Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations

Saccharomyces cerevisiae is a model eukaryotic organism for classical genetics and genomics, and yet its ecology is still largely unknown. In this work, a population genetic analysis was performed on five yeast populations isolated from wine-making areas with different enological practices using simple sequence repeats and restriction fragment length polymorphism of mitochondrial DNA as molecular markers on 292 strains. In accordance with other studies, genome size estimation suggests that native S. cerevisiae strains are mainly homothallic and diploids. Analysis of mtDNA data showed that yeast populations from nonindustrial areas have 40% higher genetic diversity than populations isolated from industrial areas, demonstrating that industrial enological practices are likely to affect native yeast populations negatively by reducing its biodiversity. On the other hand, genetic differentiation analysis based on their microsatellite showed no correlation between genetic and geographic distance and a nonsignificant value when a Mantel test was applied. Finally, in the five populations studied, positive inbreeding ( F _is) values from 0.4 to 0.75, a low but significant level of linkage disequilibrium and a high number of multilocus genotypes were detected. These results strongly advocate that sexual reproduction is frequent enough to erase clonal signature in natural populations and that self-fertilization is the main mating system.     

A novel silicon patch‐clamp chip permits high‐fidelity recording of ion channel activity from functionally defined neurons

We report on a simple and high‐yield manufacturing process for silicon planar patch‐clamp chips, which allow low capacitance and series resistance from individually identified cultured neurons. Apertures are etched in a high‐quality silicon nitride film on a silicon wafer; wells are opened on the backside of the wafer by wet etching and passivated by a thick deposited silicon dioxide film to reduce the capacitance of the chip and to facilitate the formation of a high‐impedance cell to aperture seal. The chip surface is suitable for culture of neurons over a small orifice in the substrate with minimal leak current. Collectively, these features enable high‐fidelity electrophysiological recording of transmembrane currents resulting from ion channel activity in cultured neurons. Using cultured Lymnaea neurons we demonstrate whole‐cell current recordings obtained from a voltage‐clamp stimulation protocol, and in current‐clamp mode we report action potentials stimulated by membrane depolarization steps. Despite the relatively large size of these neurons, good temporal and spatial control of cell membrane voltage was evident. To our knowledge this is the first report of recording of ion channel activity and action potentials from neurons cultured directly on a planar patch‐clamp chip. This interrogation platform has enormous potential as a novel tool to readily provide high‐information content during pharmaceutical assays to investigate in vitro models of disease, as well as neuronal physiology and synaptic plasticity. Biotechnol. Bioeng. 2010;107:593–600. © 2010 Wiley Periodicals, Inc.     

Salinisation impacts in life cycle assessment: a review of challenges and options towards their consistent integration

Purpose

Salinisation is a threat not only to arable land but also to freshwater resources. Nevertheless, salinisation impacts have been rarely and only partially included in life cycle assessment (LCA) so far. The objectives of this review paper were to give a comprehensive overview of salinisation mechanisms due to human interventions, analyse the completeness, relevance and scientific robustness of existing published methods addressing salinisation in LCA and provide recommendations towards a comprehensive integration of salinisation within the impact modelling frameworks in LCA.

Methods

First, with the support of salinisation experts and related literature, we highlighted multiple causes of soil and water salinisation and presented induced effects on human health, ecosystems and resources. Second, existing life cycle impact assessment (LCIA) methods addressing salinisation were analysed against the International Reference Life Cycle Data System analysis grid of the European Commission. Third, adopting a holistic approach, the modelling options for salinisation impacts were analysed in agreement with up-to-date LCIA frameworks and models.

Results and discussion

We proposed a categorisation of salinisation processes in four main types based on salinisation determinism: land use change, irrigation, brine disposal and overuse of a water body. For each salinisation type, key human management and biophysical factors involved were identified. Although the existing methods addressing salinisation in LCA are important and relevant contributions, they are often incomplete with regards to both the salinisation pathways they address and their geographical validity. Thus, there is a lack of a consistent framework for salinisation impact assessment in LCA. In analysing existing LCIA models, we discussed the inventory and impact assessment boundary options. The land use/land use change framework represents a good basis for the integration of salinisation impacts due to a land use change but should be completed to account for off-site impacts. Conversely, the land use/land use change framework is not appropriate to model salinisation due to irrigation, overuse of a water body and brine disposal. For all salinisation pathways, a bottom-up approach describing the environmental mechanisms (fate, exposure and effect) is recommended rather than an empirical or top-down approach because (i) salts and water are mobile and theirs effects are interconnected; (ii) water and soil characteristics vary greatly spatially; (iii) this approach allows the evaluation of both on- and off-site impacts and (iv) it is the best way to discriminate systems and support a reliable eco-design.

Conclusions

This paper highlights the importance of including salinisation impacts in LCA. Much research effort is still required to include salinisation impacts in a global, consistent and operational manner in LCA, and this paper provides the basis for future methodological developments.

     

Allometric space and allometric disparity: a developmental perspective in the macroevolutionary analysis of morphological disparity

Here, we advance novel uses of allometric spaces--multidimensional spaces specifically defined by allometric coefficients--with the goal of investigating the focal role of development in shaping the evolution of morphological disparity. From their examination, operational measures of allometric disparity can be derived, complementing standard signals of morphological disparity through an intuitive and process-oriented refinement of established analytical protocols used in disparity studies. Allometric spaces thereby become a promising context to reveal different patterns of evolutionary developmental changes and to assess their relative prevalence and importance. Such spaces offer a novel domain of investigation of phenotypic variation and should help in detecting large-scale trends, thus placing various macroevolutionary phenomena in an explicitly developmental context. Ammonoidea (Cephalopoda) at the Lower-Middle Jurassic transition were chosen as a case study to illustrate this methodological approach. We constructed two phenotypic spaces: a static, adult one (adult morphospace) and a dynamic, developmental one (allometric space). Comparative disparity analyses show a strikingly stable occupation in both spaces, despite extensive change in taxonomic composition. In contrast, disparity analyses of subclades reveal clearly distinct morphological and allometric disparity dynamics. Allometric approaches allow developmental insights into morphological diversification otherwise intractable from the analysis of adult morphospace alone.     

Nuclear prostaglandin signaling system: biogenesis and actions via heptahelical receptors

Prostaglandins are ubiquitous lipid mediators that play pivotal roles in cardiovascular homeostasis, reproduction, and inflammation, as well as in many important cellular processes including gene expression and cell proliferation. The mechanism of action of these lipid messengers is thought to be primarily dependent on their interaction with specific cell surface receptors that belong to the heptahelical transmembrane spanning G protein-coupled receptor superfamily. Accumulating evidence suggests that these receptors may co-localize at the cell nucleus where they can modulate gene expression through a series of biochemical events. In this context, we have recently demonstrated that prostaglandin E2-EP3 receptors display an atypical nuclear compartmentalization in cerebral microvascular endothelial cells. Stimulation of these nuclear EP3 receptors leads to an increase of eNOS RNA in a cell-free isolated nuclear system. This review will emphasize these findings and describe how nuclear prostaglandin receptors, notably EP3 receptors, may affect gene expression, specifically of eNOS, by identifying putative transducing elements located within this organelle. The potential sources of lipid ligand activators for these intracellular sites will also be addressed. The expressional control of G-protein-coupled receptors located at the perinuclear envelope constitutes a novel and distinctive mode of gene regulation.     

A Virulent Phage Infecting Lactococcus garvieae,with Homology to Lactococcus lactis Phages

A new virulent phage belonging to the Siphoviridae family and able to infect Lactococcus garvieae strains was isolated from compost soil. Phage GE1 has a prolate capsid (56 by 38 nm) and a long noncontractile tail (123 nm). It had a burst size of 139 and a latent period of 31 min. Its host range was limited to only two L. garvieae strains out of 73 tested. Phage GE1 has a double-stranded DNA genome of 24,847 bp containing 48 predicted open reading frames (ORFs). Putative functions could be assigned to only 14 ORFs, and significant matches in public databases were found for only 17 ORFs, indicating that GE1 is a novel phage and its genome contains several new viral genes and encodes several new viral proteins. Of these 17 ORFs, 16 were homologous to deduced proteins of virulent phages infecting the dairy bacterium Lactococcus lactis, including previously characterized prolate-headed phages. Comparative genome analysis confirmed the relatedness of L. garvieae phage GE1 to L. lactis phages c2 (22,172 bp) and Q54 (26,537 bp), although its genome organization was closer to that of phage c2. Phage GE1 did not infect any of the 58 L. lactis strains tested. This study suggests that phages infecting different lactococcal species may have a common ancestor.     

Cyto-nuclear discordance in the phylogeny of Ficus section Galoglychia and host shifts in plant-pollinator associations

Background  

Hybridization events are relatively common in vascular plants. However, the frequency of these events is unevenly distributed across the plant phylogeny. Plant families in which individual species are pollinated by specific pollinator species are predicted to be less prone to hybridization than other families. However, exceptions may occur within these families, when pollinators shift host-plant species. Indeed, host shifts are expected to increase the rate of hybridization events. Pollinators of Ficus section Galoglychia are suspected to have changed host repeatedly, based on several cases of incongruence between plant phylogeny and taxonomy, and insect phylogeny and taxonomy. We tracked cyto-nuclear discordance across section Galoglychia as evidence for hybridization. To achieve a proper global view, we first clarified the monophyly of section Galoglychia as it had been questioned by recent phylogenetic studies. Moreover, we investigated if fig size could be a factor facilitating host shifts.     

Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data

Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete‐case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete‐case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices.     

Mapping of schistosomiasis and soil-transmitted helminthiases across 15 provinces of Angola

IntroductionSchistosomiasis (SCH) and soil transmitted helminthiases (STH) have been historically recognized as a major public health problem in Angola. However, lack of reliable, country wide prevalence data on these diseases has been a major hurdle to plan and implement programme actions to target these diseases. This study aimed to characterize SCH and STH prevalence and distribution in Angola.MethodsA country wide mapping was conducted in October 2018 (1 province) and from July to December 2019 (14 provinces) in school aged (SAC) children in 15 (of 18) provinces in Angola, using WHO protocols and procedures. A total of 640 schools and an average of 50 students per school (N = 31,938 children) were sampled. Stool and urine samples were collected and processed using the Kato-Katz method and Urine Filtration. Prevalence estimates for SCH and STH infections were calculated for each province and district with 95% confidence intervals. Factors associated with SCH and STH infection, respectively, were explored using multivariable logistic regression accounting for clustering by school.ResultsOf the 131 districts surveyed, 112 (85.5%) are endemic for STH, 30 (22.9%) have a prevalence above 50%, 24 (18.3%) are at moderate risk (prevalence 20%-50%), and 58 (44.3%) are at low risk (<20% prevalence); similarly, 118 (90,1%) of surveyed districts are endemic for any SCH, 2 (1.5%) are at high risk (>50% prevalence), 59 (45.0%) are at moderate risk (10%-50% prevalence), and 57 (43.5%) are at low risk (<10% prevalence). There were higher STH infection rates in the northern provinces of Malanje and Lunda Norte, and higher SCH infection rates in the southern provinces of Benguela and Huila.ConclusionsThis mapping exercise provides essential information to Ministry of Health in Angola to accurately plan and implement SCH and STH control activities in the upcoming years. Data also provides a useful baseline contribution for Angola to track its progress towards the 2030 NTD roadmap targets set by WHO.     

One for all and all for one: the energetic benefits of huddling in endotherms

Huddling can be defined as “an active and close aggregation of animals”. It is a cooperative group behaviour, permitting individuals involved in social thermoregulation to minimize heat loss and thereby lower their energy expenditure, and possibly allowing them to reallocate the saved energy to other functions such as growth or reproduction. Huddling is especially important in the case of animals faced with high heat loss due to a high surface‐to‐volume ratio, poor insulation, or living in cold environments. Although numerous experimental studies have focused on the huddling behaviour of a wide range of species, to our knowledge, this is the first attempt to review the various implications of this widely used behavioural strategy. Huddling allows individuals to maximise energy savings by (1) decreasing their cold‐exposed body surface area, (2) reducing their heat loss through warming of ambient temperatures surrounding the group, and (3) eventually lowering their body temperature through physiological processes. Huddling provides substantial energy savings and is estimated to reduce energy expenditure by between 6 and 53%. Broad variations in the energetic benefits of huddling depend on the number of individuals and species involved in huddles, the ambient temperatures to which individuals are exposed and the density of the aggregations. It has been shown that huddling individuals have increased survival, a lower food intake, a decreased body mass loss, increased growth rate, reduced water loss, and/or a more constant body temperature together with a significant reduction in metabolic rate. Though huddling has been studied widely, this review reveals the intricacies of this adaptive behaviour.