Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria.

Breast milk enhances the predominance of Bifidobacterium species in the infant gut, probably due to its large concentration of human milk oligosaccharides (HMO). Here we screened infant-gut isolates of Bifidobacterium longum subsp. infantis and Bifidobacterium bifidum using individual HMO, and compared the global transcriptomes of representative isolates on major HMO by RNA-seq. While B. infantis displayed homogeneous HMO-utilization patterns, B. bifidum were more diverse and some strains did not use fucosyllactose (FL) or sialyllactose (SL). Transcriptomes of B. bifidum SC555 and B. infantis ATCC 15697 showed that utilization of pooled HMO is similar to neutral HMO, while transcriptomes for growth on FL were more similar to lactose than HMO in B. bifidum. Genes linked to HMO-utilization were upregulated by neutral HMO and SL, but not by FL in both species. In contrast, FL induced the expression of alternative gene clusters in B. infantis. Results also suggest that B. bifidum SC555 does not utilize fucose or sialic acid from HMO. Surprisingly, expression of orthologous genes differed between both bifidobacteria even when grown on identical substrates. This study highlights two major strategies found in Bifidobacterium species to process HMO, and presents detailed information on the close relationship between HMO and infant-gut bifidobacteria

Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq

Background: The European red mite, Panonychus ulmi, is among the most important mite pests in fruit orchards, where it is controlled primarily by acaricide application. However, the species rapidly develops pesticide resistance, and the elucidation of resistance mechanisms for P. ulmi has not kept pace with insects or with the closely related spider mite Tetranychus urticae. The main reason for this lack of knowledge has been the absence of genomic resources needed to investigate the molecular biology of resistance mechanisms. Results: Here, we provide a comprehensive strand-specific RNA-seq based transcriptome resource for P. ulmi derived from strains susceptible and resistant to the widely used acaricide spirodiclofen. From a de novo assembly of the P. ulmi transcriptome, we manually annotated detoxification enzyme families, target-sites of commonly used acaricides, and horizontally transferred genes implicated in plant-mite interactions and pesticide resistance. In a comparative analysis that incorporated sequences available for Panonychus citri, T. urticae, and insects, we identified radiations for detoxification gene families following the divergence of Panonychus and Tetranychus genera. Finally, we used the replicated RNA-seq data from the spirodiclofen susceptible and resistant strains to describe gene expression changes associated with resistance. A cytochrome P450 monooxygenase, as well as multiple carboxylcholinesterases, were differentially expressed between the susceptible and resistant strains, and provide a molecular entry point for understanding resistance to spirodiclofen, widely used to control P. ulmi populations. Conclusions: The new genomic resources and data that we present in this study for P. ulmi will substantially facilitate molecular studies of underlying mechanisms involved in acaricide resistance

By Product Synergy Analysis

The United States Air Forces generates various waste during the repair and overhaul activities. These wastes can involve hazardous material. Depending on the material, technologies exist or could be readily developed to convert wastes into feed-stock for other processes. The old concept of managing material from cradle-to-grave now has evolved into cradle-to-cradle. This concept goes beyond the disposal of waste and can be even more cost-effective than recycling. The objective is to generate food by identifying and developing other processes to use current wastes in its own production processes. By shifting from waste disposal to an endless reusing model improves cost efficiency and reduces the overall environmental impact (not limited to landfill space, water consumption and carbon footprint). This research will develop a methodology to employ state-of-the-art commercial practices to analyze depot waste production processes. The goal is to identify and classify waste generated by volume, hazard, and costs, then analyze the environmental flow by comparing government and commercial users of by-products in a synergy model. Optimal solutions for current product flow will be identified, along with potential areas for investment in by-product technologies. Solutions are mutually beneficial for both parties not only economically but also from social and environmental concerns

Tool Support for a Method and a Language Integrating Model Refinements and Project Management

International audienceComplexity of Embedded Systeme (ES) development is increasing due of several cumulative sources. Some of them are directly related to constraints on the ES themselves, like computing power, resource constraints, and multi- or many-core programming, while other are related to the industrial context, like teamwork and parallelisation of concurrent development. In this paper we present CanHOE2, a Model Driven Engineering (MDE) tool that addresses two issues of ES development: expression of parallelism by means of objects and Hierarchical State Machines (HSM), and teamwork synchronisation

Numerical Investigation of Porous and Non-Porous Pipe with Free Overfall

This dissertation presents results of a computational investigation into the discharge characteristics of two stormwater runoff management approach, i.e., a perforated pipe-aggregate underdrain system, a common setup used in various Low Impact Development (LID) strategies and Best Management Practices (BMPs), and a circular pipe free overfall. A three-dimensional model of a perforated pipe-aggregate underdrain system was developed and validated using previously published experimental results for saturated subsurface flow (flow where the water surface is above the top of the aggregate) for a 10.2 cm perforated pipe shrouded in loose laid aggregate. Results showed that for the saturated case, the orifice flow approximation was valid; for the unsaturated case (water surface level is below the top of the aggregate level), energy losses in the aggregate layer were significant and the orifice approximation was not valid. The effects of several controlling geometric parameters, i.e., aggregate depth over the pipe, trench width, total head, pipe length, pipe wall perforation area per unit length of pipe, and the area of individual perforations on discharge characteristics of pipe-aggregate system were also investigated. For any combinations of these geometric parameters, there was a finite length of pipe, after which discharge did not increase with increasing pipe length. That length was defined as the critical length and was found to be sensitive to changes in pipe geometry only. A non-dimensional equation was proposed for predicting the peak discharge coefficient for porous pavements and infiltration trenches that use perforated pipe underdrains. The discharge characteristics of a free overfall from a smooth, horizontal circular pipe was also investigated. A free overfall can be used as a simple discharge measuring approach and is also common as an outflow condition for storm sewers. Based on the characteristics of flow, two different flow regimes i.e. cavity outflow flow and bubble washout flow were investigated. A constant End Depth Ratio (EDR) was found for the cavity outflow regime but it varied linearly with dimensionless critical depth for the bubble washout flow. The limiting discharge for a pipe flowing full and the cavity outflow, and bubble washout regimes has been established. Several important parameters, i.e., Froude number, pressure and momentum coefficients at the upstream and brink sections, and the minimum slope of the water surface behaved differently in the two flow regimes. However, the non-dimensional pressure distribution at the brink section showed same trend for both flow regimes. An expression for predicting discharge in the bubble washout flow regime has been proposed incorporating appropriate pressure and momentum coefficients and shows very good agreement with the computational data and available experimental data. Possible reasons of transition between cavity outflow and bubble washout flow was also explained. Findings from this dissertation have practical applications in design and analysis of porous pipe underdrain-aggregate systems as well as in flow rate control and improving the design methods of urban drainage facilities