Modifier effects between regulatory and protein-coding variation

Genome-wide associations have shown a lot of promise in dissecting the genetics of complex traits in humans with single variants, yet a large fraction of the genetic effects is still unaccounted for. Analyzing genetic interactions between variants (epistasis) is one of the potential ways forward. We investigated the abundance and functional impact of a specific type of epistasis, namely the interaction between regulatory and protein-coding variants. Using genotype and gene expression data from the 210 unrelated individuals of the original four HapMap populations, we have explored the combined effects of regulatory and protein-coding single nucleotide polymorphisms (SNPs). We predict that about 18% (1,502 out of 8,233 nsSNPs) of protein-coding variants are differentially expressed among individuals and demonstrate that regulatory variants can modify the functional effect of a coding variant in cis. Furthermore, we show that such interactions in cis can affect the expression of downstream targets of the gene containing the protein-coding SNP. In this way, a cis interaction between regulatory and protein-coding variants has a trans impact on gene expression. Given the abundance of both types of variants in human populations, we propose that joint consideration of regulatory and protein-coding variants may reveal additional genetic effects underlying complex traits and disease and may shed light on causes of differential penetrance of known disease variants.     

Foraminiferal ecological zonation along a Brazilian mangrove transect: Diversity, morphotypes and the influence of subaerial exposure time

Two foraminiferal associations comprising only arenaceous species define two distinct environments in a 340 m-long mangrove transect at Cardoso Island, Trapandé Bay (Cananéia-Iguape estuarine system, SP, Brazil). The “lower muddy flat” (LMF), from the outer mangrove fringe inwards towards land (100 m), is positioned in the lower plain between 0.04 and 0.23 m above the mean sea level (msl), and remains subaerially exposed between 48.5 and 65.6% of the time. This environment is characterized by higher foraminiferal diversity and evenness (McIntosh's D = 0.54 ± 0.21 and Pielou's E = 0.68 ± 0.25, respectively) and is dominated by Arenoparrella mexicana and Trochammina inflata, and to a lesser extent by Ammotium directum and Textularia earlandi. The mangrove plant of this segment is a Rhizophoretum with average height of 8.4 ± 1.2 m. The sediment is characterized by higher concentration of organic matter (93.5 ± 32.3 g dm⁻³) and metals (e.g. V = 53.4 ± 21.8 ppm and Zn = 46.4 ± 21.3 ppm). The “upper sandy flat” (USF), 240 m wide along the transect, is positioned in the upper plain between 0.28 and 0.89 m above the msl, and remains subaerially exposed between 69.7 and 98.5% of the time. This environment is characterized by a lower diversity and evenness (D = 0.33 ± 0.17 and E = 0.49 ± 0.20, respectively). The association is dominated by species T. inflata and Miliammina fusca. The Rhizophoretum exhibits a lower average height of 3.6 ± 0.6 m. The sediment is poorer in organic matter (39.3 ± 15.0 g dm⁻³) and metals (e.g. V = 13.0 ± 6.8 ppm and Zn = 6.9 ± 3.7 ppm). Whereas “elongate” tests (uniserial, biserial and planospiral followed by a uniserial portion) are restricted to the LMF, “spiraled” species dominate the USF. Subaerial exposure time seems to exert a primary influence on species distribution, in addition to salinity and sediment type. Species may be adapted to different exposure times, a factor dependent on their position on the intertidal zone and the tidal regime, which should be taken into account in relative sea level reconstructions based on intertidal foraminifera. These patterns have important implications for studies investigating the ecology and paleoecology of foraminifera and subtle fluctuations in relative sea level during the Quaternary.     

Fragment quality and matrix affect epiphytic performance in a Mediterranean forest landscape

Destruction and fragmentation of habitats represent one of the most important threats for biodiversity. Here, we examined the effects of fragmentation in Mediterranean forests on the epiphytic lichen Lobaria pulmonaria (Lobariaceae). We tested the hypothesis that not only the level of fragmentation affects L. pulmonaria populations, but also the quality of the habitat and the nature of the surrounding matrix affect them. The presence and abundance of the lichen was recorded on 2039 trees in a total of 31 stands. We recorded habitat quality and landscape variables at three hierarchical levels: tree, plot, and patch. We found that L. pulmonaria tends to occur in trees with larger diameters in two types of surveyed forests. In Quercus pyrenaica patches, the mean diameter of colonized trees was smaller, suggesting the importance of bark roughness. Factors affecting the presence and cover of the lichen in each type of forest were different. There was a strong positive influence of distance from a river in beech forests, whereas proximity to forest edge positively affected in oak forests. The influence of the surrounding matrix was also an important factor explaining the epiphytic lichen abundance.     

Action of ferric and aluminium ions on the dormancy breakage of <Emphasis Type="Italic">Stylosanthes humilis</Emphasis> seeds

Dormancy of scarified seeds of Stylosanthes humilis was broken by acidic Al³⁺ and Fe³⁺ solutions. Fe⁺³-stimulated seeds exhibited a high activity of 1-aminocyclopropane-1-carboxylate (ACC) oxidase and produced great amounts of ethylene, which showed correlated with the germination process. In addition, specific inhibitors of ethylene biosynthesis and action largely depressed the Fe³⁺-stimulated germination, leading to the conclusion that the ion broke dormancy by triggering ethylene production by the seeds. By contrast, inhibitors of ethylene biosynthesis and action did not impair germination of Al³⁺-stimulated dormant seeds. Moreover, ethylene production and activity of ACC oxidase of Al³⁺-treated seeds was substantially decreased by inhibitors of ethylene biosynthesis, but germination kept large. Together these data suggest that ethylene biosynthesis was not required in the chain of events triggered by Al³⁺ leading to dormancy breakage. Methyl viologen (MV), a reactive oxygen species-generating compound, broke dormancy of seeds to the same extent as Al³⁺ did. Germination of both Al³⁺- and MV-stimulated dormant seeds was inhibited by sodium selenate, an antioxidant compound; selenate, however had no effect on germination of Fe³⁺-stimulated seeds. Together these data indicate that the mechanisms underlying the germination of Al³⁺- and Fe³⁺-treated seeds are not the same.     

Leaf Stripe and Stem Rot Caused by Burkholderia gladioli,a New Maize Disease in Mexico

A disease in maize plants, not previously observed, appeared in 2003–2004 in Cosoleacaque, Tlalixcoyan and Paso de Ovejas counties, in the state of Veracruz, Mexico. Initial symptoms on leaves were small white‐yellow watery spots, which coalesced into dry necrotic stripes 0.3 wide and up to 8 cm long. Reddening sometimes developed on these leaves. Stems developed a rot in the crown. The flag leaf became rot and necrotic at the base, rolled inwards and dried out. Necrosis developed at the base of the corn ears and their growth was inhibited. These symptoms were initially observed in Asgrow‐7573 commercial maize plantings. A bacterium characterized by white colonies, gram negative, aerobic, rod‐shape, opaque, round colonies with entire margins on casaaminoacid peptone and glucose media was consistently isolated from diseased maize plants. On King’s Medium B, the isolates produced yellow, non‐mucoid colonies, with the majority of the strains secreting a diffusible yellow pigment into the media. The bacterium identity was confirmed by PCR amplification and sequencing of 16S and 23S genes rDNA fragments. The bacterium was identified as Burkholderia gladioli. Its pathogenicity on maize plants in Mexico is a new record.     

Ethylene and polyamine interactions in morphogenesis of <Emphasis Type="Italic">Passiflora cincinnata</Emphasis>: effects of ethylene biosynthesis and action modulators,as well as ethylene scavengers

Ethylene is a plant hormone that is of fundamental importance to in vitro morphogenesis, but in many species, it has not been thoroughly studied. Its relationship with polyamines has been studied mainly because the two classes of hormones share a common biosynthetic precursor, S-adenosylmethionine (SAM). In order to clarify whether competition between polyamines and ethylene influences in vitro morphogenetic responses of Passiflora cincinnata Mast., a climacteric species, different compounds were used that act on ethylene biosynthesis and action, or as ethylene scavengers. Treatment with the ethylene inhibitor, aminoethoxyvinylglycine (AVG) caused a greater regeneration frequency in P. cincinnata, whereas treatment with the ethylene precursor, 1-aminocyclopropane-1-carboxylic-acid (ACC) lessened regeneration frequencies. The data suggested that levels of polyamines and ethylene are not correlated with morphogenic responses in P. cincinnata. It was ascertained that neither the absolute ethylene and polyamine levels, nor competition between the compounds, correlated to the obtained morphogenic responses. However, sensitivity to, and signaling by, ethylene appears to play an important role in differentiation. This study reinforces previous reports regarding the requirement of critical concentrations and temporal regulation of ethylene levels for morphogenic responses. Temporal regulation also appeared to be a key factor in competition between the two biosynthetic pathways, without having any effects on morphogenesis. Further studies investigating the silencing or overexpression of genes related to ethylene perception, under the influence of polyamines in cell differentiation are extremely important for the complete understanding of this process.     

Ecology and management of mahogany (Swietenia macrophylla King) in the Chimanes Forest, Bed, Bolivia

Mahogany ( Swietenia macrophylla King) regenerates in areas of erosion on high terraces and in forest killed by flooding and deposition of alluvial sediments in the Chimanes Forest, Bolivia. These hydrological disturbances are patchy, and only one of five stands of mahogany that we inventoried was regenerating. Mahogany survives these disturbances significantly better than the common tree species. The long time between disturbances appears to favour late maturation. Mahogany trees allocate little photosynthates to reproduction until they are very large emergents, at least 80 cm in diameter. The episodic nature of the regeneration sites means that mahogany stands are composed of one or a few cohorts, which are vulnerable to overharvesting, particularly with the current use of a minimum cutting diameter to regulate harvest. The delayed onset of fecundity means that the small trees that escape harvest are not very fecund, resulting in minimal seed input to logged forest. Only 7–9% of the gaps created by logging contain natural regeneration after 20 + yr. A successful management plan for mahogany would entail a monocyclic harvest, with a rotation age of 100 + years, the estimated time that it takes for trees to achieve commercial size in natural forest. Since the number of seed trees that will be left is small, they should be concentrated in sites that are likely to be conducive to natural regeneration, such as near rivers and flood damaged forest. Seed production will be maximized for a given basal area (opportunity cost to loggers) if trees c. 110 cm dbh are selected as seed trees. The mahogany stocks in the Chimanes Forest are nearly exhausted, but the findings of this study could be used to help rebuild the mahogany populations, or to design management plans for the commercial species that have similar ecologies to mahogany.