A combinatorial approach of Proteomics and Systems Biology in unravelling the mechanisms of acute kidney injury (AKI): involvement of NMDA receptor GRIN1 in murine AKI

BACKGROUND: Acute kidney injury (AKI) is a frequent condition in hospitalised patients undergoing major surgery or the critically ill and is associated with increased mortality. Based on the volume of the published literature addressing this condition, reporting both supporting as well as conflicting molecular evidence, it is apparent that a comprehensive analysis strategy is required to understand and fully delineate molecular events and pathways which can be used to describe disease induction and progression as well as lead to a more targeted approach in intervention therapies.<p></p> RESULTS: We used a Systems Biology approach coupled with a de-novo high-resolution proteomic analysis of kidney cortex samples from a mouse model of folic acid-induced AKI (12 animals in total) and show comprehensive mapping of signalling cascades, gene activation events and metabolite interference by mapping high-resolution proteomic datasets onto a de-novo hypothesis-free dataspace. The findings support the involvement of the glutamatergic signalling system in AKI, induced by over-activation of the N-methyl-D-aspartate (NMDA)-receptor leading to apoptosis and necrosis by Ca2+-influx, calpain and caspase activation, and co-occurring reactive oxygen species (ROS) production to DNA fragmentation and NAD-rundown. The specific over-activation of the NMDA receptor may be triggered by the p53-induced protein kinase Dapk1, which is a known non-reversible cell death inducer in a neurological context. The pathway mapping is consistent with the involvement of the Renin-Angiotensin Aldosterone System (RAAS), corticoid and TNFalpha signalling, leading to ROS production and gene activation through NFkappaB, PPARgamma, SMAD and HIF1alpha trans-activation, as well as p53 signalling cascade activation. Key elements of the RAAS-glutamatergic axis were assembled as a novel hypothetical pathway and validated by immunohistochemistry.<p></p> CONCLUSIONS: This study shows to our knowledge for the first time in a molecular signal transduction pathway map how AKI is induced, progresses through specific signalling cascades that may lead to end-effects such as apoptosis and necrosis by uncoupling of the NMDA receptor. Our results can potentially pave the way for a targeted pharmacological intervention in disease progression or induction.<p></p&gt

Urine peptidomic biomarkers for diagnosis of patients with systematic lupus erythematosus

Background: Systematic lupus erythematosus (SLE) is characterized with various complications which can cause serious organ damage in the human body. Despite the significant improvements in disease management of SLE patients, the non-invasive diagnosis is entirely missing. In this study, we used urinary peptidomic biomarkers for early diagnosis of disease onset to improve patient risk stratification, vital for effective drug treatment. Methods: Urine samples from patients with SLE, lupus nephritis (LN) and healthy controls (HCs) were analyzed using capillary electrophoresis coupled to mass spectrometry (CE-MS) for state-of-the-art biomarker discovery. Results: A biomarker panel made up of 65 urinary peptides was developed that accurately discriminated SLE without renal involvement from HC patients. The performance of the SLE-specific panel was validated in a multicentric independent cohort consisting of patients without SLE but with different renal disease and LN. This resulted in an area under the receiver operating characteristic (ROC) curve (AUC) of 0.80 (p < 0.0001, 95% confidence interval (CI) 0.65–0.90) corresponding to a sensitivity and a specificity of 83% and 73%, respectively. Based on the end terminal amino acid sequences of the biomarker peptides, an in silico methodology was used to identify the proteases that were up or down-regulated. This identified matrix metalloproteinases (MMPs) as being mainly responsible for the peptides fragmentation. Conclusions: A laboratory-based urine test was successfully established for early diagnosis of SLE patients. Our approach determined the activity of several proteases and provided novel molecular information that could potentially influence treatment efficacy

The detection of tightly closed flaws by nondestructive testing (NDT) methods

Liquid penetrant, ultrasonic, eddy current and X-radiographic techniques were optimized and applied to the evaluation of 2219-T87 aluminum alloy test specimens in integrally stiffened panel, and weld panel configurations. Fatigue cracks in integrally stiffened panels, lack-of-fusion in weld panels, and fatigue cracks in weld panels were the flaw types used for evaluation. A 2319 aluminum alloy weld filler rod was used for all welding to produce the test specimens. Forty seven integrally stiffened panels containing a total of 146 fatigue cracks, ninety three lack-of-penetration (LOP) specimens containing a total of 239 LOP flaws, and one-hundred seventeen welded specimens containing a total of 293 fatigue cracks were evaluated. Nondestructive test detection reliability enhancement was evaluated during separate inspection sequences in the specimens in the 'as-machined or as-welded', post etched and post proof loaded conditions. Results of the nondestructive test evaluations were compared to the actual flaw size obtained by measurement of the fracture specimens after completing all inspection sequences. Inspection data were then analyzed to provide a statistical basis for determining the flaw detection reliability

Psyllid Resistance in the Leucaena Genus

Leucaena species varied from highly susceptible to highly resistant in their response to the psyllid insect (Heteropsylla cubana) at 2 sites, a high psyllid environment at Brisbane, Australia and a moderate psyllid environment at Los Baños, Philippines. L. leucocephala was the most susceptible species. There was considerable intraspecific variation in psyllid resistance within L. collinsii, L. diversifolia and L. pallida. Plant reponse to psyllid challenge between environments was highly correlated but not linear. The higher psyllid challenge environment at Brisbane permitted greater discrimination between species and fewer Leucaena species were ranked as psyllid resistant

FluxSimulator: An R Package to Simulate Isotopomer Distributions in Metabolic Networks

The representation of biochemical knowledge in terms of fluxes (transformation rates) in a metabolic network is often a crucial step in the development of new drugs and efficient bioreactors. Mass spectroscopy (MS) and nuclear magnetic resonance spectroscopy (NMRS) in combination with ^13C labeled substrates are experimental techniques resulting in data that may be used to quantify fluxes in the metabolic network underlying a process. The massive amount of data generated by spectroscopic experiments increasingly requires software which models the dynamics of the underlying biological system. In this work we present an approach to handle isotopomer distributions in metabolic networks using an object-oriented programming approach, implemented using S4 classes in R. The developed package is called FluxSimulator and provides a user friendly interface to specify the topological information of the metabolic network as well as carbon atom transitions in plain text files. The package automatically derives the mathematical representation of the formulated network, and assembles a set of ordinary differential equations (ODEs) describing the change of each isotopomer pool over time. These ODEs are subsequently solved numerically. In a case study FluxSimulator was applied to an example network. Our results indicate that the package is able to reproduce exact changes in isotopomer compositions of the metabolite pools over time at given flux rates.

Detection of tightly closed flaws by nondestructive testing (NDT) methods in steel and titanium

X-radiographic, liquid penetrant, ultrasonic, eddy current and magnetic particle testing techniques were optimized and applied to the evaluation of 4340 steel (180 KSI-UTS) and 6Al-4V titanium (STA) alloy specimens. Sixty steel specimens containing a total of 176 fatigue cracks and 60 titanium specimens containing a total of 135 fatigue cracks were evaluated. The cracks ranged in length from .043 cm (0.017 inch) to 1.02 cm (.400 inch) and in depth from .005 cm (.002 inch) to .239 cm (.094 inch) for steel specimens. Lengths ranged from .048 cm (0.019 inch) to 1.03 cm (.407 inch) and depths from 0.010 cm (.004 inch) to .261 cm (0.103 inch) for titanium specimens. Specimen thicknesses were nominally .152 cm (0.060 inch) and 0.635 cm (0.250 inch) and surface finishes were nominally 125 rms. Specimens were evaluated in the "as machined" surface condition, after etch surface and after proof loading in a randomized inspection sequence

Social Media and Professional School Counselors: Ethical and Legal Considerations

The use of social media continues to expand in prevalence and is a medium of communication for individuals of all ages. Schools are using social media to engage their stakeholders at increasing rates. Therefore, school counselors require the knowledge and appreciation of ethical and legal issues regarding the use of such technology. The purpose of this manuscript is to: (a) introduce the development and prevalence of social media; (b) review legal and ethical issues related to social media use in schools; and (c) present strategies in which school counselors can engage in ethical interactions via social media

Fluorescence Lifetime Imaging Microscopy (FLIM) Data Analysis with TIMP

Fluorescence Lifetime Imaging Microscopy (FLIM) allows fluorescence lifetime images of biological objects to be collected at 250 nm spatial resolution and at (sub-)nanosecond temporal resolution. Often n_comp kinetic processes underlie the observed fluorescence at all locations, but the intensity of the fluorescence associated with each process varies per-location, i.e., per-pixel imaged. Then the statistical challenge is global analysis of the image: use of the fluorescence decay in time at all locations to estimate the n_comp lifetimes associated with the kinetic processes, as well as the amplitude of each kinetic process at each location. Given that typical FLIM images represent on the order of 10^2 timepoints and 10^3 locations, meeting this challenge is computationally intensive. Here the utility of the TIMP package for R to solve parameter estimation problems arising in FLIM image analysis is demonstrated. Case studies on simulated and real data evidence the applicability of the partitioned variable projection algorithm implemented in TIMP to the problem domain, and showcase options included in the package for the visual validation of models for FLIM data.

Geometrical Defects in Josephson Junction Arrays

Dislocations and disclinations in a lattice of Josephson junctions will affect the dynamics of vortex excitations within the array. These defects effectively distort the space in which the excitations move and interact. The interaction energy between such defects and excitations are determined and vortex trajectories in twisted lattices are calculated. Finally, possible experiments observing these effects are presented.Comment: 26 pages including 5 figure