Revision of Recreation and Leisure Practicum

In a 1-ha plot divided into 100 subplots of 10 x 10 m, all trees with at least 15 cm of perimeter at breast height (DBH = 4.8 cm) were marked and had their heights estimated and perimeter taken. The rock cover (rocks over 50 cm diameter) was estimated in five classes of frequency, and records were made for individuals growing directly on rocks. We found 1,274 trees matching the sampling criteria, which belong to 41 botanical families (highlighting Myrtaceae, Rubiaceae and Fabaceae) and 142 species or morphotypes. The most important (Importance Value Index) species are: Euterpe edulis, Mollinedia schottiana, Bathysa mendoncaei, Coussarea accedens, Rustia formosa and Guapira opposita. Shannon's diversity index was 4.05 nats/ind and Pielou's equability was 0.82. The average tree height is of 9 m and the canopy is at around 18 m. The trees' average diameter is 13.9 cm, and 29 individuals surpass 50 cm DBH. The basal area for the I-ha plot (live trees only) is 30.27 m(2). A direct relation was found between rock cover and lesser species richness and number of individuals per subplot. No relationship was found between rock cover and the mean height or mean diameter of stems in the subplots. 34 tree species in this area are able to grow on rocks; 11 of which do not grow roots to the soil, particularly Euterpe edulis and Guapira opposita. The height and diameter of the individuals that grow on rocks is not statistically different from the remaining in the plot

Floristic composition and similaritie between areas of Montane Atlantic Rainforest, Sao Paulo, Brazil

The study was conducted in two areas of Montana Atlantic Rainforest at Nucleo Santa Virginia, Serra do Mar State Park, Brazil. The aim was to investigate structural and floristic composition of each area and the differences between them, knowing that one has not been disturbed recently and the other was subjected to selective logging until 1970, as reported by local people. We installed two 1 ha (PLOT K and PLOT N), approximately 4 km away from each other, and within this plots all individuals with DBH >= 4.8 cm were recorded. Considering the two plots we sampled 3,503 individuals (2,269 trees - 64.7%; 860 palms - 24.5%; and 159 ferns - 4.5%), distributed in 265 species and 51 families. The rest (215 individuals) was dead. Among the most abundant families (Arecaceae, Myrtaceae, Lauraceae, Cyatheaceae) Monimiaceae is the only one classified as typical of the Montane Ombrophylus Dense Atlantic Forest. Euterpe edulis Mart. (Arecaceae) is the dominant species in PLOT K (old), where we recorded 1,852 individuals, 189 species and 43 families, with Myrtaceae (48), Lauraceae (26) and Monimiaceae (13) presenting the higher number of species. It is important to mention that clumps of a native bamboo (Merostachys neesii Ruprecht, Poaceae) are present in 93 of the 100 subparcels of PLOT K, summing up 3,813 culms. In contrast, in PLOT N (secondary) where palm heart (Euterpe edulis) is also the dominant species but bamboos are not so conspicuous, we recorded 1436 individuals, 149 species and 40 families, with Myrtaceae (27), Lauraceae (15) and Fabaceae (eight) being the ones with higher number of species. In the plot of secondary forest (N) Shannon's diversity index (H' = 4.05) and the eveness index (J' = 0.8) are higher than those recorded in the old plot of forest (K) where H' = 3,72 nats.ind(-1) and J' = 0.7. Plots K and N have a low similarity (Jaccard index C(J) = 0,3), with only 94 species (34,47%) in common, and 102(38,5%) occurring exclusively in PLOT K. However, the maximum estimate of species expected at the point of rarefaction of PLOT N (IC 95% - 158.54) overlaps with the minimum estimate of species at the same point of PLOT K (95% - 157.12), showing that the number of species of both areas would be equivalent in the number of 1,420 individuals. Although the largest tree sampled was found in PLOT K, where forest stratification is more evident, there is no significant difference between the sums of basal area of living individuals. Considering the disturbance history of the region, the results suggest that forest structure recovery may occur within 25 years but, as shown by the total number of species and by the diversity parameters determined, species richness does not recover within this time frame.11213915

Study of the arboreal component in two areas of the Submontane Rainforest in Ubatuba, Sao Paulo State

We studied the floristic composition and structure of the arboreal component (trees, palms and ferns with DBH equal to or greater than 4.8 cm) of two plots of Lower Montane Rain Forest in Ubatuba, SP, one with a history of selective logging and the other more preserved. We sampled 50 families, 114 genera and 193 species (four undetermined). The richest families were Myrtaceae, Fabaceae, Lauraceae, Rubiaceae, Melastomataceae and Sapotaceae. In the disturbed plot we sampled 104 species, 72 genera and 39 families, and in the more preserved area, 152 species, 98 genera and 43 families. There were differences in species richness, in the prevalence of their succesional status and in the structure of the areas, and the multivariate analysis allowed recognition of two floristic blocks. Among all species, 33 were exclusive of the first plot and 95 were exclusive of the second plot. Almost half of the species (45%) occurred with only one or two individuals and 29 have some degree of rarity. Five species are in the category of vulnerable in the List of brazilian plant species threatened of extinction. The differences observed between the sites studied, as well as the occurrence of rare and endangered species highlight the importance of the conservation of the area.11231333

Soil-atmosphere exchange of nitrous oxide, methane and carbon dioxide in a gradient of elevation in the coastal Brazilian Atlantic forest

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Soils of tropical forests are important to the global budgets of greenhouse gases. The Brazilian Atlantic Forest is the second largest tropical moist forest area of South America, after the vast Amazonian domain. This study aimed to investigate the emissions of nitrous oxide (N2O), carbon dioxide (CO2) and methane (CH4) fluxes along an altitudinal transect and the relation between these fluxes and other climatic, edaphic and biological variables (temperature, fine roots, litterfall, and soil moisture). Annual means of N2O flux were 3.9 (+/- 0.4), 1.0 (+/- 0.1), and 0.9 (+/- 0.2) ng N cm(-2) h(-1) at altitudes 100, 400, and 1000 m, respectively. On an annual basis, soils consumed CH4 at all altitudes with annual means of -1.0 (+/- 0.2), -1.8 (+/- 0.3), and -1.6 (+/- 0.1) mg m(-2) d(-1) at 100 m, 400 m and 1000 m, respectively. Estimated mean annual fluxes of CO2 were 3.5, 3.6, and 3.4 mu mol m(-2) s(-1) at altitudes 100, 400 and 1000 m, respectively. N2O fluxes were significantly influenced by soil moisture and temperature. Soil-atmosphere exchange of CH4 responded to changes in soil moisture. Carbon dioxide emissions were strongly influenced by soil temperature. While the temperature gradient observed at our sites is only an imperfect proxy for climatic warming, our results suggest that an increase in air and soil temperatures may result in increases in decomposition rates and gross inorganic nitrogen fluxes that could support consequent increases in soil N2O and CO2 emissions and soil CH4 consumption.83733742Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAPESP [2005/57549-8]FAPESP [FAPESP 03/12595-7

Habitat fragmentation and the future structure of tree assemblages in a fragmented Atlantic forest landscape

The biodiversity value of human-modified landscapes has become a central question in the tropical forest conservation biology, yet the degree to which plant populations and communities are restructured in response to environmental change remains unclear. Here, we address tree species density in a fragmented Atlantic forest landscape to test the hypothesis that tree assemblages inhabiting edge-dominated forest habitats approach typical conditions of early successional systems. Seedlings and adults from 141 tree species were sampled across 39 0.1-ha plots: 19 in small fragments (55 % of all tree species exhibiting higher densities in small fragments than in mature forest, particularly pioneers (>60 % of all species). Seedlings and adults of these proliferating species differed from species exhibiting population declines in terms of wood density and seed size, respectively. Additionally, pioneers were more abundant than shade-tolerant species, as were hardwood species in the case of seedlings. Tree species showing highest population increases consisted largely of long-lived, light-demanding canopy species bearing soft or hardwood and small-to-medium-sized seeds. Tree assemblage structure also differed in terms of forest habitats with small forest fragments supporting few rare species, whereas the most rapidly proliferating species were much more widespread and abundant in fragments. However, 60 % of all adult pioneer species recorded in small fragments were not recorded as seedlings in this habitat type, although both seedling and adult assemblages were dominated by pioneer species. Edge-dominated tree assemblages are likely to experience long-term shifts toward greater dominance of long-lived, pioneer canopy species

Pantropical modelling of canopy functional traits using Sentinel-2 remote sensing data

Tropical forest ecosystems are undergoing rapid transformation as a result of changing environmental conditions and direct human impacts. However, we cannot adequately understand, monitor or simulate tropical ecosystem responses to environmental changes without capturing the high diversity of plant functional characteristics in the species-rich tropics. Failure to do so can oversimplify our understanding of ecosystems responses to environmental disturbances. Innovative methods and data products are needed to track changes in functional trait composition in tropical forest ecosystems through time and space. This study aimed to track key functional traits by coupling Sentinel-2 derived variables with a unique data set of precisely located in-situ measurements of canopy functional traits collected from 2434 individual trees across the tropics using a standardised methodology. The functional traits and vegetation censuses were collected from 47 field plots in the countries of Australia, Brazil, Peru, Gabon, Ghana, and Malaysia, which span the four tropical continents. The spatial positions of individual trees above 10 cm diameter at breast height (DBH) were mapped and their canopy size and shape recorded. Using geo-located tree canopy size and shape data, community-level trait values were estimated at the same spatial resolution as Sentinel-2 imagery (i.e. 10 m pixels). We then used the Geographic Random Forest (GRF) to model and predict functional traits across our plots. We demonstrate that key plant functional traits can be accurately predicted across the tropicsusing the high spatial and spectral resolution of Sentinel-2 imagery in conjunction with climatic and soil information. Image textural parameters were found to be key components of remote sensing information for predicting functional traits across tropical forests and woody savannas. Leaf thickness (R2 = 0.52) obtained the highest prediction accuracy among the morphological and structural traits and leaf carbon content (R2 = 0.70) and maximum rates of photosynthesis (R2 = 0.67) obtained the highest prediction accuracy for leaf chemistry and photosynthesis related traits, respectively. Overall, the highest prediction accuracy was obtained for leaf chemistry and photosynthetic traits in comparison to morphological and structural traits. Our approach offers new opportunities for mapping, monitoring and understanding biodiversity and ecosystem change in the most species-rich ecosystems on Earth

Ancient DNA Resolves Identity and Phylogeny of New Zealand's Extinct and Living Quail (Coturnix sp.)

BACKGROUND: The New Zealand quail, Coturnix novaezealandiae, was widespread throughout New Zealand until its rapid extinction in the 1870's. To date, confusion continues to exist concerning the identity of C. novaezealandiae and its phylogenetic relationship to Coturnix species in neighbouring Australia, two of which, C. ypsilophora and C. pectoralis, were introduced into New Zealand as game birds. The Australian brown quail, C. ypsilophora, was the only species thought to establish with current populations distributed mainly in the northern part of the North Island of New Zealand. Owing to the similarities between C. ypsilophora, C. pectoralis, and C. novaezealandiae, uncertainty has arisen over whether the New Zealand quail is indeed extinct, with suggestions that remnant populations of C. novaezealandiae may have survived on offshore islands. METHODOLOGY/PRINCIPAL FINDINGS: Using fresh and historical samples of Coturnix sp. from New Zealand and Australia, DNA analysis of selected mitochondrial regions was carried out to determine phylogenetic relationships and species status. Results show that Coturnix sp. specimens from the New Zealand mainland and offshore island Tiritiri Matangi are not the New Zealand quail but are genetically identical to C. ypsilophora from Australia and can be classified as the same species. Furthermore, cytochrome b and COI barcoding analysis of the New Zealand quail and Australia's C. pectoralis, often confused in museum collections, show that they are indeed separate species that diverged approximately 5 million years ago (mya). Gross morphological analysis of these birds suggests a parallel loss of sustained flight with very little change in other phenotypic characters such as plumage or skeletal structure. CONCLUSION/SIGNIFICANCE: Ancient DNA has proved invaluable for the detailed analysis and identification of extinct and morphologically cryptic taxa such as that of quail and can provide insights into the timing of evolutionary changes that influence morphology

Aspergillus fumigatus Stimulates the NLRP3 Inflammasome through a Pathway Requiring ROS Production and the Syk Tyrosine Kinase

Invasive aspergillosis (IA) is a life-threatening disease that occurs in immunodepressed patients when infected with Aspergillus fumigatus. This fungus is the second most-common causative agent of fungal disease after Candida albicans. Nevertheless, much remains to be learned about the mechanisms by which A. fulmigatus activates the innate immune system. We investigated the inflammatory response to conidia and hyphae of A. fumigatus and specifically, their capacity to trigger activation of an inflammasome. Our results show that in contrast to conidia, hyphal fragments induce NLRP3 inflammasome assembly, caspase-1 activation and IL-1β release from a human monocyte cell line. The ability of Aspergillus hyphae to activate the NLRP3 inflammasome in the monocytes requires K+ efflux and ROS production. In addition, our data show that NLRP3 inflammasome activation as well as pro-IL-1β expression relies on the Syk tyrosine kinase, which is downstream from the pathogen recognition receptor Dectin-1, reinforcing the importance of Dectin-1 in the innate immune response against fungal infection. Furthermore, we show that treatment of monocytes with corticosteroids inhibits transcription of the gene encoding IL-1β. Thus, our data demonstrate that the innate immune response against A. fumigatus infection involves a two step activation process, with a first signal promoting expression and synthesis of pro-IL-1β; and a second signal, involving Syk-induced activation of the NLRP3 inflammasome and caspase-1, allowing processing and secretion of the mature cytokine

The route to transcription initiation determines the mode of transcriptional bursting in E. coli

Transcription is fundamentally noisy, leading to significant heterogeneity across bacterial populations. Noise is often attributed to burstiness, but the underlying mechanisms and their dependence on the mode of promotor regulation remain unclear. Here, we measure E. coli single cell mRNA levels for two stress responses that depend on bacterial sigma factors with different mode of transcription initiation (σ70 and σ54). By fitting a stochastic model to the observed mRNA distributions, we show that the transition from low to high expression of the σ70-controlled stress response is regulated via the burst size, while that of the σ54-controlled stress response is regulated via the burst frequency. Therefore, transcription initiation involving σ54 differs from other bacterial systems, and yields bursting kinetics characteristic of eukaryotic systems

A Novel Role for the NLRC4 Inflammasome in Mucosal Defenses against the Fungal Pathogen Candida albicans

Candida sp. are opportunistic fungal pathogens that colonize the skin and oral cavity and, when overgrown under permissive conditions, cause inflammation and disease. Previously, we identified a central role for the NLRP3 inflammasome in regulating IL-1β production and resistance to dissemination from oral infection with Candida albicans. Here we show that mucosal expression of NLRP3 and NLRC4 is induced by Candida infection, and up-regulation of these molecules is impaired in NLRP3 and NLRC4 deficient mice. Additionally, we reveal a role for the NLRC4 inflammasome in anti-fungal defenses. NLRC4 is important for control of mucosal Candida infection and impacts inflammatory cell recruitment to infected tissues, as well as protects against systemic dissemination of infection. Deficiency in either NLRC4 or NLRP3 results in severely attenuated pro-inflammatory and antimicrobial peptide responses in the oral cavity. Using bone marrow chimeric mouse models, we show that, in contrast to NLRP3 which limits the severity of infection when present in either the hematopoietic or stromal compartments, NLRC4 plays an important role in limiting mucosal candidiasis when functioning at the level of the mucosal stroma. Collectively, these studies reveal the tissue specific roles of the NLRP3 and NLRC4 inflammasome in innate immune responses against mucosal Candida infection