 lines were placed in 915 patients. There were 892 postoperative CXRs (82.6%). An abnormality was seen on 40 radiographs (4.5%, n = 891), with 16 false-positive (1.3%) and 5 false-negative (0.6%) CXRs. The sensitivity and specificity of CXR to identify complications requiring intervention were 50.0% (95% confidence interval [95% CI], 10.0-90.0) and 95.8% (95% CI, 94.5-97.1), respectively. Positive predictive value of CXR was 7.5% (95% CI, 0-15.7) with a negative predictive value of 99.6% (95% CI, 99.2-100). A clinically driven approach to postoperative imaging was associated with 41% decrease in CXR (P < 0.001) without increased incidence of missed complications. Only three complications requiring intervention (0.3%) were suspected on postoperative CXR alone, and all of those were symptomatic before intervention. CONCLUSIONS: Routine postoperative CXR offers minimal value in identifying technical complications requiring intervention after image-guided CVL placement in asymptomatic children. We recommend abandoning this practice in favor of a clinical symptom-driven approach to postoperative imaging.

A Natural History of Gastrojejunostomy Tubes in Children.

BACKGROUND: Gastrojejunostomy (GJ) tubes are frequently used to provide nutrition in patients who do not tolerate gastric feeding. Despite their widespread use, there is little literature on the lifespan of GJ tubes, reasons for failure, and recommendations for optimal techniques and timing of replacement. We aimed to evaluate the natural history of GJ tubes in pediatric patients. MATERIALS AND METHODS: We reviewed all pediatric patients who underwent GJ tube placement or exchange at our institution from January 2012 to July 2018. Demographic data, time, and indication for replacement or removal of GJ tubes were collected. End points were permanent removal of GJ tube or mortality. RESULTS: Seventy-nine patients underwent 205 GJ tube procedures with a median of 2 GJ tubes per patient. Median GJ tube lifespan was 98 d (interquartile range = 54-166). The two most common indications for tube exchange were structural or mechanical problems (43.1%) and GJ tube dislodgement (34.6%). Although most GJ tube exchanges (66%) were performed under general anesthesia or with moderate sedation, 34% of exchanges were done without sedation. During the study period, 12 patients (15.2%) died from their primary disease, nine patients (11.4%) required subsequent fundoplication, one (1.3%) underwent a jejunostomy, and 23 (29.1%) progressed to gastric feeds without fundoplication at a median time of 208 d. CONCLUSIONS: GJ tubes offer a safe and effective feeding option in patients intolerant of gastric feeding. GJ tubes fail most commonly from intrinsic structural or mechanical issues, and many patients ultimately tolerate gastric feeds without need for further intervention. Exchange of tubes without anesthesia is a viable option.

Significant practice variability exists in the prevention of venous thromboembolism in injured children: results from a joint survey of the Pediatric Trauma Society and the Trauma Center Association of America.

BACKGROUND/PURPOSE: The purpose of this study was to characterize current practices to prevent venous thromboembolism (VTE) in children and measure adherence to recent joint consensus guidelines from the Pediatric Trauma Society and Eastern Association for the Surgery of Trauma (PTS/EAST). METHODS: An 18-question survey was sent to the membership of PTS and the Trauma Center Association of American. Responses were compared with Chi-square test. RESULTS: One hundred twenty-nine members completed the survey. Most respondents were from academic (84.5%), Level 1 pediatric (62.0%) trauma centers. Criteria for VTE prophylaxis varied between hospitals with freestanding pediatric trauma centers significantly more likely to stratify children by risk factors than adult trauma centers (p = 0.020). While awareness of PTS/EAST guidelines (58.7% overall) was not statistically different between hospital types (44% freestanding adult, 52% freestanding pediatric, 71% combined adult pediatric, p = 0.131), self-reported adherence to these guidelines was uniformly low at 37.2% for all respondents. Lastly, in three clinical scenarios, respondents chose VTE screening and prophylaxis plans in accordance with a prospective application of PTS/EAST guidelines 55.0% correctly. CONCLUSION: Currently no consensus regarding the prevention of VTE in pediatric trauma exists. Prospective application of PTS/EAST guidelines has been limited, likely due to poor quality of evidence and a reliance on post-injury metrics. Results of this survey suggest that further investigation is needed to more clearly define the risk of VTE in children, evaluate, and prospectively validate alternative scoring systems for VTE prevention in injured children. LEVEL OF EVIDENCE: N/A-Survey.

Pediatric trauma venous thromboembolism prediction algorithm outperforms current anticoagulation prophylaxis guidelines: a pilot study.

PURPOSE: Venous thromboembolism (VTE) in injured children is rare, but sequelae can be morbid and life-threatening. Recent trauma society guidelines suggesting that all children over 15 years old should receive thromboprophylaxis may result in overtreatment. We sought to evaluate the efficacy of a previously published VTE prediction algorithm and compare it to current recommendations. METHODS: Two institutional trauma registries were queried for all pediatric (age < 18 years) patients admitted from 2007 to 2018. Clinical data were applied to the algorithm and the area under the receiver operating characteristic (AUROC) curve was calculated to test algorithm efficacy. RESULTS: A retrospective review identified 8271 patients with 30 episodes of VTE (0.36%). The VTE prediction algorithm classified 51 (0.6%) as high risk (> 5% risk), 322 (3.9%) as moderate risk (1-5% risk) and 7898 (95.5%) as low risk (< 1% risk). AUROC was 0.93 (95% CI 0.89-0.97). In our population, prophylaxis of the 'moderate-' and 'high-risk' cohorts would outperform the sensitivity (60% vs. 53%) and specificity (96% vs. 77%) of current guidelines while anticoagulating substantially fewer patients (373 vs. 1935, p < 0.001). CONCLUSION: A VTE prediction algorithm using clinical variables can identify injured children at risk for venous thromboembolic disease with more discrimination than current guidelines. Prospective studies are needed to investigate the validity of this model. LEVEL OF EVIDENCE: III-Clinical decision rule evaluated in a single population.

RAZA: A Rapid 3D z-crossings algorithm to segment electron tomograms and extract organelles and macromolecules.

Resolving the 3D architecture of cells to atomic resolution is one of the most ambitious challenges of cellular and structural biology. Central to this process is the ability to automate tomogram segmentation to identify sub-cellular components, facilitate molecular docking and annotate detected objects with associated metadata. Here we demonstrate that RAZA (Rapid 3D z-crossings algorithm) provides a robust, accurate, intuitive, fast, and generally applicable segmentation algorithm capable of detecting organelles, membranes, macromolecular assemblies and extrinsic membrane protein domains. RAZA defines each continuous contour within a tomogram as a discrete object and extracts a set of 3D structural fingerprints (major, middle and minor axes, surface area and volume), enabling selective, semi-automated segmentation and object extraction. RAZA takes advantage of the fact that the underlying algorithm is a true 3D edge detector, allowing the axes of a detected object to be defined, independent of its random orientation within a cellular tomogram. The selectivity of object segmentation and extraction can be controlled by specifying a user-defined detection tolerance threshold for each fingerprint parameter, within which segmented objects must fall and/or by altering the number of search parameters, to define morphologically similar structures. We demonstrate the capability of RAZA to selectively extract subgroups of organelles (mitochondria) and macromolecular assemblies (ribosomes) from cellular tomograms. Furthermore, the ability of RAZA to define objects and their contours, provides a basis for molecular docking and rapid tomogram annotation.

Cap mesenchyme cell swarming during kidney development is influenced by attraction, repulsion, and adhesion to the ureteric tip.

Morphogenesis of the mammalian kidney requires reciprocal interactions between two cellular domains at the periphery of the developing organ: the tips of the epithelial ureteric tree and adjacent regions of cap mesenchyme. While the presence of the cap mesenchyme is essential for ureteric branching, how it is specifically maintained at the tips is unclear. Using ex vivo timelapse imaging we show that cells of the cap mesenchyme are highly motile. Individual cap mesenchyme cells move within and between cap domains. They also attach and detach from the ureteric tip across time. Timelapse tracks collected for >800 cells showed evidence that this movement was largely stochastic, with cell autonomous migration influenced by opposing attractive, repulsive and cell adhesion cues. The resulting swarming behaviour maintains a distinct cap mesenchyme domain while facilitating dynamic remodelling in response to underlying changes in the tip.

Functional characterization of retromer in GLUT4 storage vesicle formation and adipocyte differentiation.

Insulin-stimulated translocation of glucose transporter 4 (GLUT4) storage vesicles (GSVs), the specialized intracellular compartments within mature adipocytes, to the plasma membrane (PM) is a fundamental cellular process for maintaining glucose homeostasis. Using 2 independent adipocyte cell line models, human primary Simpson-Golabi-Behmel syndrome and mouse 3T3-L1 fibroblast cell lines, we demonstrate that the endosome-associated protein-sorting complex retromer colocalizes with GLUT4 on the GSVs by confocal microscopy in mature adipocytes. By use of both confocal microscopy and differential ultracentrifugation techniques, retromer is redistributed to the PM of mature adipocytes upon insulin stimulation. Furthermore, stable knockdown of the retromer subunit-vacuolar protein-sorting 35, or the retromer-associated protein sorting nexin 27, by lentivirus-delivered small hairpin RNA impaired the adipogenesis process when compared to nonsilence control. The knockdown of retromer decreased peroxisome proliferator activated receptor γ expression during differentiation, generating adipocytes with decreased levels of GSVs, lipid droplet accumulation, and insulin-stimulated glucose uptake. In conclusion, our study demonstrates a role for retromer in the GSV formation and adipogenesis.

Rapid Expansion of Human Epithelial Stem Cells Suitable for Airway Tissue Engineering.

RATIONALE: Stem cell-based tracheal replacement represents an emerging therapeutic option for patients with otherwise untreatable airway diseases including long-segment congenital tracheal stenosis and upper airway tumors. Clinical experience demonstrates that restoration of mucociliary clearance in the lungs after transplantation of tissue-engineered grafts is critical, with preclinical studies showing that seeding scaffolds with autologous mucosa improves regeneration. High epithelial cell-seeding densities are required in regenerative medicine, and existing techniques are inadequate to achieve coverage of clinically suitable grafts. OBJECTIVES: To define a scalable cell culture system to deliver airway epithelium to clinical grafts. METHODS: Human respiratory epithelial cells derived from endobronchial biopsies were cultured using a combination of mitotically inactivated fibroblasts and Rho-associated protein kinase (ROCK) inhibition using Y-27632 (3T3+Y). Cells were analyzed by immunofluorescence, quantitative polymerase chain reaction, and flow cytometry to assess airway stem cell marker expression. Karyotyping and multiplex ligation-dependent probe amplification were performed to assess cell safety. Differentiation capacity was tested in three-dimensional tracheospheres, organotypic cultures, air-liquid interface cultures, and an in vivo tracheal xenograft model. Ciliary function was assessed in air-liquid interface cultures. MEASUREMENTS AND MAIN RESULTS: 3T3-J2 feeder cells and ROCK inhibition allowed rapid expansion of airway basal cells. These cells were capable of multipotent differentiation in vitro, generating both ciliated and goblet cell lineages. Cilia were functional with normal beat frequency and pattern. Cultured cells repopulated tracheal scaffolds in a heterotopic transplantation xenograft model. CONCLUSIONS: Our method generates large numbers of functional airway basal epithelial cells with the efficiency demanded by clinical transplantation, suggesting its suitability for use in tracheal reconstruction.

The Vps35 D620N mutation linked to Parkinson's disease disrupts the cargo sorting function of retromer.

The retromer is a trimeric cargo-recognition protein complex composed of Vps26, Vps29 and Vps35 associated with protein trafficking within endosomes. Recently, a pathogenic point mutation within the Vps35 subunit (D620N) was linked to the manifestation of Parkinson's disease (PD). Here, we investigated details underlying the molecular mechanism by which the D620N mutation in Vps35 modulates retromer function, including examination of retromer's subcellular localization and its capacity to sort cargo. We show that expression of the PD-linked Vps35 D620N mutant redistributes retromer-positive endosomes to a perinuclear subcellular localization and that these endosomes are enlarged in both model cell lines and fibroblasts isolated from a PD patient. Vps35 D620N is correctly folded and binds Vps29 and Vps26A with the same affinity as wild-type Vps35. While PD-linked point mutant Vps35 D620N interacts with the cation-independent mannose-6-phosphate receptor (CI-M6PR), a known retromer cargo, we find that its expression disrupts the trafficking of cathepsin D, a CI-M6PR ligand and protease responsible for degradation of α-synuclein, a causative agent of PD. In summary, we find that the expression of Vps35 D620N leads to endosomal alterations and trafficking defects that may partly explain its action in PD.

A cost and outcome analysis of pediatric single-incision appendectomy.

BACKGROUND: For appendicitis, single-incision laparoscopic appendectomy (SIA) has been proposed as an alternative to 3-port appendectomy (3PA). However, there remains controversy regarding outcomes and cost of SIA. We sought to review our experience with these two techniques to identify differences in these factors. MATERIALS AND METHODS: The charts of children (0-17 y) who underwent appendectomy at a tertiary pediatric hospital from 2011-2014 were retrospectively reviewed. Appendectomy was either performed through traditional 3PA or SIA (laparoscopically assisted via externalization through an umbilical incision). Demographic data including age, body mass index, comorbidities, and gender were examined. Information on perforation, operative time and cost, length of stay, and infectious complications for both SIA and 3PA was identified. Data were analyzed using student t tests and chi square analysis. RESULTS: A total of 337 patients underwent appendectomy (141 SIA and 197 3PA), 35.6% of whom (40 SIA, 80 3PA) had perforated appendicitis. For nonperforated appendicitis, SIA had significantly shorter operative times, decreased operative costs, and length of stay. However, these differences were not found for perforated appendicitis. Regardless of appendicitis severity, there was no difference in rates of wound infection, abscess, or readmission between the two techniques. CONCLUSIONS: Our study suggests that SIA is a faster, more cost effective alternative than 3PA for acute appendicitis. SIA did not result in increased infection rates for acute or perforated appendicitis and can be considered an equivalent alternative to 3PA in the surgical management of appendicitis.

Comparing and distinguishing the structure of biological branching.

Bifurcating developmental branching morphogenesis gives rise to complex organs such as the lung and the ureteric tree of the kidney. However, a few quantitative methods or tools exist to compare and distinguish, at a structural level, the critical features of these important biological systems. Here we develop novel graph alignment techniques to quantify the structural differences of rooted bifurcating trees and demonstrate their application in the analysis of developing kidneys from in normal and mutant mice. We have developed two graph based metrics: graph discordance, which measures how well the graphs representing the branching structures of distinct trees graphs can be aligned or overlayed; and graph inclusion, which measures the degree of containment of a tree graph within another. To demonstrate the application of these approaches we first benchmark the discordance metric on a data set of 32 normal and 28Tgfß(+/-) mutant mouse ureteric trees. We find that the discordance metric better distinguishes control and mutant mouse kidneys than alternative metrics based on graph size and fingerprints - the distribution of tip depths. Using this metric we then show that the structure of the mutant trees follows the same pattern as the normal kidneys, but undergo a major delay in elaboration at later stages. Analysis of both controls and mutants using the inclusion metric gives strong support to the hypothesis that ureteric tree growth is stereotypic. Additionally, we present a new generalised multi-tree alignment algorithm that minimises the sum of pairwise graph discordance and which can be used to generate maximum consensus trees that represent the archetype for fixed developmental stages. These tools represent an advance in the analysis and quantification of branching patterns and will be invaluable in gaining a deeper understanding of the mechanisms that drive development. All code is being made available with documentation and example data with this publication.

Inhibition of the PtdIns(5) kinase PIKfyve disrupts intracellular replication of Salmonella.

3-phosphorylated phosphoinositides (3-PtdIns) orchestrate endocytic trafficking pathways exploited by intracellular pathogens such as Salmonella to gain entry into the cell. To infect the host, Salmonellae subvert its normal macropinocytic activity, manipulating the process to generate an intracellular replicative niche. Disruption of the PtdIns(5) kinase, PIKfyve, be it by interfering mutant, siRNA-mediated knockdown or pharmacological means, inhibits the intracellular replication of Salmonella enterica serovar typhimurium in epithelial cells. Monitoring the dynamics of macropinocytosis by time-lapse 3D (4D) videomicroscopy revealed a new and essential role for PI(3,5)P(2) in macropinosome-late endosome/lysosome fusion, which is distinct from that of the small GTPase Rab7. This PI(3,5)P(2)-dependent step is required for the proper maturation of the Salmonella-containing vacuole (SCV) through the formation of Salmonella-induced filaments (SIFs) and for the engagement of the Salmonella pathogenicity island 2-encoded type 3 secretion system (SPI2-T3SS). Finally, although inhibition of PIKfyve in macrophages did inhibit Salmonella replication, it also appears to disrupt the macrophage's bactericidal response.

On linear models and parameter identifiability in experimental biological systems.

A key problem in the biological sciences is to be able to reliably estimate model parameters from experimental data. This is the well-known problem of parameter identifiability. Here, methods are developed for biologists and other modelers to design optimal experiments to ensure parameter identifiability at a structural level. The main results of the paper are to provide a general methodology for extracting parameters of linear models from an experimentally measured scalar function - the transfer function - and a framework for the identifiability analysis of complex model structures using linked models. Linked models are composed by letting the output of one model become the input to another model which is then experimentally measured. The linked model framework is shown to be applicable to designing experiments to identify the measured sub-model and recover the input from the unmeasured sub-model, even in cases that the unmeasured sub-model is not identifiable. Applications for a set of common model features are demonstrated, and the results combined in an example application to a real-world experimental system. These applications emphasize the insight into answering "where to measure" and "which experimental scheme" questions provided by both the parameter extraction methodology and the linked model framework. The aim is to demonstrate the tools' usefulness in guiding experimental design to maximize parameter information obtained, based on the model structure.