Biodiversity responses to land‐use and restoration in a global biodiversity hotspot: Ant communities in Brazilian Cerrado

Given that land‐use change is the main cause of global biodiversity decline, there is widespread interest in adopting land‐use practices that maintain high levels of biodiversity, and in restoring degraded land that previously had high biodiversity value. In this study, we use ant taxonomic and functional diversity to examine the effects of different land uses (agriculture, pastoralism, silviculture and conservation) and restoration practices on Cerrado (Brazilian savanna) biodiversity. We also examine the extent to which ant diversity and composition can be explained by vegetation attributes that apply across the full land management spectrum. We surveyed vegetation attributes and ant communities in five replicate plots of each of 13 land‐use and restoration treatments, including two types of native vegetation as reference sites: cerrado sensu stricto and cerradão. Several land‐use and restoration treatments had comparable plot richness to that of the native reference habitats. Ant species and functional composition varied systematically among land‐use treatments following a gradient from open habitats such as agricultural fields to forested sites. Tree basal area and grass cover were the strongest predictors of ant species richness. Losses in ant diversity were higher in land‐use systems that transform vegetation structure. Among productive systems, therefore, uncleared pastures and old pine plantations had similar species composition to that occurring in cerrado sensu stricto. Restoration techniques currently applied to sites that were previously Cerrado have focused on returning tree cover, and have failed to restore ant communities typical of savanna. To improve restoration outcomes for Cerrado biodiversity, greater attention needs to be paid to the re‐establishment and maintenance of the grass layer, which requires frequent fire. At the broader scale, conservation planning in agricultural landscapes, should recognize the value of land‐use mosaics and the risks of homogenization.     

Indicators of restoration success in riparian tropical forests using multiple reference ecosystems

Forest restoration by planting trees often accelerates succession, but the trajectories toward reference ecosystems have rarely been evaluated. Using a chronosequence (4–53 years) of 26 riparian forest undergoing restoration in the Brazilian Atlantic Forest, we modeled how the variables representing forest structure, tree species richness and composition, and the proportion of plant functional guilds change through time. We also estimated the time required for these variables to reach different types of reference ecosystems: old‐growth forest (OGF), degraded forest, and secondary forest. Among the attributes which follow a predictable trajectory over time are: the basal area, canopy cover, density and tree species richness, as well as proportions of shade tolerant and slow growing species or individuals. Most of the variation in density of pteridophythes, lianas, shrubs and phorophythes, proportion of animal‐dispersed individuals, rarefied richness and floristic similarity with reference ecosystems remain unexplained. Estimated time to reach the reference ecosystems is, in general, shorter for structural attributes than for species composition or proportion of functional guilds. The length of this time varies among the three types of reference ecosystems for most attributes. For instance, tree species richness and proportion of shade tolerant or slow growing individuals become similar to secondary forests in about 40 years, but is estimated to take 70 years or more to reach the OGF. Of all the variables considered, canopy cover, basal area, density, and richness of the understory—by their ecological relevance and predictability—are recommended as ecological indicators for monitoring tropical forest restoration success.     

Are atopy and eosinophilic bronchial inflammation associated with relapsing forms of chronic rhinosinusitis with nasal polyps?

Background

The aetiopathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP) is still unknown. The role of atopy and the concept of united airways in such patients are still a matter of debate. In this pilot study we aimed at evaluating the degree of eosinophilic inflammation and the frequency of atopy in a cohort of CRSwNP patients candidate for Functional Endoscopic Sinus Surgery (FESS) and assessing the association between these factors and relapsing forms of CRSwNP.

Methods

30 patients (18 men, 12 women) with CRSwNP eligible for FESS were evaluated before and after surgery. Preoperative investigation included: history of previous relapse after FESS, clinical and laboratory allergologic assessment, spirometry, methacholine challenge, blood eosinophilia and determination of the fraction of nitric oxide in exhaled air (FeNO). Nasal fibroendoscopy, spirometry and FeNO determination were also assessed prospectively at 3 and 27 months post-FESS.

Results

18/30 subjects were atopic, 6/18 (33 %) were monosensitized, 16/30 (53 %) were asthmatics and 10/30 (33 %) had non steroidalantinflammatory drugs (NSAIDs) hypersensitivity. Twenty-one patients (70 %) were classified as relapsers, 15/18 (83 %) among atopics, 6/12 (50 %) among non atopics (p = 0.05). Among patients with NSAIDs hypersensitivity, 9/10 (90 %) were relapsers. The median IgE concentration was 161.5 UI/mL in relapsers and 79 UI/mL in non-relapsers (ns). The mean FeNO decreased after FESS (43.1–26.6 ppb) in 84 % of patients, but this effect disappeared over time (FeNO = 37.7 ppb at 27 months). Higher levels of FeNO pre-FESS were detected in atopics, and in particular in relapsing ones (median 51.1 ppb vs 22.1, ns). Higher levels of FeNO pre-FESS were detected in asthmatic patients, especially in those who relapsed (median: 67 vs 64.85 ppb in non-relapsed patients, ns). The Tiffeneau Index (FEV1/FVC) was significantly lower in asthmatic relapsers than in non relapsers asthmatics (94.7 ± 11.1 versus 105 ± 5.9—p = 0.04). Patients with asthma and atopy had a major risk of relapse (p = 0.05).

Conclusion

In our pilot study, atopy, severe asthma, bronchial inflammation, NSAIDs hypersensitivity and high level of total IgE are possible useful prognostic factors for the proneness to relapse after FESS. The role of allergy in CRSwNP pathogenesis should consequently be given deeper consideration. Allergen specific immunotherapy, combined with anti-IgE therapy, may have an immunomodulatory effect preventing polyps relapse and need to be investigated.

Electronic supplementary material

The online version of this article (doi:10.1186/s12948-015-0026-8) contains supplementary material, which is available to authorized users.     

An experimental evaluation of a loop versus a reference design for two-channel microarrays

MOTIVATION: Despite theoretical arguments that so-called 'loop designs' for two-channel DNA microarray experiments are more efficient, biologists continue to use 'reference designs'. We describe two sets of microarray experiments with RNA from two different biological systems (TPA-stimulated mammalian cells and Streptomyces coelicolor). In each case, both a loop and a reference design were used with the same RNA preparations with the aim of studying their relative efficiency. RESULTS: The results of these experiments show that (1) the loop design attains a much higher precision than the reference design, (2) multiplicative spot effects are a large source of variability, and if they are not accounted for in the mathematical model, for example, by taking log-ratios or including spot effects, then the model will perform poorly. The first result is reinforced by a simulation study. Practical recommendations are given on how simple loop designs can be extended to more realistic experimental designs and how standard statistical methods allow the experimentalist to use and interpret the results from loop designs in practice. AVAILABILITY: The data and R code are available at http://exgen.ma.umist.ac.uk CONTACT: veronica.vinciotti@brunel.ac.uk.     

Molecular analysis of 23 exons of the CFTR gene in Brazilian patients leads to the finding of rare cystic fibrosis mutations

To define mutations present in 23 exons and flanking intronic sequences of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in 95 patients from Rio de Janeiro, Brazil, we carried out single-strand conformation polymorphism analysis and automated direct sequencing. Mutation detection was achieved in 45% of the alleles presented, and complete genotyping (two mutated alleles) was accomplished in 34.7% of the patients. Twenty patients (21.1%) were found to carry only one mutation, whereas mutated alleles could not be observed in 42 patients (44.2%). Eleven mutations were found, of which four were characterized as rare mutations: P205S (1.05%), Y1092X (0.53%), S549R (0.53%), and S4X (0.53%). The DF508 mutation in this population sample showed a frequency of 28.42%. The low number of individuals (10 of 95; 10.5%) with compound heterozygous (DF508/non-DF508) genotypes could indicate the presence of another severe mutation leading to the premature death of these individuals. In 4 of the aforementioned 10 individuals with compound heterozygous genotypes, the D-7-2-1-2 (XV2c-KM19-IVS6a-TUB9-M470-T854) haplotype was defined.     

Changes in cerrado vegetation after disturbance by frost (São Paulo State,Brazil)

We report changes after frost in cerrado species populations and community structure in Assis, São Paulo State, Brazil and consider the possible impacts of frost on cerrado types and their distribution. Four permanent plots (10 m × 10 m) were established and 736 individuals were marked with enumerated plastic labels and measured one week after the frost. Frost damage for each individual was assessed: 0 - not affected; 1 - slightly affected; 2 - substantially affected; and 3 - strongly affected. The frost impact on vegetation structure was high, reducing tree canopy cover from 88% to 19% in the upper stratum and that of the lower stratum from 48% to 8.5%. Floristic richness did not change, even though a small number (3%) of individuals of some species died. Conversely, the relative dominance of species changed dramatically in the short-term because of varying susceptibility to frost of different species. The largest reductions in crown cover were observed in Xylopia aromatica and Vochysia tucanorum. Of the 57 species recorded, 15% were unaffected, 19% had only their leaves damaged, 25% had some of their leaves and branches damaged, and 41% had all their aerial parts killed. The majority of individuals in the community belonged to frost tolerant species. The regeneration of the stand structure was remarkably rapid; height and canopy cover of the lower stratum recovered completely after five months, and those of the arboreal stratum showed a recovery of about 80% after 11 months. We consider that the frequency and intensity of frosts can maintain more open forms of cerrado vegetation even in sites where both water and nutrient availability could support denser vegetation. It is also probable that some frost-resistant heliophyte species are confined to areas where frosts prevent the development of denser cerrado vegetation. Much of the characteristic floristic composition of the southern region of the cerrado biome may be related to the selection of frost-resistant species. Our study shows, however, that a full complement of cerrado plants is capable of occupying and colonizing frost susceptible sites.     

HLA-A*01 allele: a risk factor for dengue haemorrhagic fever in Brazil's population

Severe forms of dengue, such as dengue haemorrhagic fever (DHF) and dengue shock syndrome, are examples of a complex pathogenic mechanism in which the virus, environment and host immune response interact. The influence of the host's genetic predisposition to susceptibility or resistance to infectious diseases has been evidenced in several studies. The association of the human leukocyte antigen gene (HLA) class I alleles with DHF susceptibility or resistance has been reported in ethnically and geographically distinct populations. Due to these ethnic and viral strain differences, associations occur in each population, independently with a specific allele, which most likely explains the associations of several alleles with DHF. As the potential role of HLA alleles in the progression of DHF in Brazilian patients remains unknown, we then identified HLA-A alleles in 67 patients with dengue fever and 42 with DHF from Rio de Janeiro, Brazil, selected from 2002-2008 by the sequence-based typing technique. Statistical analysis revealed an association between the HLA-A*01 allele and DHF [odds ratio (OR) = 2.7, p = 0.01], while analysis of the HLA-A*31 allele (OR = 0.5, p = 0.11) suggested a potential protective role in DHF that should be further investigated. This study provides evidence that HLA class I alleles might be important risk factors for DHF in Brazilian patients.     

The use of dexamethasone administered to mares at breeding time in the modulation of persistent mating induced endometritis

The present study describes the effect of a single dose of dexamethasone administered to mares at time of breeding. In an initial experiment, the authors investigated safety of treatment. In a second experiment the effect of treatment on the uterine environment, fetal development and pregnancy outcome was examined. In the final part of the study, mares susceptible to persistent mating induced endometritis were identified, by means of a risk factor score system and the effect of treatment evaluated. Results indicated that dexamethasone administered at breeding time did not negatively impact on mares medical and reproductive traits. A reduced inflammatory response was observed post-mating in treated versus control mares and mares with multiple risk factors for susceptibility to persistent mating induced endometritis showed improved pregnancy rates following treatment. The authors concluded that a single dose of dexamethasone administered at the time of breeding is safe and can be used to modulate the uterine inflammatory response to breeding in susceptible mares.     

Environment and landscape rather than planting design are the drivers of success in long‐term restoration of riparian Atlantic forest

Question

Identifying the factors that lead to the success of restoration projects has been a major challenge in ecological restoration. Here we ask which factors, aside from time since restoration began, drive the recovery of tree biomass, density and richness of the understorey in riparian forests undergoing restoration.

Location

Semideciduous Atlantic Forest with tropical climate and deep, fertile soils, southeast Brazil.

Methods

We sampled tree basal area (DBH ≥ 5 cm), density and richness of the understorey (DBH < 5 cm) in 26 riparian forests undergoing restoration (a chronosequence spanning 4–53 years). We assessed the following variables as possible factors, besides time, influencing community attributes: (1) planting design: density and richness of seedlings planted; (2) landscape features: proximity index measuring forest cover within a 1.5‐km radius, distance and size of the nearest forest remnant; and (3) environmental factors: invasive grasses, soil fertility, drought, average annual precipitation and proportion of fine particles in the soil. We performed correlation analyses including predictor and response variables, followed by stepwise backward regression (AIC), multiple and simple linear regressions, to investigate the relationships between those factors and the community attributes.

Results

Tree basal area was primarily influenced by the proportion of small particles in the soil (+) and secondarily by rainfall (?). Understorey richness was influenced by the combination of size (+) and distance (?) of the nearest patch, rainfall (?) and soil fertility (+). Understorey density was primarily influenced by the size of the nearest forest remnant (+) and secondarily by invasive grasses (?). No influence of density or richness of the seedlings planted was observed.

Conclusion

Environmental factors and landscape configuration drive the recovery of tree biomass, density and richness in communities undergoing restoration. The most relevant ecological filters influencing restoration success are availability of soil water and nutrients and the distance and size of the nearest remnant of native vegetation. The expected influence of richness and density of seedlings planted, considered for many years as important drivers of forest restoration success, was not confirmed in this study.