Rapid identification and interpretation of gene–environment associations using the new R.SamBada landscape genomics pipeline

sam βada is a genome–environment association software, designed to search for signatures of local adaptation. However, pre‐ and postprocessing of data can be labour‐intensive, preventing wider uptake of the method. We have now developed R.SamBada, an r ‐package providing a pipeline for landscape genomic analysis based on sam βada , spanning from the retrieval of environmental conditions at sampling locations to gene annotation using the Ensembl genome browser. As a result, R.SamBada standardizes the landscape genomics pipeline and eases the search for candidate genes of local adaptation, enhancing reproducibility of landscape genomic studies. The efficiency and power of the pipeline is illustrated using two examples: sheep populations from Morocco with no evident population structure and Lidia cattle from Spain displaying population substructuring. In both cases, R.SamBada enabled rapid identification and interpretation of candidate genes, which are further discussed in the light of local adaptation. The package is available in the r CRAN package repository and on GitHub (github.com/SolangeD/R.SamBada).     

Operationalisation and application of water supply mix (WSmix) at worldwide scale: how does WSmix influence the environmental profile of water supply for different users?

The International Journal of Life Cycle Assessment - A worldwide-regionalized water supply mix (WSmix) has been developed for use in life cycle assessment (LCA) studies. The WSmix is the...     

Towards Productive Cities: Environmental Assessment of the Food‐Energy‐Water Nexus of the Urban Roof Mosaic

Cities are rapidly growing and need to look for ways to optimize resource consumption. Metropolises are especially vulnerable in three main systems, often referred to as the FEW (i.e., food, energy, and water) nexus. In this context, urban rooftops are underutilized areas that might be used for the production of these resources. We developed the Roof Mosaic approach, which combines life cycle assessment with two rooftop guidelines, to analyze the technical feasibility and environmental implications of producing food and energy, and harvesting rainwater on rooftops through different combinations at different scales. To illustrate, we apply the Roof Mosaic approach to a densely populated neighborhood in a Mediterranean city. The building‐scale results show that integrating rainwater harvesting and food production would avoid relatively insignificant emissions (13.9–18.6 kg CO₂ eq/inhabitant/year) in the use stage, but their construction would have low environmental impacts. In contrast, the application of energy systems (photovoltaic or solar thermal systems) combined with rainwater harvesting could potentially avoid higher CO₂ eq emissions (177–196 kg CO₂ eq/inhabitant/year) but generate higher environmental burdens in the construction phase. When applied at the neighborhood scale, the approach can be optimized to meet between 7% and 50% of FEW demands and avoid up to 157 tons CO₂ eq/year. This approach is a useful guide to optimize the FEW nexus providing a range of options for the exploitation of rooftops at the local scale, which can aid cities in becoming self‐sufficient, optimizing resources, and reducing CO₂ eq emissions.     

Hepatic effects of long‐term tamoxifen administration to cycling female rats

The metabolic implications of tamoxifen (TAM) used as preventive therapy of young premenopausal women with high risk of breast cancer is unknown. To unravel this problem, an animal model of long‐term TAM administration to cycling young adult female rats was used to evaluate its effects in the liver. Body weight and food consumption were monitored, and at the end of the study, both parameters were lower in TAM‐treated rats. Biochemical measurements showed that the TAM administration induced alterations in serum levels of liver enzymes when compared with control rats at different stages of the estrous cycle. In TAM‐treated rats, lower glycogen storage was observed in hepatocytes close to the portal areas and pericentrolobular cells had a higher concentration of glycogen. Liver sections of TAM‐treated rats presented mild steatosis—a high percentage of area occupied by lipid droplets in the hepatocytes. These results point to metabolic changes upon long‐term TAM therapy.     

Simple and rapid method determination for metformin in human plasma using high performance liquid chromatography tandem mass spectrometry: application to pharmacokinetic studies

A rapid and simple method for quantitation of metformin (MET) in human plasma by HPLC-MS/MS was developed and validated. The sample preparation consists of plasma deproteinization using acetonitrile. The mobile phase consisted of water-acetonitrile and formic acid (55/45/0.048, v/v/%) and the run time was 3 min. A pursuit C(18) (100 mm x 2.0 mm i.d., 3 microm) column connected to a guard column MS-pursuit (0.20 mm x 0.20 mm i.d., 5 microm) was used. The range of the calibration curve was from 20 to 5000 ng/mL, the limit of quantitation being 20 ng/mL. The detection was performed on a mass spectrometer (ESI+), using metoprolol as internal standard. The calibration curves have r(2) values of 0.995 (CV=0.24%, n=10). The accuracy and precision were between 90.74 and 106.7% and coefficients of variations (CV) of 1.10 and 4.35%, respectively. The method was applied to determine the pharmacokinetic parameters: C(max) (1667.25 ng/mL) and T(max) (3.89 h).     

Parameterization of the stomatal component of the DO3SE model for Mediterranean evergreen broadleaf species

An ozone (O3) deposition model (DO3SE) is currently used in Europe to define the areas where O3 concentrations lead to absorbed O3 doses that exceed the flux-based critical levels above which phytotoxic effects would be likely recorded. This mapping exercise relies mostly on the accurate estimation of O3 flux through plant stomata. However, the present parameterization of the modulation of stomatal conductance (g(s)) behavior by different environmental variables needs further adjustment if O3 phytotoxicity is to be assessed accurately at regional or continental scales. A new parameterization of the model is proposed for Holm oak (Quercus ilex), a tree species that has been selected as a surrogate for all Mediterranean evergreen broadleaf species. This parameterization was based on a literature review, and was calibrated and validated using experimentally measured data of g(s) and several atmospheric and soil parameters recorded at three sites of the Iberian Peninsula experiencing long summer drought, and very cold and dry winter air (El Pardo and Miraflores) or milder conditions (Tietar). A fairly good agreement was found between modeled and measured data (R2 = 0.64) at Tietar. However, a reasonable performance (R2 = 0.47-0.62) of the model was only achieved at the most continental sites when g(s) and soil moisture deficit relationships were considered. The influence of root depth on g(s) estimation is discussed and recommendations are made to build up separate parameterizations for continental and marine-influenced Holm oak sites in the future.     

Watch-ing out for chick limb development

Time control is a crucial issue during embryonic development.Nevertheless, little is known about how embryonic cells measuretime. Until recently, the only molecular clock known to operateduring vertebrate embryonic development was the somitogenesisclock, exclusively functioning in coordinating the precise timingof each new pair of somites formed from the presomitic mesoderm.We have recently evidenced that a similar molecular clock alsounderlies the timing at which autopod chondrogenic precursorsare laid down to form a skeletal limb element. In addition,we herein suggest that the molecular clock is not the only parallelismthat can be established between somitogenesis and limb-bud development.In an evolutionary perspective, we support the previously proposedidea that the molecular mechanisms involved in the segmentationof the body axis may have been partially reused in the mesodermof the lateral plate, thereby allowing the emergence of pairedappendages.     

Janus: a framework to boost HPC applications in the cloud based on SDN path provisioning

Data centers, clusters, and grids have historically supported High-Performance Computing (HPC) applications. Due to the high capital and operational expenditures associated with such infrastructures, we have witnessed consistent efforts to run HPC applications in the cloud in the recent past. The potential advantages of this shift include higher scalability and lower costs. If, on the one hand, app instantiation—through customized Virtual Machines (VMs)—is a well-solved issue, on the other, the network still represents a significant bottleneck. When switching HPC applications to be executed on the cloud, we lose control of where VMs will be positioned and of the paths that will be traversed for processes to communicate with one another. To bridge this gap, we present Janus, a framework for dynamic, just-in-time path provisioning in cloud infrastructures. By leveraging emerging software-defined networking principles, the framework allows for an HPC application, once deployed, to have interprocess communication paths configured upon usage based on least-used network links (instead of resorting to shortest, pre-computed paths). Janus is fully configurable to cope with different operating parameters and communication strategies, providing a rich ecosystem for application execution speed up. Through an extensive experimental evaluation, we provide evidence that the proposed framework can lead to significant gains regarding runtime. Moreover, we show what one can expect in terms of system overheads, providing essential insights on how better benefiting from Janus.