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).     

Synthesis and biological evaluation of 3-amino-, 3-alkoxy- and 3-aryloxy-6-(hetero)arylpyridazines as potent antitumor agents

Various 3-amino-, 3-aryloxy- and alkoxy-6-arylpyridazines have been synthesized by an electrochemical reductive cross-coupling between 3-amino-, 3-aryloxy- or 3-alkoxy-6-chloropyridazines and aryl or heteroaryl halides. In vitro antiproliferative activity of these products was evaluated against a representative panel of cancer cell lines (HuH7, CaCo-2, MDA-MB-231, HCT116, PC3, NCI-H727, HaCaT) and oncogenicity prevention of the more efficient derivatives was highlighted on human breast cancer cell line MDA-MB 468-Luc prior establishing their interaction with p44/42 and Akt-dependent signaling pathways.     

SETAC Europe Young Scientist LCA award 2019 for P. James Joyce

The International Journal of Life Cycle Assessment - At the 29th SETAC Europe annual meeting, May 26–30, 2019, Helsinki (Finland), P. James Joyce received the SETAC Europe Young Scientist LCA...     

Adaptation to developmental diet influences the response to selection on age at reproduction in the fruit fly

Experimental evolution (EE) is a powerful tool for addressing how environmental factors influence life‐history evolution. While in nature different selection pressures experienced across the lifespan shape life histories, EE studies typically apply selection pressures one at a time. Here, we assess the consequences of adaptation to three different developmental diets in combination with classical selection for early or late reproduction in the fruit fly Drosophila melanogaster. We find that the response to each selection pressure is similar to that observed when they are applied independently, but the overall magnitude of the response depends on the selection regime experienced in the other life stage. For example, adaptation to increased age at reproduction increased lifespan across all diets; however, the extent of the increase was dependent on the dietary selection regime. Similarly, adaptation to a lower calorie developmental diet led to faster development and decreased adult weight, but the magnitude of the response was dependent on the age‐at‐reproduction selection regime. Given that multiple selection pressures are prevalent in nature, our findings suggest that trade‐offs should be considered not only among traits within an organism, but also among adaptive responses to different—sometimes conflicting—selection pressures, including across life stages.     

Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis

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Two functionally distinct Axin-like proteins regulate canonical Wnt signaling in C. elegans

Axin is a central component of the canonical Wnt signaling pathway that interacts with the adenomatous polyposis coli protein APC and the kinase GSK3beta to downregulate the effector beta-catenin. In the nematode Caenorhabditis elegans, canonical Wnt signaling is negatively regulated by the highly divergent Axin ortholog PRY-1. Mutation of pry-1 leads to constitutive activation of BAR-1/beta-catenin-dependent Wnt signaling and results in a range of developmental defects. The pry-1 null phenotype is however not fully penetrant, indicating that additional factors may partially compensate for PRY-1 function. Here, we report the cloning and functional analysis of a second Axin-like protein, which we named AXL-1. We show that despite considerable sequence divergence with PRY-1 and other Axin family members, AXL-1 is a functional Axin ortholog. AXL-1 functions redundantly with PRY-1 in negatively regulating BAR-1/beta-catenin signaling in the developing vulva and the Q neuroblast lineage. In addition, AXL-1 functions independently of PRY-1 in negatively regulating canonical Wnt signaling during excretory cell development. In contrast to vertebrate Axin and the related protein Conductin, AXL-1 and PRY-1 are not functionally equivalent. We conclude that Axin function in C. elegans is divided over two different Axin orthologs that have specific functions in negatively regulating canonical Wnt signaling.     

Proteomics data validation: why all must provide data

The field of proteomics has gained considerable momentum over the last years as new technologies and better instrumentation allowed the field to mature from what resembled a cottage industry into a high-throughput means to identify, characterize and quantify hundreds of proteins. The identifications and (relative) quantitation values obtained are often controversial however, as various techniques and different software platforms are used in the many laboratories worldwide. This Opinion attempts to shed some light on some of the underlying issues, and proposes certain guidelines authors can adhere to in order to allow others to validate their findings.     

High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK

The Wellcome Trust Conference Centre at Hinxton, UK, was the meeting place of the 7th HUPO Brain Proteome Project Workshop entitled "High Performance Proteomics". It started on Wednesday, March 7, 2007 with a steering committee meeting followed by a two days series of talks dealing with the standardization and handling of tissues, body fluids as well as of proteomics data. The presentation and accompanying vivid discussions created a picture of actual strategies and standards in recent proteomics.     

Comparison of Emulsifying Properties of Plant and Animal Proteins in Oil-in-Water Emulsions: Whey,Soy, and RuBisCo Proteins

There is increasing interest within the food industry in replacing animal-derived ingredients with plant-derived alternatives. In this study, we compared the emulsifying properties of an emerging plant protein (RuBisCo protein) with those of a well-established plant (soy protein) and animal (whey protein) protein. The RuBisCo protein (ribulose 1,5-bisphosphate carboxylase) was isolated from duckweed (lemna minor), which is an abundant plant material with a higher protein yield and biomass per unit area than most other plant protein sources. The ability of the three proteins to form and stabilize 10 wt% soybean oil-in-water emulsions was examined. The minimum amount of protein required to produce small droplets (d <?350 nm) decreased in the following order: RuBisCo > soy > whey protein. This effect was mainly attributed to the fact that the molar mass of the proteins decreased in the same order. Even so, the RuBisCo proteins were able to form stable emulsions when used at sufficiently high concentrations (≥ 1%). All three types of protein-coated oil droplets aggregated at pH values near their isoelectric points and at high ionic strengths but there were differences between them. In the absence of added salt, extensive droplet aggregation occurred from pH 4 to 5 for whey protein, from pH 2 to 5 for soy protein, and from pH 2 to 6 for RuBisCo protein. The isoelectric points of all three protein-coated droplets were around pH 5, but the magnitude of the surface potential at low and high pH values was higher for whey protein than for the two plant proteins. At pH 7, extensive droplet aggregation occurred at ≥100 mM NaCl for RuBisCo- and soy protein-coated droplets, but only at ≥400 mM NaCl for whey protein-coated ones. The RuBisCo-coated oil droplets were more prone to flocculation when heated, especially in the presence of salt (100 mM NaCl). Overall, these results show that RuBisCo protein can be used to form and stabilize oil-in-water emulsions, but the pH, salt, and temperature conditions must be carefully controlled to avoid droplet aggregation. We should note that droplet aggregation is advantageous in some applications because it leads to an increase in emulsion viscosity or gelation.