KinView: A visual comparative sequence analysis tool for integrated kinome research

Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats. Here, we present the Multiple Sequence Alignment Ontology (MSAOnt), which represents a profile or consensus alignment in an ontological format. Subsets of the alignment are easily selected through the SPARQL Protocol and RDF Query Language for downstream statistical analysis or visualization. We have also created the Kinome Viewer (KinView), an interactive integrative visualization that places eukaryotic protein kinase cancer variants in the context of natural sequence variation and experimentally determined post-translational modifications, which play central roles in the regulation of cellular signaling pathways. Using KinView, we identified differential phosphorylation patterns between tyrosine and serine/threonine kinases in the activation segment, a major kinase regulatory region that is often mutated in proliferative diseases. We discuss cancer variants that disrupt phosphorylation sites in the activation segment, and show how KinView can be used as a comparative tool to identify differences and similarities in natural variation, cancer variants and post-translational modifications between kinase groups, families and subfamilies. Based on KinView comparisons, we identify and experimentally characterize a regulatory tyrosine (Y177PLK4) in the PLK4 C-terminal activation segment region termed the P+1 loop. To further demonstrate the application of KinView in hypothesis generation and testing, we formulate and validate a hypothesis explaining a novel predicted loss-of-function variant (D523NPKCβ) in the regulatory spine of PKCβ, a recently identified tumor suppressor kinase. KinView provides a novel, extensible interface for performing comparative analyses between subsets of kinases and for integrating multiple types of residue specific annotations in user friendly formats

Cigarette Smoke-Related Hydroquinone Dysregulates MCP-1, VEGF and PEDF Expression in Retinal Pigment Epithelium in Vitro and in Vivo

Age-related macular degeneration (AMD) is the leading cause of legal blindness in the elderly population. Debris (termed drusen) below the retinal pigment epithelium (RPE) have been recognized as a risk factor for dry AMD and its progression to wet AMD, which is characterized by choroidal neovascularization (CNV). The underlying mechanism of how drusen might elicit CNV remains undefined. Cigarette smoking, oxidative damage to the RPE and inflammation are postulated to be involved in the pathophysiology of the disease. To better understand the cellular mechanism(s) linking oxidative stress and inflammation to AMD, we examined the expression of pro-inflammatory monocyte chemoattractant protein-1 (MCP-1), pro-angiogenic vascular endothelial growth factor (VEGF) and anti-angiogenic pigment epithelial derived factor (PEDF) in RPE from smoker patients with AMD. We also evaluated the effects of hydroquinone (HQ), a major pro-oxidant in cigarette smoke on MCP-1, VEGF and PEDF expression in cultured ARPE-19 cells and RPE/choroids from C57BL/6 mice.MCP-1, VEGF and PEDF expression was examined by real-time PCR, Western blot, and ELISA. Low levels of MCP-1 protein were detected in RPE from AMD smoker patients relative to controls. Both MCP-1 mRNA and protein were downregulated in ARPE-19 cells and RPE/choroids from C57BL/6 mice after 5 days and 3 weeks of exposure to HQ-induced oxidative injury. VEGF protein expression was increased and PEDF protein expression was decreased in RPE from smoker patients with AMD versus controls resulting in increased VEGF/PEDF ratio. Treatment with HQ for 5 days and 3 weeks increased the VEGF/PEDF ratio in vitro and in vivo.We propose that impaired RPE-derived MCP-1-mediated scavenging macrophages recruitment and phagocytosis might lead to incomplete clearance of proinflammatory debris and infiltration of proangiogenic macrophages which along with increased VEGF/PEDF ratio favoring angiogenesis might promote drusen accumulation and progression to CNV in smoker patients with dry AMD

Doyne lecture 2016:intraocular health and the many faces of inflammation

Dogma for reasons of immune privilege including sequestration (sic) of ocular antigen, lack of lymphatic and immune competent cells in the vital tissues of the eye has long evaporated. Maintaining tissue and cellular health to preserve vision requires active immune responses to prevent damage and respond to danger. A priori the eye must contain immune competent cells, undergo immune surveillance to ensure homoeostasis as well as an ability to promote inflammation. By interrogating immune responses in non-infectious uveitis and compare with age-related macular degeneration (AMD), new concepts of intraocular immune health emerge. The role of macrophage polarisation in the two disorders is a tractable start. TNF-alpha regulation of macrophage responses in uveitis has a pivotal role, supported via experimental evidence and validated by recent trial data. Contrast this with the slow, insidious degeneration in atrophic AMD or in neovasular AMD, with the compelling genetic association with innate immunity and complement, highlights an ability to attenuate pathogenic immune responses and despite known inflammasome activation. Yolk sac-derived microglia maintains tissue immune health. The result of immune cell activation is environmentally dependent, for example, on retinal cell bioenergetics status, autophagy and oxidative stress, and alterations that skew interaction between macrophages and retinal pigment epithelium (RPE). For example, dead RPE eliciting macrophage VEGF secretion but exogenous IL-4 liberates an anti-angiogenic macrophage sFLT-1 response. Impaired autophagy or oxidative stress drives inflammasome activation, increases cytotoxicity, and accentuation of neovascular responses, yet exogenous inflammasome-derived cytokines, such as IL-18 and IL-33, attenuate responses

Improving predictions of swash dynamics in XBeach: The role of groupiness and incident-band runup

In predicting storm impacts on sandy coasts, possibly with structures, accurate runup and overtopping simulation is an important aspect. Recent investigations (Stockdon et al., 2014; Palmsten and Splinter, 2016) show that despite accurate predictions of the morphodynamics of dissipative sandy beaches, the XBeach model (Roelvink et al., 2009) does not correctly simulate the individual contributions of set-up, and infragravity and incident-band swash to the wave run-up. In this paper we describe an improved numerical scheme and a different way of simulating the propagation of directionally-spread short wave groups in XBeach to better predict the groupiness of the short waves and the resulting infragravity waves. The new approach is tested against field measurements from the DELILAH campaign at Duck, NC, and against video-derived runup measurements at Praia de Faro, a relatively steep sandy beach. Compared to the empirical fit by Vousdoukas et al. (2012) the XBeach model performs much better for more extreme wave conditions, which are severely underestimated by existing empirical formulations. For relatively steep beaches incident-band swash cannot be neglected and a wave-resolving simulation mode is required. Therefore in this paper we also test the non-hydrostatic, wave-resolving model within XBeach for runup and overtopping against three datasets. Results for a high-quality flume test show non-hydrostatic XBeach predicts the run-up height with good accuracy (maximum deviation 15%). A case with a very shallow foreshore typical for the Belgian coast at Wenduine was compared against detailed measurements. Overall the model shows correct behavior for this case. Finally, the model is tested against a large number (551) of physical model tests of overtopping from the CLASH database. For relatively high overtopping discharges the non-hydrostatic XBeach performs quite well, with increasing accuracy for increasing overtopping rates. However, for relatively low overtopping rates of less than 10–20 l/m/s, the model systematically underestimates measured overtopping rates

Treatment chamber with turbulent flow for liquid food pasteurization

The pulsed electric field (PEF) is a suitable technological option for pasteurization but the laminar flow inside the treatment chamber is a reason for treatment inhomogeneity in most of the treatment chambers. This work was performed to measure the efficiency of PEF treatment of the liquid food by using the helical sterilization chamber. The helical shape shows significant advantages during the flow of fruit juices by disrupting the laminar flow inside the treatment zone. Thus, it provides a uniform electric field to the whole treated sample with little temperature rise and longer exposure time. The effectiveness of the chamber was determined experimentally and simulated using COMSOL Multiphysics. Three different lengths of the chamber at 30 kV/cm were used to sterilize the liquid samples of pineapple, mango, and coconut milk. The treated samples were assessed by monitoring the chemical changes and log reduction. Helical chamber length of 30 cm exhibited inactivation effects of 7.5, 5.7, and 5.55-CFU/mL for the treated samples of mango, pineapple, and coconut milk, respectively. This study provides new insight into industrial set up with multiple helical chambers in a continuous flow

The Impact of storm-induced breaches on barrier coast systems subject to climate change - A stochastic modelling study

Storms can have devastating impacts on barrier coasts causing coastal erosion, partial inundation, and possibly the breaching of barrier islands. The breaching of barrier islands provides a mechanism for the creation of new tidal inlets that connect the backbarrier basin (or lagoon) and the outer sea. As a new tidal inlet affects both the basin and the hydrodynamics of existing inlets, it is important to understand why an initial breach either closes or may evolve into a new tidal inlet. To this end, we performed a Monte Carlo analysis using an idealized model capable of simulating the long-term morphological evolution of multiple tidal inlets connected to a single backbarrier basin. To do so required the creation of a stochastic shell, as a new element around this existing barrier coast model. Our results demonstrate that barrier coast systems tend towards an equilibrium value for the number of inlets per kilometer of barrier coast and total inlet cross section. This even holds with the continuous stochastic forcing of storm-induced breaches. This finding implies that if a new breach opens in a coast that is already in equilibrium, existing inlets will shrink and may close if the new breach remains open. Furthermore, we find that climate-driven changes in storm frequency will modify the timescales in which barrier coasts reach their equilibrium state. Finally, we find that the distance between a new breach and its nearest neighbor is more important for its survival than the size of the breach or the degree of saturation of the barrier coast

Diagnostic value of physical examination for topographic detection of infratentorial lesions in patients with cerebrovascular syndromes

Background and Objective: The Detection of neurologic signs for topographical disorders in central nerves system can prevent unnecessary neuroimaging techniques such as MRI. This study was performed to determine the diagnostic value of physical examination for topographic detection of infratentorial lesions in patients with cerebrovascular syndromes. Methods: This descriptive study was done on 200 patients with cerebrovascular syndrome in Qaem Hospital in Mashhad, north-east Iran during 2011. Regarding to topographic physical examination, sensitivity, specificity, positive and negative predictive value and accuracy of signs of syndromes were compared to MRI as gold standard method. Results: The accuracy of tetraparesis and crossed syndromes for localization of brain lesion in brainstem was 79% and 83%, respectively. The accuracy of hemiataxia for localization of brain lesion in ipsilateral cerebellar hemisphere was 98%. The accuracy of Wallenberg syndrome for localization of brain lesion in posterolateral medulla was 98%. Conclusion: Using clinical neuro-examination skills and accurate topographic physical examination can prevent unwanted MRI technique for the diagnoses of cerebrovascular syndromes