Presumed normal ultrasonographic findings of the testis and epididymis of Botos (Inia Geoffrensis)

Fifteen live adult male botos, or Amazon river dolphins (Inia geoffrensis), were examined using ultrasonography during the yearly capture expedition, between October and November 2005, at the Mamiraua Sustainable Development Reserve, within the Brazilian Amazon (3 degrees S, 65 degrees W). All examinations were performed with a Sonosite 180 plus ultrasound unit in conjunction with a 2- to 5-MHz multifrequency transducer convex array 180 Plus/Elite-C60. Age and maturity estimates were determined considering the body length, weight, and external characteristics. In all examinations, the testes were discerned by the presence of a hyperechoic central line, called the mediastinum testis, a landmark for their identification during ultrasonography. No significant differences in echogenicity were detected on the ultrasonographic appearance of the testes among the studied animals. On adult male botos, apparent parenchymal nodulation of the testis was observed on scanning in most of the animals and probably constituted evidence of reproductive maturity. Using the color Doppler technique, blood flow was detected along the mediastinum testis that progressively decreased toward the periphery of this organ. Little blood flow could be identified by color Doppler. Power Doppler allowed better accuracy to identify testicular vessels, their topography, and their differentiation from adjacent structures. Ultrasonographic examination provides useful data for morphologic characterization of the boto's testes. Examination using Doppler techniques was considered a valuable tool to evidence blood flow through the testicular parenchyma.

Unraveling the drivers of community dissimilarity and species extinction in fragmented landscapes

Communities in fragmented landscapes are often assumed to be structured by species extinction due to habitat loss, which has led to extensive use of the species-area relationship (SAR) in fragmentation studies. However, the use of the SAR presupposes that habitat loss leads species to extinction but does not allow for extinction to be offset by colonization of disturbed-habitat specialists. Moreover, the use of SAR assumes that species richness is a good proxy of community changes in fragmented landscapes. Here, we assessed how communities dwelling in fragmented landscapes are influenced by habitat loss at multiple scales; then we estimated the ability of models ruled by SAR and by species turnover in successfully predicting changes in community composition, and asked whether species richness is indeed an informative community metric. To address these issues, we used a data set consisting of 140 bird species sampled in 65 patches, from six landscapes with different proportions of forest cover in the Atlantic Forest of Brazil. We compared empirical patterns against simulations of over 8 million communities structured by different magnitudes of the power-law SAR and with species-specific rules to assign species to sites. Empirical results showed that, while bird community composition was strongly influenced by habitat loss at the patch and landscape scale, species richness remained largely unaffected. Modeling results revealed that the compositional changes observed in the Atlantic Forest bird metacommunity were only matched by models with either unrealistic magnitudes of the SAR or by models ruled by species turnover, akin to what would be observed along natural gradients. We show that, in the presence of such compositional turnover, species richness is poorly correlated with species extinction, and z values of the SAR strongly underestimate the effects of habitat loss. We suggest that the observed compositional changes are driven by each species reaching its individual extinction threshold: either a threshold of forest cover for species that disappear with habitat loss, or of matrix cover for species that benefit from habitat loss.

Decisions on Temporal Sampling Protocol Influence the Detection of Ecological Patterns

Within-site variability in species detectability is a problem common to many biodiversity assessments and can strongly bias the results. Such variability can be caused by many factors, including simple counting inaccuracies, which can be solved by increasing sample size, or by temporal changes in species behavior, meaning that the way the temporal sampling protocol is designed is also very important. Here we use the example of mist-netted tropical birds to determine how design decisions in the temporal sampling protocol can alter the data collected and how these changes might affect the detection of ecological patterns, such as the species-area relationship (SAR). Using data from almost 3400 birds captured from 21,000 net-hours at 31 sites in the Brazilian Atlantic Forest, we found that the magnitude of ecological trends remained fairly stable, but the probability of detecting statistically significant ecological patterns varied depending on sampling effort, time of day and season in which sampling was conducted. For example, more species were detected in the wet season, but the SAR was strongest in the dry season. We found that the temporal distribution of sampling effort was more important than its total amount, discovering that similar ecological results could have been obtained with one-third of the total effort, as long as each site had been equally sampled over 2 yr. We discuss that projects with the same sampling effort and spatial design, but with different temporal sampling protocol are likely to report different ecological patterns, which may ultimately lead to inappropriate conservation strategies.

Possible early foraminiferans in post-Sturtian (716-635 Ma) cap carbonates

Foraminifera are an ecologically important group of modern heterotrophic amoeboid eukaryotes whose naked and testate ancestors are thought to have evolved similar to 1 Ga ago. However, the single-chambered agglutinated tests of these protists appear in the fossil record only after ca. 580 Ma, coinciding with the appearance of macroscopic and mineralized animals. Here we report the discovery of small, slender tubular microfossils in the Sturtian (ca. 716-635 Ma) cap carbonate of the Rasthof Formation in Namibia. The tubes are 200-1300 mu m long and 20-70 mu m wide, and preserve apertures and variably wide lumens, folds, constrictions, and ridges. Their sometimes flexible walls are composed of carbonaceous material and detrital minerals. This combination of morphological and compositional characters is also present in some species of modern single-chambered agglutinated tubular foraminiferans, and is not found in other agglutinated eukaryotes. The preservation of possible early Foraminifera in the carbonate rocks deposited in the immediate aftermath of Sturtian low-latitude glaciation indicates that various morphologically modern protists thrived in microbially dominated ecosystems, and contributed to the cycling of carbon in Neoproterozoic oceans much before the rise of complex animals.

Nuculidae (Bivalvia) in the Cape Melville Formation, King George Island, Antarctica, with an overview of the bivalve fauna

Nuculid bivalves of the Cape Melville Formation (Early Miocene, King George Island) are reviewed. Ten bivalve taxa are listed from the formation in the families Nuculidae (two species), Sareptidae, Malletiidae, Limopsidae (two species), Limidae, Pectinidae, Hiatellidae, and Periplomatidae. The Nuculidae consist of two species of Leionucula Quenstedt, 1930. One of these, L. melvilleana n. sp., is described and the other consists of the two species named previously by Anelli et al. (2006), which are demonstrated to be synonymous and are assigned to the species Leionucula frigida (Anelli, Rocha-Campos, Santos, Perinotto & Quaglio 2006). This assemblage, dominated by protobranchs (89% of specimens), is a typical fauna of offshore soft substrates, with a few specimens transported from hard substrates nearby. The diversity of Nuculidae has decreased in the Antarctic region through the Cenozoic.

GENETIC VARIABILITY OF SUGARCANE-ASSOCIATED DIAZOTROPHIC BACTERIA CAPABLE OF INORGANIC PHOSPHATE SOLUBILIZING

The sugarcane is a culture of great importance for the Brazilian agriculture. Every year this culture consumes great amounts of nitrogen and phosphate fertilizers. However, the use of plant growth-promoting bacteria can reduce the use of the chemical fertilizers, contributing to the economy and the environment conservation. So, the goal of this study was to select sugarcane-associated diazotrophic bacteria able to solubilize inorganic phosphate and to evaluate the genetic diversity of these bacteria. A total of 68 diazotrophic bacteria, leaf and root endophytic and rizoplane, of three sugarcane varieties. The selection of inorganic phosphate solubilizing diazotrophic bacteria was assayed by the solubilization index (SI) in solid medium containing insoluble phosphate. The genetic variability was analyzed by the BOX-PCR technique. The results showed that 74% of the diazotrophic strains were able to solubilize inorganic phosphate, presenting classes of different SI. The results showed that the vegetal tissue and the genotype plant influenced in the interaction between phosphate solubilizing diazotrophic bacteria and sugarcane plants. BOX-PCR revealed high genetic variability among the strains analyzed. So, sugarcane-associated diazotrophic bacteria express the capacity to solubilize inorganic phosphate and they present high genetic diversity.

Giant magnetofossils and hyperthermal events

Magnetotactic bacteria biomineralize magnetic minerals with precisely controlled size, morphology, and stoichiometry. These cosmopolitan bacteria are widely observed in aquatic environments. If preserved after burial, the inorganic remains of magnetotactic bacteria act as magnetofossils that record ancient geomagnetic field variations. They also have potential to provide paleoenvironmental information. In contrast to conventional magnetofossils, giant magnetofossils (most likely produced by eukaryotic organisms) have only been reported once before from Paleocene-Eocene Thermal Maximum (PETM; 55.8 Ma) sediments on the New Jersey coastal plain. Here, using transmission electron microscopic observations, we present evidence for abundant giant magnetofossils, including previously reported elongated prisms and spindles, and new giant bullet-shaped magnetite crystals, in the Southern Ocean near Antarctica, not only during the PETM, but also shortly before and after the PETM. Moreover, we have discovered giant bullet-shaped magnetite crystals from the equatorial Indian Ocean during the Mid-Eocene Climatic Optimum (similar to 40 Ma). Our results indicate a more widespread geographic, environmental, and temporal distribution of giant magnetofossils in the geological record with a link to "hyperthermal" events. Enhanced global weathering during hyperthermals, and expanded suboxic diagenetic environments, probably provided more bioavailable iron that enabled biomineralization of giant magnetofossils. Our micromagnetic modelling indicates the presence of magnetic multi-domain (i.e., not ideal for navigation) and single domain (i.e., ideal for navigation) structures in the giant magnetite particles depending on their size, morphology and spatial arrangement. Different giant magnetite crystal morphologies appear to have had different biological functions, including magnetotaxis and other non-navigational purposes. Our observations suggest that hyperthermals provided ideal conditions for giant magnetofossils, and that these organisms were globally distributed. Much more work is needed to understand the interplay between magnetofossil morphology, climate, nutrient availability, and environmental variability.

Chemically Resolved Particle Fluxes Over Tropical and Temperate Forests

Chemically resolved submicron (PM1) particlemass fluxes were measured by eddy covariance with a high resolution time-of-flight aerosolmass spectrometer over temperate and tropical forests during the BEARPEX-07 and AMAZE-08 campaigns. Fluxes during AMAZE-08 were small and close to the detection limit (<1 ng m−2 s−1) due to low particle mass concentrations (<1 μg m−3). During BEARPEX-07, concentrations were five times larger, with mean mid-day deposition fluxes of −4.8 ng m−2 s−1 for total nonrefractory PM1 (Vex,PM1 = −1 mm s−1) and emission fluxes of +2.6 ng m−2 s−1 for organic PM1 (Vex,org = +1 mm s−1). Biosphere–atmosphere fluxes of different chemical components are affected by in-canopy chemistry, vertical gradients in gas-particle partitioning due to canopy temperature gradients, emission of primary biological aerosol particles, and wet and dry deposition. As a result of these competing processes, individual chemical components had fluxes of varying magnitude and direction during both campaigns. Oxygenated organic components representing regionally aged aerosol deposited, while components of fresh secondary organic aerosol (SOA) emitted. During BEARPEX-07, rapid incanopy oxidation caused rapid SOA growth on the timescale of biosphere-atmosphere exchange. In-canopy SOA mass yields were 0.5–4%. During AMAZE-08, the net organic aerosol flux was influenced by deposition, in-canopy SOA formation, and thermal shifts in gas-particle partitioning.Wet deposition was estimated to be an order ofmagnitude larger than dry deposition during AMAZE-08. Small shifts in organic aerosol concentrations from anthropogenic sources such as urban pollution or biomass burning alters the balance between flux terms. The semivolatile nature of the Amazonian organic aerosol suggests a feedback in which warmer temperatures will partition SOA to the gas-phase, reducing their light scattering and thus potential to cool the region.

Distribution of microphytobenthic biomass in Martel Inlet, King George Island (Antarctica)

The spatial and temporal variation of microphytobenthic biomass in the nearshore zone of Martel Inlet (King George Island, Antarctica) was estimated at several sites and depths (10-60 m), during three summer periods (1996/1997, 1997/1998, 2004/2005). The mean values were inversely related to the bathymetric gradient: higher ones at 10-20 m depth (136.2 +/- A 112.5 mg Chl a m(-2), 261.7 +/- A 455.9 mg Phaeo m(-2)), intermediate at 20-30 m (55.6 +/- A 39.5 mg Chl a m(-2), 108.8 +/- A 73.0 mg Phaeo m(-2)) and lower ones at 40-60 m (22.7 +/- A 23.7 mg Chl a m(-2), 58.3 +/- A 38.9 mg Phaeo m(-2)). There was also a reduction in the Chl a/Phaeo ratio with depth, from 3.2 +/- A 3.2 (10-20 m) to 0.7 +/- A 1.0 (40-60 m), showing a higher contribution of senescent phytoplankton and/or macroalgae debris at the deeper sites and the limited light flux reaching the bottom. Horizontal differences found in the biomass throughout the inlet could not be clearly related to hydrodynamics or proximity to glaciers, but with sediment characteristics. An inter-summer variation was observed: the first summer presented the highest microphytobenthic biomass apparently related to more hydrodynamic conditions, which causes the deposition of allochthonous material.

New Brazilian Floristic List Highlights Conservation Challenges

A comprehensive new inventory of Brazilian plants and fungi was published just in time to meet a 2010 Convention on Biological Diversity target and offers important insights into this biodiversity's global significance. Brazil is the home to the world's richest flora (40,989 species; 18,932 endemic) and includes two of the hottest hotspots: Mata Atlantica (19,355 species) and Cerrado (12,669 species). Although the total number of known species is one-third lower than previous estimates, the absolute number of endemic vascular plant species is higher than was previously estimated, and the proportion of endemism (56%) is the highest in the Neotropics. This compilation serves not merely to quantify the scale of the challenge faced in conserving Brazil's unique flora but also serves as a key resource to direct action and monitor progress. Similar efforts by other megadiverse countries are urgently required if the 2020 targets of the Convention on Biological Diversity and the Global Strategy for Plant Conservation are to be attained.

An integrated GIS for sedimentological and geomorphological analysis of a lagoon environment. Barra de Cananeia inlet region, (Southeastern Brazil)

The aim of this work is to use GIS integration data to characterize sedimentary processes in a SubTropical lagoon environment. The study area was the Canan,ia Inlet estuary in the southeastern section of the Canan,ia Lagoon Estuarine System (CLES), state of So Paulo, Brazil (25A degrees 03'S/47A degrees 53'W). The area is formed by the confluence of two estuarine channels forming a bay-shaped water body locally called "Trapand, Bay". The region is surrounded by one of the most preserved tracts of Atlantic Rain Forest in Southwestern Brazil and presents well-developed mangroves and marshes. In this study a methodology was developed using integrated a GIS database based on bottom sediment parameters, geomorphological data, remote sensing images, Hidrodynamical Modeling data and geophysical parameters. The sediment grain size parameters and the bottom morphology of the lagoon were also used to develop models of net sediment transport pathways. It was possible to observe that the sediment transport vectors based on the grain size model had a good correlation with the transport model based on the bottom topography features and Hydrodynamic model, especially in areas with stronger energetic conditions, with a minor contribution of finer sediments. This relation is somewhat less evident near shallower banks and depositional features. In these regions the organic matter contents in the sediments was a good complementary tool for inferring the hydrodynamic and depositional conditions (i.e. primary productivity, sedimentation rates, sources, oxi-reduction rates).

Phylogenetic relationships of rock-wallabies, Petrogale (Marsupialia: Macropodidae) and their biogeographic history within Australia

The rock-wallaby genus Petrogale comprises a group of habitat-specialist macropodids endemic to Australia. Their restriction to rocky outcrops, with infrequent interpopulation dispersal, has been suggested as the cause of their recent and rapid diversification. Molecular phylogenetic relationships within and among species of Petrogale were analysed using mitochondrial (cytochrome oxidase c subunit 1, cytochrome b. NADH dehydrogenase subunit 2) and nuclear (omega-globin intron, breast and ovarian cancer susceptibility gene) sequence data with representatives that encompassed the morphological and chromosomal variation within the genus, including for the first time both Petrogale concinna and Petrogale purpureicollis. Four distinct lineages were identified, (1) the brachyotis group, (2) Petrogale persephone, (3) Petrogale xanthopus and (4) the lateralis-penicillata group. Three of these lineages include taxa with the ancestral karyotype (2n = 22). Paraphyletic relationships within the brachyotis group indicate the need for a focused phylogeographic study. There was support for P. purpureicollis being reinstated as a full species and P. concinna being placed within Petrogale rather than in the monotypic genus Peradorcas. Bayesian analyses of divergence times suggest that episodes of diversification commenced in the late Miocene-Pliocene and continued throughout the Pleistocene. Ancestral state reconstructions suggest that Petrogale originated in a mesic environment and dispersed into more arid environments, events that correlate with the timing of radiations in other arid zone vertebrate taxa across Australia. Crown Copyright (C) 2011 Published by Elsevier Inc. All rights reserved.

A novel strategy for building interoperable MPI environment in heterogeneous high performance systems

Breakthrough advances in microprocessor technology and efficient power management have altered the course of development of processors with the emergence of multi-core processor technology, in order to bring higher level of processing. The utilization of many-core technology has boosted computing power provided by cluster of workstations or SMPs, providing large computational power at an affordable cost using solely commodity components. Different implementations of message-passing libraries and system softwares (including Operating Systems) are installed in such cluster and multi-cluster computing systems. In order to guarantee correct execution of message-passing parallel applications in a computing environment other than that originally the parallel application was developed, review of the application code is needed. In this paper, a hybrid communication interfacing strategy is proposed, to execute a parallel application in a group of computing nodes belonging to different clusters or multi-clusters (computing systems may be running different operating systems and MPI implementations), interconnected with public or private IP addresses, and responding interchangeably to user execution requests. Experimental results demonstrate the feasibility of this proposed strategy and its effectiveness, through the execution of benchmarking parallel applications.