Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer

Background

Horizontal gene transfer (HGT) is the stable transmission of genetic material between organisms by means other than vertical inheritance. HGT has an important role in the evolution of prokaryotes but is relatively rare in eukaryotes. HGT has been shown to contribute to virulence in eukaryotic pathogens. We studied the importance of HGT in plant pathogenic fungi by identifying horizontally transferred genes in the genomes of three members of the genus Colletotrichum.

Results

We identified eleven HGT events from bacteria into members of the genus Colletotrichum or their ancestors. The HGT events include genes involved in amino acid, lipid and sugar metabolism as well as lytic enzymes. Additionally, the putative minimal dates of transference were calculated using a time calibrated phylogenetic tree. This analysis reveals a constant flux of genes from bacteria to fungi throughout the evolution of subphylum Pezizomycotina.

Conclusions

Genes that are typically transferred by HGT are those that are constantly subject to gene duplication and gene loss. The functions of some of these genes suggest roles in niche adaptation and virulence. We found no evidence of a burst of HGT events coinciding with major geological events. In contrast, HGT appears to be a constant, albeit rare phenomenon in the Pezizomycotina, occurring at a steady rate during their evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-16-2) contains supplementary material, which is available to authorized users.     

Environmental impacts of European trade: interpreting results of process-based LCA and environmentally extended input–output analysis towards hotspot identification

Purpose

Trade is increasingly considered a significant contributor to environmental impacts. The assessment of the impacts of trade is usually performed via environmentally extended input–output analysis (EEIOA). However, process-based life cycle assessment (LCA) applied to traded goods allows increasing the granularity of the analysis and may be essential to unveil specific impacts due to traded products.

Methods

This study assesses the environmental impacts of the European trade, considering two modelling approaches: respectively EEIOA, using EXIOBASE 3 as supporting database, and process-based LCA. The interpretation of the results is pivotal to improve the robustness of the assessment and the identification of hotspots. The hotspot identification focuses on temporal trends and on the contribution of products and substances to the overall impacts. The inventories of elementary flows associated with EU trade, for the period 2000–2010, have been characterized considering 14 impact categories according to the Environmental Footprint (EF2017) Life Cycle Impact Assessment method.

Results and discussion

The two modelling approaches converge in highlighting that in the period 2000–2010: (i) EU was a net importer of environmental impacts; (ii) impacts of EU trade and EU trade balance (impacts of imports minus impacts of exports) were increasing over time, regarding most impact categories under study; and (iii) similar manufactured products were the main contributors to the impacts of exports from EU, regarding most impact categories. However, some results are discrepant: (i) larger impacts are obtained from IO analysis than from process-based LCA, regarding most impact categories, (ii) a different set of most contributing products is identified by the two approaches in the case of imports, and (iii) large differences in the contributions of substances are observed regarding resource use, toxicity, and ecotoxicity indicators.

Conclusions

The interpretation step is crucial to unveil the main hotspots, encompassing a comparison of the differences between the two methodologies, the assumptions, the data coverage and sources, the completeness of inventory as basis for impact assessment. The main driver for the observed divergences is identified to be the differences in the impact intensities of goods, both induced by inherent properties of the IO and life cycle inventory databases and by some of this study’s modelling choices. The combination of IO analysis and process-based LCA in a hybrid framework, as performed in other studies but generally not at the macro-scale of the full trade of a country or region, appears a potential important perspective to refine such an assessment in the future.

     

Gap junctions in skeletal development and function

Gap junctions play a critical role in the coordinated function and activity of nearly all of the skeletal cells. This is not surprising, given the elaborate orchestration of skeletal patterning, bone modeling and subsequent remodeling, as well as the mechanical stresses, strains and adaptive responses that the skeleton must accommodate. Much remains to be learned regarding the role of gap junctions and hemichannels in these processes. A common theme is that without connexins none of the cells of bone function properly. Thus, connexins play an important role in skeletal form and function.     

Life cycle assessment of bio-based products: a disposable diaper case study

Purpose

In this study, a life cycle assessment of a bioplastic based diaper was performed. The product has several innovative elements, due to the implementation of eco-design principles, such as: (1) introduction of biopolymers (namely polylactic acid (PLA) and Mater-bi®), (2) relevant reduction of petrochemical plastics, and (3) minimization of energy consumptions and use of renewable energy in manufacturing. The aim of the study is to evaluate the environmental benefits gained through eco-innovation, while identifying further areas of improvement.

Methods

The bio-based diaper has been evaluated using a “cradle-to-gate” analysis. The functional unit is one diaper, assuming an average size among the different commercial options. A case study of an enterprise in Italy (WIP S.p.A) was carried out to collect as much reliable primary data as possible. In order to highlight potential areas of improvement and to compare the environmental performance of the product, a sensitivity analysis based on three different impact assessment methods (adopting ReCiPe 2008, IMPACT 2002+ and Cumulative Energy Demand (CED)) and a comparison with a standard commercial diaper were performed. Finally, three possible end-of-life scenarios including composting of WIP diaper were hypothesized and tested.

Results and discussion

Contribution analysis suggested that sourcing and production of raw materials used in WIP diaper manufacturing contributed most significantly to the potential environmental impacts. Adopting ReCiPe method, pulp, and sodium polyacrylate present the highest environmental burdens in WIP diaper system. Applying IMPACT2002+ method, PLA relative contribution to the toxicity increases, due to the generation of the electricity used in corn production and in PLA production phases. For both methods, impacts related to energy consumption of the WIP diapers’ production process look to be negligible. WIP diaper performance has room for improvement, since critical points were detected in the life cycle stages of raw materials used. However, the results of the normalization step, according to ReCiPe method, state that WIP diapers can bring environmental benefits, compared to standard ones. Moreover, if composting end-of-life scenario is included in the assessment, there is a significant improvement in WIP diaper environmental performance compared to a standard diaper.

Conclusions

Integrating eco-innovation and eco-design principles in the production of the bio-based diaper leads to a better environmental profile, compared to the standard one. Nevertheless, there are several areas of concerns to be considered in order to further improve its environmental performance. So far, the possible improvements identified from the case study are: (1) the selection of biopolymers suppliers with better production systems from an environmental point of view, (2) the reduction of distances along the supply chain, and (3) the implementation of composting procedures for the end of life. In conclusion, the introduction of biopolymers in diaper composition could lead them to be preferable compared to standard diapers, but criticisms arise, which need to be solved, to avoid the risk of burdens shifting.     

A distance-to-target weighting method for Europe 2020

Purpose

Distance-to-target (DTT) methods are weighting methods aimed at assessing the distance of an existing situation from a desired state (the target). Weighting factors in DTT methods could be based on calculation which is performed on normalization factors (NFs) developed for life cycle assessment (LCA). At present, some DTT weighting sets have been developed. However, there is no DTT weighting set assessing the distance of EU domestic impacts from the desired state set by EU binding or non-binding policy targets (e.g., those related to the “Climate and Energy Package” and the “Roadmap to a Resource Efficient Europe”).

Methods

In the present work, a methodology to derive target references from policy-based targets in 2020 (TRs2020), both binding (A) and non-binding (B), is presented. Resulting target factors and DTT weighting factors are then compared to the current normalisation factors (based on 2010 normalization references). The resulting weighting factor (WF) sets are presented and discussed in light of their use for decision support in policy and business contexts. We applied the WF sets to characterization results to an example (the EU energy mix process) aiming at illustrating key differences and effects on the results.

Results and discussion

The three reference sets (NRs2010, TRs2020A, and TRs2020B) show, in some impact categories, a relatively small difference. WFs referred to set A and set B result to be quite similar, with the only exception of water depletion impact category, for which a very relevant change is foreseen when considering the effect of the non-binding target of limiting the abstraction of water resource to 20 % of the available renewable water resources. This is mainly due to the higher difficulty in deriving quantitative targets from non-binding strategies and policies rather than from binding ones.

Conclusions

The resulting weighting sets present strengths and limitations. The translation of policy targets into quantitative modifications to the baseline inventories appeared to be not a straightforward task, due to several reasons discussed in the paper (e.g., not all the policy targets are expressed in quantitative terms or can be translated into quantitative reductions and modifications of the elementary flows in the existing baseline inventories). Aiming at improving the effectiveness in supporting policies, further development of the methodology may be the integration with other DTT approaches such those based on carrying capacity, developed to integrate Earth’s carrying capacity concept and planetary boundaries.

     

Alfalfa plant-derived biostimulant stimulate short-term growth of salt stressed Zea mays L. plants

Background & Aims

The effects of an alfalfa plant (Medicago sativa L.) hydrolysate-based biostimulant (EM) containing triacontanol (TRIA) and indole-3-acetic acid (IAA) were tested in salt-stressed maize plants.

Methods

Plants were grown for 2 weeks in the absence of NaCl or in the presence (25, 75 and 150 mM). On the 12th day, plants were supplied for 48 h with 1.0 mg L^?1 EM or 11.2 μM TRIA.

Results

EM and TRIA stimulated the growth and nitrogen assimilation of control plants to a similar degree, while NaCl reduced plant growth, SPAD index and protein content. EM or TRIA increased plant biomass under salinity conditions. Furthermore, EM induced the activity of enzymes functioning in nitrogen metabolism. The activity of antioxidant enzymes and the synthesis of phenolics were induced by salinity, but decreased after EM treatment. The enhancement of phenylalanine ammonia-lyase (PAL) activity and gene expression by EM was consistent with the increase of flavonoids.

Conclusion

The present study proves that the EM increases plant biomass even when plants are grown under salinity conditions. This was likely because EM stimulated plant nitrogen metabolism and antioxidant systems. Therefore, EM may be proposed as bioactive product in agriculture to help plants overcome stress situations.     

NEFA-glucose comodulation model of beta-cell insulin secretion in 24-h multiple-meal test

There is experimental evidence that a source of fatty acids (FAs) that is either exogenous or endogenous is necessary to support normal insulin secretion. Therefore, FAs comodulate the glucose-induced pancreatic insulin secretion. To assess the role of FAs, 16 morbidly obese nondiabetic patients and 6 healthy volunteers were studied. The controls and the obese subjects, before and after diet-induced weight loss, spent 24 h in a calorimetric chamber, where they consumed standardized meals. Hourly blood samples were drawn from a central venous catheter for the measurement of glucose, C-peptide, and nonesterified fatty acid (NEFA) concentrations. Insulin sensitivity was measured (as the M value) by euglycemic hyperinsulinemic clamp. In the present study, we propose a mathematical model in which insulin secretion rate (ISR) is expressed as a function of both plasma glucose and NEFA concentrations. Model parameters, obtained by fitting the individual experimental data of plasma C-peptide concentration, gave an estimated ISR comparable with that obtained by the deconvolution method. To evaluate the performance of the model in an experimental condition in which incretin effect was minimized, previous data on insulin secretion following a butter load and subsequent hyperglycemic clamp were reanalyzed. This model of nutrient-stimulated insulin secretion is the first attempt to represent in a simple way the interaction between glucose and NEFA in the regulation of insulin secretion in the beta-cell and explains, at least in part, the "potentiation factor" used in previous models to account for other control factors different from glucose after either an intravenous infusion of glucose or a mixed meal.     

The basic N-terminal domain of TRF2 limits recombination endonuclease action at human telomeres

The stability of mammalian telomeres depends upon TRF2, which prevents inappropriate repair and checkpoint activation. By using a plasmid integration assay in yeasts carrying humanized telomeres, we demonstrated that TRF2 possesses the intrinsic property to both stimulate initial homologous recombination events and to prevent their resolution via its basic N-terminal domain. In human cells, we further showed that this TRF2 domain prevents telomere shortening mediated by the resolvase-associated protein SLX4 as well as GEN1 and MUS81, 2 different types of endonucleases with resolvase activities. We propose that various types of resolvase activities are kept in check by the basic N-terminal domain of TRF2 in order to favor an accurate repair of the stalled forks that occur during telomere replication.