Does chromosome number count? Mapping karyological knowledge on Italian flora in a phylogenetic framework

Italian vascular flora is highly representative of the Euro-Mediterranean area, because the region includes high mountain territories, temperate areas, and regions dominated by the Mediterranean climate. Chromosome number information about the Italian flora stored in the online database Chrobase.it includes 6,756 records, referable to 3,539 cytotypes and 2,785 accepted species and subspecies (approx. 35% of the national flora). Appropriate queries to Chrobase.it enabled us to map chromosome numbers, at order rank, in a robust phylogenetic framework, derived from APGIII and other recent phylogenetic studies on vascular plants. Similar work was conducted for selected families and genera. Chromosome number data were available for 41 out of 80 vascular plant orders (51%) currently recognized world-wide and 107 out of 428 families (25%), represented by 661 genera (4.5%). The large number of records enabled us to compute the mean chromosome number for each taxon, and to highlight significant differences among all orders and among subsets of families and genera. For each taxon, we analysed the variability in chromosome number by use of common statistical methods, and computed the frequency of chromosome numbers, the coefficient of variation of chromosome number (CV_CN), the frequency of B-chromosomes (fB), and that of odd chromosome numbers (fOCN). The phylogenetic relevance of our results is discussed and the usefulness of basic karyological data, often neglected in current phylogenetic studies, is stressed.     

Mapping Genetic Variants Underlying Differences in the Central Nitrogen Metabolism in Fermenter Yeasts

Different populations within a species represent a rich reservoir of allelic variants, corresponding to an evolutionary signature of withstood environmental constraints. Saccharomyces cerevisiae strains are widely utilised in the fermentation of different kinds of alcoholic beverages, such as, wine and sake, each of them derived from must with distinct nutrient composition. Importantly, adequate nitrogen levels in the medium are essential for the fermentation process, however, a comprehensive understanding of the genetic variants determining variation in nitrogen consumption is lacking. Here, we assessed the genetic factors underlying variation in nitrogen consumption in a segregating population derived from a cross between two main fermenter yeasts, a Wine/European and a Sake isolate. By linkage analysis we identified 18 main effect QTLs for ammonium and amino acids sources. Interestingly, majority of QTLs were involved in more than a single trait, grouped based on amino acid structure and indicating high levels of pleiotropy across nitrogen sources, in agreement with the observed patterns of phenotypic co-variation. Accordingly, we performed reciprocal hemizygosity analysis validating an effect for three genes, GLT1, ASI1 and AGP1. Furthermore, we detected a widespread pleiotropic effect on these genes, with AGP1 affecting seven amino acids and nine in the case of GLT1 and ASI1. Based on sequence and comparative analysis, candidate causative mutations within these genes were also predicted. Altogether, the identification of these variants demonstrate how Sake and Wine/European genetic backgrounds differentially consume nitrogen sources, in part explaining independently evolved preferences for nitrogen assimilation and representing a niche of genetic diversity for the implementation of practical approaches towards more efficient strains for nitrogen metabolism.     

Detection of DNA in Ancient Bones Using Histochemical Methods

We describe histochemical techniques for detecting DNA within the osteocytic lacunae of ancient bones. The bones examined were fragments of femurs from two human individuals found in the Pompeian C. I. Polybius house and fragments of metacarpals from two horses (Equus sp.) found in the Pompeian “Casti Amanti” house. Both buildings were buried by the 79 A. D. Vesuvius eruption. Fragments of femurs from a modern horse, a modern swine and a modern amphibian also were studied as controls. Some bone sections were stained with two different DNA-specific fluorochromes, 4' -' 6-diamidino-2-phenylindole (DAPI) and chromomycin A3 (CMA), while others were stained by the Feulgen reaction. All of the techniques gave a positive reaction within the osteocytic lacunae. Histological analysis of the undecalcified, ground and unstained sections agreed well with results of bone sections stained with either the fluorochromes or the Feulgen reaction. Bones showing good histology also were positive by our DNA-specific stain. Histochemical and histological analyses correlated well with the success of DNA extraction and amplification. Using conventional DNA-specific histochemical techniques in conjunction with histological analysis can be useful in the study of DNA extracted from ancient bone remains while reducing both the amount of time and cost.     

How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein?

The mechanism of interaction of an intrinsically disordered protein (IDP) with its physiological partner is characterized by a disorder-to-order transition in which a recognition and a binding step take place. Even if the mechanism is quite complex, IDPs tend to bind their partner in a cooperative manner such that it is generally possible to detect experimentally only the disordered unbound state and the structured complex. The interaction between the disordered C-terminal domain of the measles virus nucleoprotein (N_TAIL) and the X domain (XD) of the viral phosphoprotein allows us to detect and quantify the two distinct steps of the overall reaction. Here, we analyze the robustness of the folding of N_TAIL upon binding to XD by measuring the effect on both the folding and binding steps of N_TAIL when the structure of XD is modified. Because it has been shown that wild-type XD is structurally heterogeneous, populating an on-pathway intermediate under native conditions, we investigated the binding to 11 different site-directed variants of N_TAIL of one particular variant of XD (I504A XD) that populates only the native state. Data reveal that the recognition and the folding steps are both affected by the structure of XD, indicating a highly malleable pathway. The experimental results are briefly discussed in the light of previous experiments on other IDPs.     

ARGoS: a modular, parallel, multi-engine simulator for multi-robot systems

We present a novel multi-robot simulator named ARGoS. ARGoS is designed to simulate complex experiments involving large swarms of robots of different types. ARGoS is the first multi-robot simulator that is at the same time both efficient (fast performance with many robots) and flexible (highly customizable for specific experiments). Novel design choices in ARGoS have enabled this breakthrough. First, in ARGoS, it is possible to partition the simulated space into multiple sub-spaces, managed by different physics engines running in parallel. Second, ARGoS?? architecture is multi-threaded, thus designed to optimize the usage of modern multi-core CPUs. Finally, the architecture of ARGoS is highly modular, enabling easy addition of custom features and appropriate allocation of computational resources. We assess the efficiency of ARGoS and showcase its flexibility with targeted experiments. Experimental results demonstrate that simulation run-time increases linearly with the number of robots. A 2D-dynamics simulation of 10,000 e-puck robots can be performed in 60?% of the time taken by the corresponding real-world experiment. We show how ARGoS can be extended to suit the needs of an experiment in which custom functionality is necessary to achieve sufficient simulation accuracy. ARGoS is open source software licensed under GPL3 and is downloadable free of charge.     

The chemical interactome space between the human host and the genetically defined gut metabotypes

The bacteria that colonize the gastrointestinal tracts of mammals represent a highly selected microbiome that has a profound influence on human physiology by shaping the host''s metabolic and immune system activity. Despite the recent advances on the biological principles that underlie microbial symbiosis in the gut of mammals, mechanistic understanding of the contributions of the gut microbiome and how variations in the metabotypes are linked to the host health are obscure. Here, we mapped the entire metabolic potential of the gut microbiome based solely on metagenomics sequencing data derived from fecal samples of 124 Europeans (healthy, obese and with inflammatory bowel disease). Interestingly, three distinct clusters of individuals with high, medium and low metabolic potential were observed. By illustrating these results in the context of bacterial population, we concluded that the abundance of the Prevotella genera is a key factor indicating a low metabolic potential. These metagenome-based metabolic signatures were used to study the interaction networks between bacteria-specific metabolites and human proteins. We found that thirty-three such metabolites interact with disease-relevant protein complexes several of which are highly expressed in cells and tissues involved in the signaling and shaping of the adaptive immune system and associated with squamous cell carcinoma and bladder cancer. From this set of metabolites, eighteen are present in DrugBank providing evidence that we carry a natural pharmacy in our guts. Furthermore, we established connections between the systemic effects of non-antibiotic drugs and the gut microbiome of relevance to drug side effects and health-care solutions.