Extracellular metabolomics: a metabolic footprinting approach to assess fiber degradation in complex media

This work reports the implementation and optimization of a method for high-throughput analysis of metabolites produced by the breakdown of natural polysaccharides by microorganisms. Our simple protocol enables simultaneous separation and quantification of more than 40 different sugars and sugar derivatives, in addition to several organic acids in complex media, using 50-mul samples and a standard gas chromatography-mass spectrometry platform that was fully optimized for this purpose. As an implementation proof-of-concept, we assayed extracellular metabolite levels of three bacterial strains cultivated on complex medium rich in polysaccharides and under identical growth conditions. We demonstrate that the metabolic footprinting profile data distinguish among sample types such as typical metabolomics data. Moreover, we demonstrate that the differential metabolite-level data provide insight on specific fibrolytic activity of the different microbial strains and lay the groundwork for integrated proteome-metabolome studies of fiber-degrading microorganisms.     

From the arcane to the mundane: engaging French publics in discussing clinical applications of genomic technology

Genomic technologies are developing at a time when greater public involvement in research and clinical governance is sought. To this end, empirical bioethics studies, although conceptualized as academic endeavors, may draw on the inclusion of laypeople to justify informing policy. Doing so, they face similar concerns as those addressed to public consultations which cannot be termed democratic a priori and may reinforce the authority of experts. We reflect on these concerns in the process of analyzing the results of a qualitative analysis of eight focus groups (64 participants) held in France during 2010–2012, designed to understand laypeople's views of the ethical debates surrounding genomic medicine. We examine how the notions of “lay” and “expert” play in the framework of the study and how participants situate themselves along this divide. This understanding of the social context in which the publics are situated enables a more reflexive and accurate ethical analysis.     

A cross-scale framework to support a mechanistic understanding and modelling of marine climate-driven species redistribution,from individuals to communities

Climate-driven species redistribution is pervasive and accelerating, yet the complex mechanisms at play remain poorly understood. The implications of large-scale species redistribution for natural systems and human societies have resulted in a large number of studies exploring the effects on individual species and ecological communities worldwide. Whilst many studies have investigated discrete components of species redistribution, the integration required for a more complete mechanistic understanding is lacking. In this paper, we provide a framework for synthesising approaches to more robustly understand and predict marine species redistributions. We conceptualise the stages and processes involved in climate-driven species redistribution at increasing levels of biological organisation, and synthesize the laboratory, field and modelling approaches used to study redistribution related processes at individual, population and community levels. We then summarise links between scales of biological organisation and methodological approaches in a hierarchical framework that represents an integrated mechanistic assessment of climate-driven species redistributions. In a rapidly expanding field of research, this framework provides direction for: 1) guiding future research, 2) highlighting key knowledge gaps, 3) fostering data exchange and collaboration between disciplines and 4) improving shared capacity to predict and therefore, inform the proactive management of climate impacts on natural systems.     

Craniofacial Ciliopathies Reveal Specific Requirements for GLI Proteins during Development of the Facial Midline

Ciliopathies represent a broad class of disorders that affect multiple organ systems. The craniofacial complex is among those most severely affected when primary cilia are not functional. We previously reported that loss of primary cilia on cranial neural crest cells, via a conditional knockout of the intraflagellar transport protein KIF3a, resulted in midfacial widening due to a gain of Hedgehog (HH) activity. Here, we examine the molecular mechanism of how a loss of primary cilia can produce facial phenotypes associated with a gain of HH function. We show that loss of intraflagellar transport proteins (KIF3a or IFT88) caused aberrant GLI processing such that the amount of GLI3FL and GLI2FL was increased, thus skewing the ratio of GLIFL to GLIR in favor of the FL isoform. Genetic addition of GLI3R partially rescued the ciliopathic midfacial widening. Interestingly, despite several previous studies suggesting midfacial development relies heavily on GLI3R activity, the conditional loss of GLI3 alone did not reproduce the ciliopathic phenotype. Only the combined loss of both GLI2 and GLI3 was able to phenocopy the ciliopathic midfacial appearance. Our findings suggest that ciliopathic facial phenotypes are generated via loss of both GLI3R and GLI2R and that this pathology occurs via a de-repression mechanism. Furthermore, these studies suggest a novel role for GLI2R in craniofacial development.     

Incorporation of cis-9,trans-11 or trans-10,cis-12 conjugated linoleic acid into plasma and cellular lipids in healthy men

This study investigated the incorporation of cis-9,trans-11 conjugated linoleic acid (c9,t11 CLA) and trans-10,cis-12-CLA (t10,c12 CLA) into plasma and peripheral blood mononuclear cell (PBMC) lipids when consumed as supplements highly enriched in these isomers. Healthy men (n = 49, age 31 +/- 8 years) consumed one, two, and four capsules containing approximately 600 mg of either c9,t11 CLA or t10,c12 CLA per capsule for sequential 8 week periods followed by a 6 week washout before consuming the alternative isomer. Both isomers were incorporated in a dose-dependent manner into plasma phosphatidylcholine (PC) (c9,t11 CLA r = 0.779, t10,c12 CLA r = 0.738; P < 0.0001) and cholesteryl ester (CE) (c9,t11 CLA r = 0.706, t10,c12 CLA r = 0.788; P < 0.0001). Only t10,c12 CLA was enriched in plasma nonesterified fatty acids. Both c9,t11 CLA and t10,c12 CLA were incorporated linearly into PBMC total lipids (r = 0.285 and r = 0.273, respectively; P < 0.0005). The highest concentrations of c9,t11 CLA and t10,c12 CLA in PBMC lipids were 3- to 4-fold lower than those in plasma PC and CE. These data suggest that the level of intake is a major determinant of plasma and PBMC CLA content, although PBMCs appear to incorporate both CLA isomers less readily.     

Oecophylla smaragdina ants provide pest control in Australian cacao

Ecosystem service‐driven methods of agricultural production that make optimal use of an ecosystem's natural services are often effective in smallholder crops, leading increases in habitat heterogeneity at large spatial scales that encourage beneficial species. Pollination services in cacao farms can be enhanced through efforts to conserve pollinator habitats, such as adding cacao fruit husks underneath trees to provide habitat and food resources for midge pollinators. However, it remains unclear how this habitat manipulation affects pest densities or biological control. Here, we evaluated the effects of the predaceous ant Oecophylla smaragdina on three major pests of Australian cacao (Helopeltis spp., Amblypelta spp., and Rhyparida nitida) in an Australian cacao farm, in the presence and absence of cacao fruit husks. We also evaluated the effect of O. smaragdina on their potentially plant‐damaging, mutualistic mealybug (Pseudococcidae) partners in the presence and absence of cacao fruit husks. Oecophylla smaragdina reduced the combined densities of Helopeltis spp. and Amblypelta spp., regardless of cacao fruit husk addition. The ants also reduced the densities of R. nitida in the absence of cacao fruit husks, but R. nitida densities were naturally low in the experimental plots that received the addition of cacao fruit husks, regardless of ant presence. In contrast, ants generally increased the densities of mealybugs. These data suggest that O. smaragdina ants provide pest control services for three major insect pests in Australian cacao farms. Furthermore, this control may be compatible with habitat manipulations (i.e., the addition of cacao fruit husks) to improve pollinator habitat.     

Analysis of methane monooxygenase genes in mono lake suggests that increased methane oxidation activity may correlate with a change in methanotroph community structure

Mono Lake is an alkaline hypersaline lake that supports high methane oxidation rates. Retrieved pmoA sequences showed a broad diversity of aerobic methane oxidizers including the type I methanotrophs Methylobacter (the dominant genus), Methylomicrobium, and Methylothermus, and the type II methanotroph Methylocystis. Stratification of Mono Lake resulted in variation of aerobic methane oxidation rates with depth. Methanotroph diversity as determined by analysis of pmoA using new denaturing gradient gel electrophoresis primers suggested that variations in methane oxidation activity may correlate with changes in methanotroph community composition.