Estimating Genetic Ancestry Proportions from Faces

Ethnicity can be a means by which people identify themselves and others. This type of identification mediates many kinds of social interactions and may reflect adaptations to a long history of group living in humans. Recent admixture in the US between groups from different continents, and the historically strong emphasis on phenotypic differences between members of these groups, presents an opportunity to examine the degree of concordance between estimates of group membership based on genetic markers and on visually-based estimates of facial features. We first measured the degree of Native American, European, African and East Asian genetic admixture in a sample of 14 self-identified Hispanic individuals, chosen to cover a broad range of Native American and European genetic admixture proportions. We showed frontal and side-view photographs of the 14 individuals to 241 subjects living in New Mexico, and asked them to estimate the degree of NA admixture for each individual. We assess the overall concordance for each observer based on an aggregated measure of the difference between the observer and the genetic estimates. We find that observers reach a significantly higher degree of concordance than expected by chance, and that the degree of concordance as well as the direction of the discrepancy in estimates differs based on the ethnicity of the observer, but not on the observers'' age or sex. This study highlights the potentially high degree of discordance between physical appearance and genetic measures of ethnicity, as well as how perceptions of ethnic affiliation are context-specific. We compare our findings to those of previous studies and discuss their implications.     

A multidimensional <Superscript>1</Superscript>H NMR lipidomics workflow to address chemical food safety issues

Introduction

Although it is still at a very early stage compared to its mass spectrometry (MS) counterpart, proton nuclear magnetic resonance (NMR) lipidomics is worth being investigated as an original and complementary solution for lipidomics. Dedicated sample preparation protocols and adapted data acquisition methods have to be developed to set up an NMR lipidomics workflow; in particular, the considerable overlap observed for lipid signals on 1D spectra may hamper its applicability.

Objectives

The study describes the development of a complete proton NMR lipidomics workflow for application to serum fingerprinting. It includes the assessment of fast 2D NMR strategies, which, besides reducing signal overlap by spreading the signals along a second dimension, offer compatibility with the high-throughput requirements of food quality characterization.

Method

The robustness of the developed sample preparation protocol is assessed in terms of repeatability and ability to provide informative fingerprints; further, different NMR acquisition schemes—including classical 1D, fast 2D based on non-uniform sampling or ultrafast schemes—are evaluated and compared. Finally, as a proof of concept, the developed workflow is applied to characterize lipid profiles disruption in serum from β-agonists diet fed pigs.

Results

Our results show the ability of the workflow to discriminate efficiently sample groups based on their lipidic profile, while using fast 2D NMR methods in an automated acquisition framework.

Conclusion

This work demonstrates the potential of fast multidimensional ¹H NMR—suited with an appropriate sample preparation—for lipidomics fingerprinting as well as its applicability to address chemical food safety issues.

     

Occurrence of ochratoxin A in <Emphasis Type="Italic">Astragalus propinquus</Emphasis> root and its transfer to decoction

The aim of this study was to conduct a survey assessing (a) the ochratoxin A (OTA) content in different samples of Astragalus propinquus root (AR), one of the fundamental herbs in traditional Chinese medicine, and (b) the rate of OTA transfer to AR decoctions that are traditionally used to reduce general weakness and increase overall vitality. A validated method of high-performance liquid chromatography with fluorescence detection (HPLC-FLD) was used to determine OTA concentrations in AR samples and AR decoctions. The limit of quantification was 0.35 ng/g; the recovery of the HPLC method for AR samples was 82%; and the relative standard deviation (SD) of repeatability was 2.6%. All 40 tested AR samples were positive, with a mean value of 451.0 ng/g (range, 28.8–1700.0 ng/g). The transfer rate of OTA to decoctions, from a naturally contaminated and homogenized AR sample (internal reference material) with a concentration of OTA of 288.9 ng/g?±?12.3 (SD), was 83.4%?±?8.5 (SD). We believe it is necessary to continue OTA monitoring in AR and other herbal products, estimate the actual human usual intake, and perform health risk assessment.     

Separating effects of species identity and species richness on predation,pathogen dissemination and resistance to invasive species in tropical ant communities

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Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilisation

Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major forms of environmental change – fertilisation and herbivore loss – are affected by species pool size and spatial compositional heterogeneity. Fertilisation led to higher rates of local extinction, whereas turnover in herbivore exclusion plots was driven by species replacement. Overall, sites with more spatially heterogeneous composition showed significantly higher rates of annual turnover, independent of species pool size and treatment. Taking into account spatial biodiversity aspects will therefore improve our understanding of consequences of global and anthropogenic change on community dynamics.     

Stand dynamics modulate water cycling and mortality risk in droughted tropical forest

Transpiration from the Amazon rainforest generates an essential water source at a global and local scale. However, changes in rainforest function with climate change can disrupt this process, causing significant reductions in precipitation across Amazonia, and potentially at a global scale. We report the only study of forest transpiration following a long‐term (>10 year) experimental drought treatment in Amazonian forest. After 15 years of receiving half the normal rainfall, drought‐related tree mortality caused total forest transpiration to decrease by 30%. However, the surviving droughted trees maintained or increased transpiration because of reduced competition for water and increased light availability, which is consistent with increased growth rates. Consequently, the amount of water supplied as rainfall reaching the soil and directly recycled as transpiration increased to 100%. This value was 25% greater than for adjacent nondroughted forest. If these drought conditions were accompanied by a modest increase in temperature (e.g., 1.5°C), water demand would exceed supply, making the forest more prone to increased tree mortality.     

Production of TNFα and IL-6 by Activated Whole Blood from HIV-1 Infected Patients Detected by a One-Stage Procedure: Relationship with the Phenotype of HIV-1 Isolates

Diluted whole blood (WB) culturing may be the most appropriate milieu in which to study cytokine production in vitro. We tested TNFα and IL-6 production using small volumes of WB (25 μl) from HIV-1 positive patients with a one-step procedure that combines WB stimulation with LPS, PHA and cytokine measurement. We studied 49 patients without secondary infection or at distance of secondary infection staged according to the 1993 classification of the CDC and 12 healthy seronegative subjects. Heparinized blood from 5 control subjects had been collected sequentially during a period of 5 months. The individual variations of TNFα and IL-6 production were limited for all these individuals. In 1 out of 20 CDC group A patients, 6 out of 17 CDC group B patients and 3 out of 12 CDC group C patients, we obtained higher values of TNFα than the mean + 2 S.D. of the control group. In 3 out of 20 CDC group A patients, 1 out of 17 CDC group B patients without AIDS and 5 out of 12 CDC group C patients, the TNFα values were lower than the mean ?2 S.D. of the control group. Low IL-6 values were obtained in 1 out of 20 CDC group A patients and 1 out of 17 CDC group B patients and 3 out of 12 CDC group C patients. There was no correlation between TNFα production in vitro and plasma level of TNFα. We found no correlation between the levels of cytokines and monocyte count or between the levels of cytokines and CD4 T-cell count in peripheral blood. Our data point out a disarray in TNFα and IL-6 production by WB from HIV-1 infected patients. The relationship between the disarray of cytokine production and cytopathogenicity of HIV-1 isolates in the P4 cell line was investigated in this study. We found a correlation between the high level of TNFα produced by WB and the phenotype of HIV-1 isolates isolated from patients. The one-stage procedure used in this work is of potential value to investigate the activation status of cells for monitoring HIV-1 positive individuals and predicting HIV-1 phenotype.     

Evolutionary and biogeographical implications of the karyological variations in the oviparous and viviparous forms of the lizard Lacerta (Zootoca) vivipara

The lizard Lacerta ( Zootoca ) vivipara has two modes of reproduction and is variable karyologically. We describe its karyological variation from literature data and from new data on two viviparous populations from France, on two oviparous populations from the Pyrenees in south-western France and on three oviparous populations recently discovered in Slovenia. Males have 36 chromosomes, whereas females have only 35 chromosomes in all viviparous populations and in the Pyrenean oviparous populations. This karyotype has been interpreted to result from a fusion of an ancestral sexual W chromosome with an autosome from the Zl or from the Z2 pair. The karyotype formula is 32 autosomes + ZIZ2W for the female and 32 autosomes + Z1Z1Z2Z2 for the male. The karyotype of the Slovenian oviparous populations, 34 autosomes + ZW in the male and 34 autosomes +ZW in the female, represents an evolutionary stage that preceded the chromosomal fusion. There is minor karyological variation, mainly concerning the W and Z2 chromosomes, within the Pyrenean oviparous populations. This parallels the geographic variation of the W-linked alleles of the MPI enzyme and suggests that allopatric differentiation of these oviparous populations might have occurred in the vicinity of the Pyrenees during the Pleistocene.
The viviparous populations from western Europe carry a metacentric W chromosome, whereas oviparous populations from south-western Europe and eastern viviparous populations both show an acrocentrie, or a subtelocentrie. W chromosome. This suggests that the acrocentric-subtelocentric W is a primitive character and that viviparity probably arose in an eastern lineage of the species.     

Wing morphology of the active flyer Calliphora vicina (Diptera: Calliphoridae) during its invasion of a sub‐Antarctic archipelago where insect flightlessness is the rule

The cosmopolitan blowfly Calliphora vicina became established in the sub‐Antarctic Kerguelen Islands in the late 1970s, following a warming period that allowed its full development. Although temperature and wind may limit flight activity, the fly invaded the archipelago, reaching sites remote from the introduction point. Most native competitors have converged to flightlessness as a response to stringent environmental conditions and therefore the flight strategy of C. vicina might be either a handicap or a competitive advantage under ongoing climate change. Using geometric morphometrics, we investigated whether the wing had changed over time in C. vicina within the archipelago (1998 vs. 2009) and compared its morphology with that of a continental population from a temperate area (1983 vs. 2009). Wing shape plasticity to temperature was also experimentally investigated. We found no clues of relaxed selection on flight morphology in the range invaded. However, rapid changes of wing shape occurred over time in females from the Kerguelen Islands compared with both males and females of the continental population, despite a shorter time‐lag between samples in the former. The thermal reaction norms for wing shape found for C. vicina from Kerguelen were also different from those of the continental population, but it remains unknown whether this resulted from or preceded the introduction. These combined findings are consistent with a fingerprint of local adaptation in the invasive population. However, the adaptive significance of the changes, in terms of their aerodynamic consequences and the future evolution of C. vicina in the Kerguelen Islands, requires further investigation. From an evolutionary standpoint, sustaining flight capability under the novel sub‐Antarctic conditions might be critical to the invasive success of C. vicina as most competitors are flightless.