Peanut gene expression profiling in developing seeds at different reproduction stages during <Emphasis Type="Italic">Aspergillus parasiticus</Emphasis>infection

Background  

Peanut (Arachis hypogaea L.) is an important crop economically and nutritionally, and is one of the most susceptible host crops to colonization of Aspergillus parasiticus and subsequent aflatoxin contamination. Knowledge from molecular genetic studies could help to devise strategies in alleviating this problem; however, few peanut DNA sequences are available in the public database. In order to understand the molecular basis of host resistance to aflatoxin contamination, a large-scale project was conducted to generate expressed sequence tags (ESTs) from developing seeds to identify resistance-related genes involved in defense response against Aspergillus infection and subsequent aflatoxin contamination.     

Sequence context affects the rate of short insertions and deletions in flies and primates

Background  

Insertions and deletions (indels) are an important evolutionary force, making the evolutionary process more efficient and flexible by copying and removing genomic fragments of various lengths instead of rediscovering them by point mutations. As a mutational process, indels are known to be more active in specific sequences (like micro-satellites) but not much is known about the more general and mechanistic effect of sequence context on the insertion and deletion susceptibility of genomic loci.     

Blood Selenium Associated with Health and Fertility in Norwegian Dairy Herds

A survey of blood selenium (Se) concentrations in Norwegian Red heifers and dry period cows was conducted to reveal possible association to management, feeding, health and fertility. Selenium contents were determined in 254 herd blood samples consisting of pooled samples from individual non-lactating animals from herds in 5 counties. The Se concentrations showed a normal distribution with mean 0.09 μg Se/g blood, with a standard deviation (SD) of 0.05, and ranged from 0.02 to 0.23 μg/g, with 50 % of the samples being between 0.06 and 0.11 μg/g. The herds with Se concentrations below 0.06 μg/g were smaller (21.4 ± 8.7 cow-years) than those with Se levels above 0.11 μg/g (27.5 ± 14.1 cow-years) (P < 0.01), but there were no differences in milk yield, incidence of replacement, proportion of animal culling, amount of concentrate or grass silage as percentage of energy consumption between the groups. Treatment registration records showed a tendency that more animals in the low Se herds were treated for all the diseases included in this investigation (64.8 animals per 100 cow-years) than those in the high Se herds (57.5 per 100 cow-years), while no such differences were revealed for individual disorders. There was, however, a significant difference in bulk milk somatic cell counts (BMSCC) between low and high Se herds, their values being 137 000 and 155 000 cells/ml, respectively. This difference was significantly influenced by herd size. Furthermore, a total of 4 916 lactations were analyzed from individual health and fertility recordings, including 2 934 first lactations and 1 982 later lactations. The present study revealed a reduced incidence of disease treatment with increased Se concentrations from 0.02 to 0.23 μg Se/g blood. In this regard, there seemed to be an optimum of 0.10 to 0.15 μg Se/g for all types of mastitis treatments summarized, and for treatment of retained placenta. Thus, herd Se concentrations below and above these values was connected with increased probability for sum mastitis and retained placenta, reflecting the effect of the quadratic term of Se. The cow (composite) milk somatic cell count (SCC) was lower in lactations from low Se herds than in high Se herds with a marked SCC increase in the Se concentration interval from 0.11–0.13 μg/g blood. In conclusion, heifers and dry period cows in Norway are low in blood Se content and there seems to be a positive association between increased blood Se concentration pre partum and decreased incidence of mastitis, ovarian cysts and anoestrus/silent oestrus post partum.     

Landscape fragmentation generates spatial variation of diet composition and quality in a generalist herbivore

Forest fragmentation may benefit generalist herbivores by increasing access to various substitutable food resources, with potential consequences for their population dynamics. We studied a European roe deer (Capreolus capreolus) population living in an agricultural mosaic of forest, woodlots, meadows and cultivated crops. We tested whether diet composition and quality varied spatially across the landscape using botanical analyses of rumen contents and chemical analyses of the plants consumed in relation to landscape metrics. In summer and non-mast winters, roe deer ate more cultivated seeds and less native forest browse with increasing availability of crops in the local landscape. This spatial variation resulted in contrasting diet quality, with more cell content and lower lignin and hemicellulose content (high quality) for individuals living in more open habitats. The pattern was less marked in the other seasons when diet composition, but not diet quality, was only weakly related to landscape structure. In mast autumns and winters, the consumption of acorns across the entire landscape resulted in a low level of differentiation in diet composition and quality. Our results reflect the ability of generalist species, such as roe deer, to adapt to the fragmentation of their forest habitat by exhibiting a plastic feeding behavior, enabling them to use supplementary resources available in the agricultural matrix. This flexibility confers nutritional advantages to individuals with access to cultivated fields when their native food resources are depleted or decline in quality (e.g. during non-mast years) and may explain local heterogeneities in individual phenotypic quality.     

Lineage-specific evolution and gene flow in Listeria monocytogenes are independent of bacteriophages

Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracking of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage-specific characteristics call for a more detailed understanding of evolution. In our work, we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage-mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages, we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.     

Patterns of Genetic Diversity in Rare and Common Orchids Focusing on the Korean Peninsula: Implications for Conservation

To provide basic information for orchid conservation, we surveyed the plant allozyme literature to summarize genetic diversity and structure data for (i) rare orchids native to the Korean Peninsula, and (ii) their congeners irrespective of being common and rare or Korean or not. A total of 68 taxa (32 taxa in Korea and 37 outside Korea; Goodyera repens being included in both datasets) were considered in this study. Overall, rare Korean orchid species had significantly lower levels of genetic diversity than their common congeners and common orchids in general at both population and species levels. However, mean values of G _ST (or F _ST) for rare and common orchids (Korean or not) did not differ significantly from each other. We found patterns of both low and high genetic diversity in rare Korean orchids. Many rare orchids harbored a complete lack of allozyme variation or extremely low within-population variation, perhaps due to rarity associated with random genetic drift and/or, for the case of warm-temperate orchids, to founder effects during post-glacial re-colonization. In contrast, high levels of genetic variation were found for a few orchids that have become recently rare (due to over-collection during the past several decades), probably because there have not been sufficient generations for the initial diversity to be substantially eroded. In addition, several orchids occurring in the main mountain system of the Korean Peninsula (the Baekdudaegan), that served as a glacial refugium, maintained moderate to high levels of within-population genetic diversity. Based on our genetic data, conservation priority should be given to rare orchid species. Particularly, urgent measures should be implemented on Jeju Island, a popular vacation spot, because it also a hotspot for threatened orchids with low levels of genetic diversity.     

Lessons on Evolution from the Study of Edaphic Specialization

Plants adapted to special soil types are ideal for investigating evolutionary processes, including maintenance of intraspecific variation, adaptation, reproductive isolation, ecotypic differentiation, and the tempo and mode of speciation. Common garden and reciprocal transplant approaches show that both local adaptation and phenotypic plasticity contribute to edaphic (soil-related) specialization. Edaphic specialists evolve rapidly and repeatedly in some lineages, offering opportunities to investigate parallel evolution, a process less commonly documented in plants than in animals. Adaptations to soil features are often under the control of major genes and they frequently have direct or indirect effects on genes that contribute to reproductive isolation. Both reduced competitiveness and greater susceptibility to herbivory have been documented among some edaphic specialists when grown in ‘normal’ soils, suggesting that a high physiological cost of tolerance may result in strong divergent selection across soil boundaries. Interactions with microbes, herbivores, and pollinators influence soil specialization either by directly enhancing tolerance to extremes in soil conditions or by reducing gene flow between divergent populations. Climate change may further restrict the distribution of edaphic specialists due to increased competition from other taxa or, expand their ranges, if preadaptations to drought or other abiotic stressors render them more competitive under a novel climate.     

Associations between primates and other mammals in a central Amazonian forest landscape

Little information exists on mixed-species groups between primates and other mammals in Neotropical forests. In this paper, we describe three such associations observed during an extensive large-vertebrate survey in central Amazonia, Brazil. Mixed-species groups between a primate species and another mammal were observed on seven occasions between squirrel monkeys (Saimiri cf. ustus) and either South American coatis (Nasua nasua) or tayras (Eira barbara) and between brown capuchins (Cebus apella) and coatis. All associations were restricted to floodplain forest during its dry stage. We suggest that the associations involving the coatis are connected to foraging and vigilance but may be induced by a common alternative food resource at a time of food shortage.     

Nonlocal Immunized Mid-Infrared Magnetic Hot Spots in Graphene Junctions

Magnetic hot spots, which implies confinements and enhancements of magnetic fields, are demonstrated in graphene junctions (GJs) in the mid-infrared range. The appearance of magnetic hot spots in GJs comes from the conduction currents in the junction. In further, the extinction resonance peaks suffer blue shift, along with the increases in the magnetic fields inside junction area, when the junction width reduces. In opposite to the circumstances for electric field enhancements, neither magnetic field enhancements nor resonance frequency of GJs is perturbed by the intrinsic nonlocal electronic response of graphene. Such nonlocality immunized magnetic enhancement could be explained by the polarization dependent property of nonlocal effect.