Transgenic papaya: a useful platform for oral vaccines

Planta - Transgenic papaya callus lines expressing the components of the S3Pvac vaccine constitute a stable platform to produce an oral vaccine against cysticercosis caused by Taenia solium or T....     

Population size,center–periphery,and seed dispersers’ effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon

The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species’ distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation (H_E: 0.04–0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long‐distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates (F_IS = 0.155–0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among‐population differentiation highlight the conservation value of large populations throughout the species’ range, particularly in light of climate change and direct human threats.     

An SSR‐based approach incorporating a novel algorithm for identification of rare maize genotypes facilitates criteria for landrace conservation in Mexico

As maize was domesticated in Mexico around 9,000 years ago, local farmers have selected and maintained seed stocks with particular traits and adapted to local conditions. In the present day, many of these landraces are still cultivated; however, increased urbanization and migration from rural areas implies a risk that this invaluable maize germplasm may be lost. In order to implement an efficient mechanism of conservation in situ, the diversity of these landrace populations must be estimated. Development of a method to select the minimum number of samples that would include the maximum number of alleles and identify germplasm harboring rare combinations of particular alleles will also safeguard the efficient ex‐situ conservation of this germplasm. To reach this goal, a strategy based on SSR analysis and a novel algorithm to define a minimum collection and rare genotypes using landrace populations from Puebla State, Mexico, was developed as a “proof of concept” for methodology that could be extended to all maize landrace populations in Mexico and eventually to other native crops. The SSR‐based strategy using bulked DNA samples allows rapid processing of large numbers of samples and can be set up in most laboratories equipped for basic molecular biology. Therefore, continuous monitoring of landrace populations locally could easily be carried out. This methodology can now be applied to support incentives for small farmers for the in situ conservation of these traditional cultivars.     

Using random forests for assistance in the curation of G-protein coupled receptor databases

Background

Biology is experiencing a gradual but fast transformation from a laboratory-centred science towards a data-centred one. As such, it requires robust data engineering and the use of quantitative data analysis methods as part of database curation. This paper focuses on G protein-coupled receptors, a large and heterogeneous super-family of cell membrane proteins of interest to biology in general. One of its families, Class C, is of particular interest to pharmacology and drug design. This family is quite heterogeneous on its own, and the discrimination of its several sub-families is a challenging problem. In the absence of known crystal structure, such discrimination must rely on their primary amino acid sequences.

Methods

We are interested not as much in achieving maximum sub-family discrimination accuracy using quantitative methods, but in exploring sequence misclassification behavior. Specifically, we are interested in isolating those sequences showing consistent misclassification, that is, sequences that are very often misclassified and almost always to the same wrong sub-family. Random forests are used for this analysis due to their ensemble nature, which makes them naturally suited to gauge the consistency of misclassification. This consistency is here defined through the voting scheme of their base tree classifiers.

Results

Detailed consistency results for the random forest ensemble classification were obtained for all receptors and for all data transformations of their unaligned primary sequences. Shortlists of the most consistently misclassified receptors for each subfamily and transformation, as well as an overall shortlist including those cases that were consistently misclassified across transformations, were obtained. The latter should be referred to experts for further investigation as a data curation task.

Conclusion

The automatic discrimination of the Class C sub-families of G protein-coupled receptors from their unaligned primary sequences shows clear limits. This study has investigated in some detail the consistency of their misclassification using random forest ensemble classifiers. Different sub-families have been shown to display very different discrimination consistency behaviors. The individual identification of consistently misclassified sequences should provide a tool for quality control to GPCR database curators.

     

Effect of volcanic ash deposition on length and radial growths of a deciduous montane tree (Nothofagus pumilio)

Extreme environmental events such as volcanic eruptions can trigger plant responses that largely exceed those recorded for moderate‐intensity disturbances. We assessed the effects of the June 2011 eruption of the Puyehue – Cordón Caulle volcano on the length and radial growths of juvenile Nothofagus pumilio trees at two sites located 20 (with >40 cm ash accretion) and 75 (without ash) km from the volcano. Variations in length and radial growth were evaluated for the periods 1999–2013 and 1993–2013 respectively; pre‐ and post‐eruption growth rates were computed. The length growth of the N. pumilio trees located close to the volcano increased significantly after the eruption: shoot extensions during the growing season after the eruption were, on average, two to three times longer than average according to ontogenetic growth trends. Variations in radial growth after the eruption were comparatively less noticeable than those in length growth. No significant effects of the eruption were observed in those trees located 75 km from the volcano. In order to explain the exceptionally positive response of N. pumilio's length growth to the volcanic eruption, three non‐exclusive explanations were proposed: (i) thick ash layers increase water retention in the soil; (ii) volcanic ash facilitates the access of plants to nutrients; and (iii) volcanic ashes decrease herbivory and competition. The comparatively lower sensitivity of radial growth to this extreme volcanic event is also noteworthy. These findings highlight the need to further examine how large‐scale volcanic events influence structure and/or functioning of ecosystem in the Patagonian forest.     

Selected contribution: Acute and sustained ventilatory responses to hypoxia in high-altitude natives living at sea level.

High-altitude (HA) natives have blunted ventilatory responses to hypoxia (HVR), but studies differ as to whether this blunting is lost when HA natives migrate to live at sea level (SL), possibly because HVR has been assessed with different durations of hypoxic exposure (acute vs. sustained). To investigate this, 50 HA natives (>3,500 m, for >20 yr) now resident at SL were compared with 50 SL natives as controls. Isocapnic HVR was assessed by using two protocols: protocol 1, progressive stepwise induction of hypoxia over 5-6 min; and protocol 2, sustained (20-min) hypoxia (end-tidal Po(2) = 50 Torr). Acute HVR was assessed from both protocols, and sustained HVR from protocol 2. For HA natives, acute HVR was 79% [95% confidence interval (CI): 52-106%, P = not significant] of SL controls for protocol 1 and 74% (95% CI: 52-96%, P < 0.05) for protocol 2. By contrast, sustained HVR after 20-min hypoxia was only 30% (95% CI: -7-67%, P < 0.001) of SL control values. The persistent blunting of HVR of HA natives resident at SL is substantially less to acute than to sustained hypoxia, when hypoxic ventilatory depression can develop.     

Comparison of transient otoacoustic emission responses from neonatal and adult ears.

Transient otoacoustic emission (TEOAE) responses from neonatal (age: 48 h) and adult subjects (age: 26.6 +/- 10.0 yr) were analyzed by the combined use of recurrence quantification analysis and singular value decomposition. The data from the two age groups showed significant differences and similarities. The neonatal responses presented less deterministic structures than those of the adults in terms of recurrent dynamic features. In both data sets, the same high level of individual specific dynamic features was observed. The results from the singular value decomposition analysis suggest that a large percentage of variability in all of the analyzed responses can be explained by four to five essential modes. This number is lower than that observed in simulated TEOAE responses generated by a five-component gammatone model. A possible explanation is presented, based on simple instrumental and morphoanatomic considerations.