Chromosome-level genome assembly of a regenerable maize inbred line A188.

BACKGROUND The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. RESULTS Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. CONCLUSIONS The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues

Oncogenic Pathway Combinations Predict Clinical Prognosis in Gastric Cancer

Many solid cancers are known to exhibit a high degree of heterogeneity in their deregulation of different oncogenic pathways. We sought to identify major oncogenic pathways in gastric cancer (GC) with significant relationships to patient survival. Using gene expression signatures, we devised an in silico strategy to map patterns of oncogenic pathway activation in 301 primary gastric cancers, the second highest cause of global cancer mortality. We identified three oncogenic pathways (proliferation/stem cell, NF-κB, and Wnt/β-catenin) deregulated in the majority (>70%) of gastric cancers. We functionally validated these pathway predictions in a panel of gastric cancer cell lines. Patient stratification by oncogenic pathway combinations showed reproducible and significant survival differences in multiple cohorts, suggesting that pathway interactions may play an important role in influencing disease behavior. Individual GCs can be successfully taxonomized by oncogenic pathway activity into biologically and clinically relevant subgroups. Predicting pathway activity by expression signatures thus permits the study of multiple cancer-related pathways interacting simultaneously in primary cancers, at a scale not currently achievable by other platforms

An Alternative Model for Scheduling on a Computational Grid

In this paper we discuss scheduling on a computational grid of autonomous nodes. A two level process involves a meta-scheduler whose objective is to generate an optimal schedule and reduce the total execution time of an work-flow, and local schedulers whose objective is to optimize the utilization of local resources. We introduce several resource allocation and consumption models and discuss issues pertinent to decision making with incomplete and/or outdated information. Then we present a stock market model for scheduling on a computer grid with autonomous nodes. 1 Introduction A computational grid is a large-scale, heterogeneous collection of autonomous systems, geographically distributed and interconnected by low latency and high bandwidth networks. The mission of a grid is to provide dependable services at a low cost for a large community of users and to support collaborative work. The term "computational grid" is based on the analogy with the "power grid", it reflects the desire t..

Bond System Monitor

Bond is a message-oriented middleware for network computing on a grid of autonomous nodes. It consists of a distributed object communication fabric, servers, and agents. Core servers are permanent objects providing services such as directory service, dispatching, authentication, monitoring, and others. The Bond system monitor is responsible for starting up core servers, keeping them running, and balancing the load among them. In this paper, we discuss the remote server start-up and the executables failure detection functions of the monitor and present the backup monitor. Contents: 1. Abbreviations and terms 2. Introduction 3. System monitor Remote server start-up Failure detection Backup monitor 4. Future work 5. Conclusions 1. Abbreviations and terms Backup system monitor: core server; it takes control of the system when the primary system monitor fails. Shadow of a Bond object: abstraction supporting communication with a remote object. A shadow is a local object acting as a prox..

Masterbatch of Chitosan Nanowhiskers for Preparation of Nylon 6,10 Nanocomposite by Melt Blending

Composite materials have been extensively studied to optimize properties such as lightness and strength, which are the advantages of plastics. We prepared a highly concentrated (30 wt %) nylon/chitosan nanowhisker (CSW) masterbatch by blending nylon 6,10 and CSW by solvent casting to achieve high dispersion efficiency while considering an industrial setting. Subsequently, 0.3 wt % nylon/CSW nanocomposites were prepared with a large quantity of nylon 6,10 via melt blending. During preparation, the materials were stirred in the presence of formic acid at different times to investigate the effect of stirring time on the structure of the CSW and the physical properties of the composite. The formation of nanocomposites by the interactions between nylon and CSW was confirmed by observing the change in hydrogen bonding using FT-IR spectroscopy and the rise in melting temperature and melting enthalpy through differential scanning calorimetry. The results demonstrated increases in complex viscosity and shear thinning. The rheological properties of the composites changed due to interactions between CSW and nylon, as indicated by the loss factor. The mechanical properties produced by the nanocomposite stirred for 1.5 h were superior, suggesting that formic acid caused minimal structural damage, thus verifying the suitability of the stirring condition

Biorenewable, Transparent, and Oxygen/Moisture Barrier Nanocellulose/Nanochitin-Based Coating on Polypropylene for Food Packaging Applications

Aluminum-coated polypropylene films are commonly used in food packaging because aluminum is a great gas barrier. However, recycling these films is not economically feasible. In addition, their end-of-life incineration generates harmful alumina-based particulate matter. In this study, coating layers with excellent gas-barrier properties are assembled on polypropylene films through layer-by-layer (LbL) deposition of biorenewable nanocellulose and nanochitin. The coating layers significantly reduce the transmission of oxygen and water vapors, two unfavorable gases for food packaging, through polypropylene films. The oxygen transmission rate of a 60 μm-thick, 20 LbL-coated polypropylene film decreases by approximately a hundredfold, from 1118 to 13.10 cc m−2 day−1 owing to the high crystallinity of nanocellulose and nanochitin. Its water vapor transmission rate slightly reduces from 2.43 to 2.13 g m−2 day−1. Furthermore, the coated film is highly transparent, unfavorable to bacterial adhesion and thermally recyclable, thus promising for advanced food packaging applications.11Ysciescopu

Strong, Multifaceted Guanidinium-Based Adhesion of Bioorganic Nanoparticles to Wet Biological Tissue

Gluing dynamic, wet biological tissue is important in injury treatment yet difficult to achieve. Polymeric adhesives are inconvenient to handle due to rapid cross-linking and can raise biocompatibility concerns. Inorganic nanoparticles adhere weakly to wet surfaces. Herein, an aqueous suspension of guanidinium-functionalized chitin nanoparticles as a biomedical adhesive with biocompatible, hemostatic, and antibacterial properties is developed. It glues porcine skin up to 3000-fold more strongly (30 kPa) than inorganic nanoparticles at the same concentration and adheres at neutral pH, which is unachievable with mussel-inspired adhesives alone. The glue exhibits an instant adhesion (2 min) to fully wet surfaces, and the glued assembly endures one-week underwater immersion. The suspension is lowly viscous and stable, hence sprayable and convenient to store. A nanomechanic study reveals that guanidinium moieties are chaotropic, creating strong, multifaceted noncovalent bonds with proteins: salt bridges comprising ionic attraction and bidentate hydrogen bonding with acidic moieties, cation−π interactions with aromatic moieties, and hydrophobic interactions. The adhesion mechanism provides a blueprint for advanced tissue adhesives.11