H19-DMR allele-specific methylation analysis reveals epigenetic heterogeneity of CTCF binding site 6 but not of site 5 in head-and-neck carcinomas: A pilot case-control analysis

Aberrant methylation of seven potential binding sites of the CTCF factor in the differentially methylated region upstream of the H19 gene (H19-DMR) has been suggested as critical for the regulation of IGF2 and H19 imprinted genes. In this study, we analyzed the allele-specific methylation pattern of CTCF binding sites 5 and 6 using methylationsensitive restriction enzyme PCR followed by RFLP analysis in matched tumoral and lymphocyte DNA from head-and-neck squamous cell carcinoma (HNSCC) patients, as well as in lymphocyte DNA from control individuals who were cancer-free. The monoallelic methylation pattern was maintained in CTCF binding site 5 in 22 heterozygous out of 91 samples analyzed. Nevertheless, a biallelic methylation pattern was detected in CTCF binding site 6 in a subgroup of HNSCC patients as a somatic acquired feature of tumor cells. An atypical biallelic methylation was also observed in both tumor and lymphocyte DNA from two patients, and at a high frequency in the control group (29 out of 64 informative controls). Additionally, we found that the C/T transition detected by HhaI RFLP suppressed one dinucleotide CpG in critical CTCF binding site 6, of a mutation showing polymorphic frequencies. Although a heterogeneous methylation pattern was observed after DNA sequencing modified by sodium bisulfite, the biallelic methylation pattern was confirmed in 9 out of 10 HNSCCs. These findings are likely to be relevant in the epigenetic regulation of the DMR, especially in pathological conditions in which the imprinting of IGF2 and H19 genes is disrupted.

Heterogeneity correction in the construction of optimized planning in radiotherapy using linear programming

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The role of habitat heterogeneity for the functional response of the spider Nesticodes rufipes (Araneae : Theridiidae) to houseflies

We investigated whether or not different degrees of refuge for prey influence the characteristic of functional response exhibited by the spider Nesticodes rufipes on Musca domestica, comparing the inherent ability of N. rufipes to kill individual houseflies in such environments at two distinct time intervals. To investigate these questions, two artificial habitats were elaborated in the laboratory. For 168 h of predator-prey interaction, logistic regression analyses revealed a type 11 functional response, and a significant decrease in prey capture in the highest prey density was observed when habitat complexity was increased. Data from habitat 1 (less complex) presented a greater coefficient of determination than those from habitat 2 (more complex), indicating a higher variation of predation of the latter. For a 24 h period of predator-prey interaction, spiders killed significantly fewer prey in habitat 2 than in habitat 1. Although prey capture did not enable data to fit properly in the random predator equation in this case, predation data from habitat 2 presented a higher variation than data from habitat 1, corroborating results from 168 h of interaction. The high variability observed on data from habitat 2 (more complex habitat) is an interesting result because it reinforces the importance of refuge in promoting spatial heterogeneity, which can affect the extent of predator-prey interactions.

THE EXTENT of SEED PREDATION BY BRUCHINE BEETLES (COLEOPTERA: CHRYSOMELIDAE: BRUCHINAE) IN A HETEROGENEOUS LANDSCAPE IN SOUTHEASTERN BRAZIL

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Short Report: Heterogeneity of Leishmania infantum chagasi Kinetoplast DNA in Teresina (Brazil)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Use of forest fragments by blue-winged macaws (Primolius maracana) within a fragmented landscape

Parrots are the most threatened group of birds in the world, mainly because of the reduction and fragmentation of their natural habitats. However, few studies have investigated the dynamics of parrot populations in disturbed landscapes on a broad scale. In this paper, we studied the ecological interactions of the vulnerable blue-winged macaw (Primolius maracana) in a fragmented landscape surrounding a large protected park in southeastern Brazil. We sampled 36 forest fragments that varied in size, characteristics, degree of isolation and type of surrounding matrix in order to assess the importance of habitat features on the maintenance of these birds. Blue-winged macaws were recorded in 70% of the satellite remnants that were sampled, which included large and small blocks of forest. These areas were used as sites for feeding, nesting or overnight rests, and also provided connectivity for birds' displacements. However, the frequency of macaw visits varied among the remnants, and this was related to habitat features such as patch size, human use of surrounding land, and the proximity to the protected park, to urban areas and to the birds' roosting areas. In general, landscape-scale parameters explained more of the variation in the frequency of visits by macaws than did patch-scale parameters. These results demonstrate the importance of landscape mosaics for the survival of blue-winged macaws.

Frugivory and habitat use by fruit-eating birds in a fragmented landscape of southeast Brazil

To investigate the movement of seeds transported by fruit-eating birds in an agricultural, fragmented landscape of the Atlantic forest of southeast Brazil, I asked which bird species are the main seed dispersers in such environment, and how they use the available habitats (small forest fragments, forest thickets, live fences, isolated trees, and active pastures) where they are most likely to drop the seeds they swallow the relative importance of fruit-eating birds as seed vectors was evaluated based on the number of fruit species eaten, the number of visits, and visitation rate to fruiting plants. Habitat use was accessed by recording the habitats where birds were seen or heard during walks conducted throughout the study area. Sixteen plant species were observed during 308.3 plant-hours. Forty-one bird species were observed eating fruits in a total of 830 visits to fruiting plants. Sayaca Tanagers (Thraupis sayaca) and Pale-breasted Thrushes (Turdus leucomelas) ate the greatest number of fruit species, were the most frequent plant visitors in terms of number and rate of visits, and had a broad range of habitat use. These two species and the Rusty-margined Guan (Penelope superciliaris), which is able to swallow large fruits with large seeds that smaller bird species cannot cat, likely have a great contribution to the movement of seeds throughout this highly degraded landscape.

Vegetation and environmental heterogeneity relationships in a Neotropical swamp forest in southeastern Brazil (Itirapina, SP)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Experimental assessment of Heliconia acuminata growth in a fragmented Amazonian landscape

1 Fragmentation severely alters physical conditions in forest understories, but few studies have connected these changes to demographic impacts on forest species using detailed experimental examination at the individual and population levels.2 Using a 32-month, reciprocal-transplant experiment, we show that individuals of the Amazonian understory herb Heliconia acuminata transplanted into forest fragments lost over 20% of their vegetative shoots, while those transplanted to continuous forest showed a slight gain. The leaf area of plants in fragments also increased at half the rate it did in continuous forest sites.3 It appears that the normal dry season stresses to which forest understorey plants are exposed are greatly exacerbated in fragments, causing plants to shed shoots and leaves.4 the observed shifts in size could help explain why populations in fragments are more skewed towards smaller demographic stage classes than those in continuous forest. These shifts in size structure could also result in reduced abundances of flowering plants, as reproduction in H. acuminata is positively correlated with shoot number.5 Fragmentation-related changes in growth rates resulting from abiotic stress may have significant demographic consequences.

Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The influence of landscape characteristics and home-range size on the quantification of landscape-genetics relationships

A common approach used to estimate landscape resistance involves comparing correlations of ecological and genetic distances calculated among individuals of a species. However, the location of sampled individuals may contain some degree of spatial uncertainty due to the natural variation of animals moving through their home range or measurement error in plant or animal locations. In this study, we evaluate the ways that spatial uncertainty, landscape characteristics, and genetic stochasticity interact to influence the strength and variability of conclusions about landscape-genetics relationships. We used a neutral landscape model to generate 45 landscapes composed of habitat and non-habitat, varying in percent habitat, aggregation, and structural connectivity (patch cohesion). We created true and alternate locations for 500 individuals, calculated ecological distances (least-cost paths), and simulated genetic distances among individuals. We compared correlations between ecological distances for true and alternate locations. We then simulated genotypes at 15 neutral loci and investigated whether the same influences could be detected in simple Mantel tests and while controlling for the effects of isolation-by distance using the partial Mantel test. Spatial uncertainty interacted with the percentage of habitat in the landscape, but led to only small reductions in correlations. Furthermore, the strongest correlations occurred with low percent habitat, high aggregation, and low to intermediate levels of cohesion. Overall genetic stochasticity was relatively low and was influenced by landscape characteristics.

Modeling the spatial and temporal heterogeneity of deforestation-driven carbon emissions: the INPE-EM framework applied to the Brazilian Amazon

We present a generic spatially explicit modeling framework to estimate carbon emissions from deforestation (INPE-EM). The framework incorporates the temporal dynamics related to the deforestation process and accounts for the biophysical and socioeconomic heterogeneity of the region under study. We build an emission model for the Brazilian Amazon combining annual maps of new clearings, four maps of biomass, and a set of alternative parameters based on the recent literature. The most important results are as follows: (a) Using different biomass maps leads to large differences in estimates of emission; for the entire region of the Brazilian Amazon in the last decade, emission estimates of primary forest deforestation range from 0.21 to 0.26 similar to Pg similar to C similar to yr-1. (b) Secondary vegetation growth presents a small impact on emission balance because of the short duration of secondary vegetation. In average, the balance is only 5% smaller than the primary forest deforestation emissions. (c) Deforestation rates decreased significantly in the Brazilian Amazon in recent years, from 27 similar to Mkm2 in 2004 to 7 similar to Mkm2 in 2010. INPE-EM process-based estimates reflect this decrease even though the agricultural frontier is moving to areas of higher biomass. The decrease is slower than a non-process instantaneous model would estimate as it considers residual emissions (slash, wood products, and secondary vegetation). The average balance, considering all biomass, decreases from 0.28 in 2004 to 0.15 similar to Pg similar to C similar to yr-1 in 2009; the non-process model estimates a decrease from 0.33 to 0.10 similar to Pg similar to C similar to yr-1. We conclude that the INPE-EM is a powerful tool for representing deforestation-driven carbon emissions. Biomass estimates are still the largest source of uncertainty in the effective use of this type of model for informing mechanisms such as REDD+. The results also indicate that efforts to reduce emissions should focus not only on controlling primary forest deforestation but also on creating incentives for the restoration of secondary forests.

Habitat heterogeneity and pollinators: Bees in fragmented landscapes (Hymenoptera : Apidae)

This text presents the main studies that report the effect of habitat degradation upon plant-pollinator interactions and the importance of the presence of native vegetation remnants to pollinators, which leads to the need for conservation measures.

Geographical variation in genetic structure of an Atlantic Coastal Forest frog reveals regional differences in habitat stability

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Influence of the environmental heterogeneity of breeding ponds on anuran assemblages from southeastern Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)