Addressing the needs of traumatic brain injury with clinical proteomics.

BackgroundNeurotrauma or injuries to the central nervous system (CNS) are a serious public health problem worldwide. Approximately 75% of all traumatic brain injuries (TBIs) are concussions or other mild TBI (mTBI) forms. Evaluation of concussion injury today is limited to an assessment of behavioral symptoms, often with delay and subject to motivation. Hence, there is an urgent need for an accurate chemical measure in biofluids to serve as a diagnostic tool for invisible brain wounds, to monitor severe patient trajectories, and to predict survival chances. Although a number of neurotrauma marker candidates have been reported, the broad spectrum of TBI limits the significance of small cohort studies. Specificity and sensitivity issues compound the development of a conclusive diagnostic assay, especially for concussion patients. Thus, the neurotrauma field currently has no diagnostic biofluid test in clinical use.ContentWe discuss the challenges of discovering new and validating identified neurotrauma marker candidates using proteomics-based strategies, including targeting, selection strategies and the application of mass spectrometry (MS) technologies and their potential impact to the neurotrauma field.SummaryMany studies use TBI marker candidates based on literature reports, yet progress in genomics and proteomics have started to provide neurotrauma protein profiles. Choosing meaningful marker candidates from such 'long lists' is still pending, as only few can be taken through the process of preclinical verification and large scale translational validation. Quantitative mass spectrometry targeting specific molecules rather than random sampling of the whole proteome, e.g., multiple reaction monitoring (MRM), offers an efficient and effective means to multiplex the measurement of several candidates in patient samples, thereby omitting the need for antibodies prior to clinical assay design. Sample preparation challenges specific to TBI are addressed. A tailored selection strategy combined with a multiplex screening approach is helping to arrive at diagnostically suitable candidates for clinical assay development. A surrogate marker test will be instrumental for critical decisions of TBI patient care and protection of concussion victims from repeated exposures that could result in lasting neurological deficits

Proximate grassland and shrub-encroached sites show dramatic restructuring of soil bacterial communities.

Background: Changes in aboveground community composition and diversity following shrub encroachment have been studied extensively. Recently, shrub encroachment was associated with differences in belowground bacterial communities relative to non-encroached grassland sites hundreds of meters away. This spatial distance between grassland and shrub sites left open the question of how soil bacterial communities associated with different vegetation types might differ within the same plot location. Methods: We examined soil bacterial communities between shrub-encroached and adjacent (one m apart) grassland soils in Chinese Inner Mongolian, using high-throughput sequencing method (Illumina, San Diego, CA, USA). Results: Shrub-encroached sites were associated with dramatic restructuring of soil bacterial community composition and predicted metabolic function, with significant increase in bacterial alpha-diversity. Moreover, bacterial phylogenic structures showed clustering in both shrub-encroached and grassland soils, suggesting that each vegetation type was associated with a unique and defined bacterial community by niche filtering. Finally, soil organic carbon (SOC) was the primary driver varied with shifts in soil bacterial community composition. The encroachment was associated with elevated SOC, suggesting that shrub-mediated shifts in SOC might be responsible for changes in belowground bacterial community. Discussion: This study demonstrated that shrub-encroached soils were associated with dramatic restructuring of bacterial communities, suggesting that belowground bacterial communities appear to be sensitive indicators of vegetation type. Our study indicates that the increased shrub-encroached intensity in Inner Mongolia will likely trigger large-scale disruptions in both aboveground plant and belowground bacterial communities across the region

Overview of Game and Content Design for a Mobile Game that Will Prepare Students in Calculus and Physics Prerequisites to the Engineering Curriculum

As part of a research project which assists veterans as they exit the military, complete engineering degrees, and enter the workforce as engineering professionals, a range of serious games for Science, Technology, Engineering, and Mathematics (STEM) education is under development. The current focus of this development is CAPTIVATE, a serious game to assist student veterans in mastering the calculus and physics skills that are necessary prerequisites to the main engineering curriculum. Building on the development and lessons learned from MAVEN, a game developed previously to help student veterans master precalculus skills, the design and initial implementation for CAPTIVATE involves careful consideration regarding game and instructional design. Many of the positive aspects from the design of MAVEN will be implemented in CAPTIVATE. First, the overall framework developed for MAVEN will be reused in CAPTIVATE. This modular framework involves both a model and process that combine game, instructional, and software design in a way that supports adaptability throughout the design and development cycle. Additionally by embedding concepts in game play similar to well-known board games such as Battleship, computer games such as Minesweeper, and console or mobile games such as Guitar Hero, students will use their calculus and physics skills to complete tasks in a familiar environment. In addition, the game itself will consist of a series of sub-games each focusing on a topic that students traditionally struggle to understand. Furthermore, students will be offered access to learning resources and assessed regularly as they progress through the game. CAPTIVATE will also overcome some shortcomings from the previous development. While MAVEN was developed for desktop deployment, CAPTIVATE is targeted for deployment on a variety of mobile device including Apple and Android phones and tablets to engage students in interactive games that support their endeavor to build a solid foundation in mathematics and science topics. Additionally by creating games that are short and easily accessible, students will be able to engage with the material at a time and place convenient for them. The development of CAPTIVATE supports student veterans as they transition from the military to engineering degree programs and helps to accelerate them through their STEM prerequisite courses

Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin / mitomycin C resistance in other bacteria

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background The phenazines are redox-active secondary metabolites that a large number of bacterial strains produce and excrete into the environment. They possess antibiotic activity owing to the fact that they can reduce molecular oxygen to toxic reactive oxygen species. In order to take advantage of this activity, phenazine producers need to protect themselves against phenazine toxicity. Whereas it is believed that phenazine-producing pseudomonads possess highly active superoxide dismutases and catalases, it has recently been found that the plant-colonizing bacterium Enterobacter agglomerans expresses a small gene ehpR to render itself resistant towards D-alanyl-griseoluteic acid, the phenazine antibiotic produced by this strain. Results To understand the resistance mechanism installed by EhpR we have determined its crystal structure in the apo form at 2.15 Å resolution and in complex with griseoluteic acid at 1.01 Å, respectively. While EhpR shares a common fold with glyoxalase-I/bleomycin resistance proteins, the ligand binding site does not contain residues that some related proteins employ to chemically alter their substrates. Binding of the antibiotic is mediated by π-stacking interactions of the aromatic moiety with the side chains of aromatic amino acids and by a few polar interactions. The dissociation constant KD between EhpR and griseoluteic acid was quantified as 244 ± 45 μM by microscale thermophoresis measurements. Conclusions The data accumulated here suggest that EhpR confers resistance by binding D-alanyl-griseoluteic acid and acting as a chaperone involved in exporting the antibiotic rather than by altering it chemically. It is tempting to speculate that EhpR acts in concert with EhpJ, a transport protein of the major facilitator superfamily that is also encoded in the phenazine biosynthesis operon of E. agglomerans. The low affinity of EhpR for griseoluteic acid may be required for its physiological function.Peer Reviewe

MRI Field-transfer Reconstruction with Limited Data: Regularization by Neural Style Transfer

Recent works have demonstrated success in MRI reconstruction using deep learning-based models. However, most reported approaches require training on a task-specific, large-scale dataset. Regularization by denoising (RED) is a general pipeline which embeds a denoiser as a prior for image reconstruction. The potential of RED has been demonstrated for multiple image-related tasks such as denoising, deblurring and super-resolution. In this work, we propose a regularization by neural style transfer (RNST) method to further leverage the priors from the neural transfer and denoising engine. This enables RNST to reconstruct a high-quality image from a noisy low-quality image with different image styles and limited data. We validate RNST with clinical MRI scans from 1.5T and 3T and show that RNST can significantly boost image quality. Our results highlight the capability of the RNST framework for MRI reconstruction and the potential for reconstruction tasks with limited data.Comment: 30 pages, 8 figures, 2 tables, 1 algorithm char

Using RNase sequence specificity to refine the identification of RNA-protein binding regions

Massively parallel pyrosequencing is a high-throughput technology that can sequence hundreds of thousands of DNA/RNA fragments in a single experiment. Combining it with immunoprecipitation-based biochemical assays, such as cross-linking immunoprecipitation (CLIP), provides a genome-wide method to detect the sites at which proteins bind DNA or RNA. In a CLIP-pyrosequencing experiment, the resolutions of the detected protein binding regions are partially determined by the length of the detected RNA fragments (CLIP amplicons) after trimming by RNase digestion. The lengths of these fragments usually range from 50-70 nucleotides. Many genomic regions are marked by multiple RNA fragments. In this paper, we report an empirical approach to refine the localization of protein binding regions by using the distribution pattern of the detected RNA fragments and the sequence specificity of RNase digestion. We present two regions to which multiple amplicons map as examples to demonstrate this approach