The role of exon shuffling in shaping protein-protein interaction networks

Background: Physical protein-protein interaction (PPI) is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions. Exon shuffling, intron-mediated recombination of exons from existing genes, is known to have been a major mechanism of domain shuffling in metazoans. Thus, we hypothesized that exon shuffling could have a significant influence in shaping the topology of PPI networks. Results: We tested our hypothesis by compiling exon shuffling and PPI data from six eukaryotic species: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Cryptococcus neoformans and Arabidopsis thaliana. For all four metazoan species, genes enriched in exon shuffling events presented on average higher vertex degree (number of interacting partners) in PPI networks. Furthermore, we verified that a set of protein domains that are simultaneously promiscuous (known to interact to multiple types of other domains), self-interacting (able to interact with another copy of themselves) and abundant in the genomes presents a stronger signal for exon shuffling. Conclusions: Exon shuffling appears to have been a recurrent mechanism for the emergence of new PPIs along metazoan evolution. In metazoan genomes, exon shuffling also promoted the expansion of some protein domains. We speculate that their promiscuous and self-interacting properties may have been decisive for that expansion.

Environmental and grazing influence on spatial variability of intertidal biofilm on subtropical rocky shores

Epilithic biofilm on rocky shores is regulated by physico-chemical and biological factors and is important as a source of food for benthic organisms. The influences of environmental and grazing pressure on spatial variability of biomass of biofilm were evaluated on shores on the north coast of Sao Paulo State (SE Brazil). A general trend of greater abundance of microalgae was observed lower on the shore, but neither of the environmental factors evaluated (wave exposure and shore level) showed consistent effects, and differences were found among specific shores or times (September 2007 and March 2008). The abundance of slow-moving grazers (limpets and littorinids) showed a negative correlation with chlorophyll a concentration on shores. However, experimental exclusion of these grazers failed to show consistent results at small spatial scales. Observations of divergent abundances of the isopod Ligia exotica and biomass of biofilm on isolated boulders on shores led to a short exclusion experiment, where the grazing pressure by L. exotica significantly decreased microalgal biomass. The result suggests that grazing activities of this fast-moving consumer probably mask the influence of slow-moving grazers at small spatial scales, while both have an additive effect at larger scales that masks environmental influences. This is the first evaluation of the impact of the fast-moving herbivore L. exotica on microalgal biomass on rocky shores and opens an interesting discussion about the role of these organisms in subtropical coastal environments.

Meiobenthic communities of seagrass beds (Zostera capricorni) and unvegetated sediments along the coast of New South Wales, Australia

Seagrass beds have higher biomass, abundance, diversity and productivity of benthic organisms than unvegetated sediments. However, to date most studies have analysed only the macrofaunal component and ignored the abundant meiofauna present in seagrass meadows. This study was designed to test if meiobenthic communities, especially the free-living nematodes, differed between seagrass beds and unvegetated sediments. Sediment samples from beds of the eelgrass Zostera capricorni and nearby unvegetated sediments were collected in three estuaries along the coast of New South Wales, Australia. Results showed that sediments below the seagrass were finer, with a higher content of organic material and were less oxygenated than sediments without seagrass. Univariate measures of the fauna (i.e. abundance, diversity and taxa richness of total meiofauna and nematode assemblages) did not differ between vegetated and unvegetated sediments. However multivariate analysis of meiofaunal higher taxa showed significant differences between the two habitats, largely due to the presence and absence of certain taxa. Amphipods, tanaidacea, ostracods, hydrozoans and isopods occurred mainly in unvegetated sediments, while kinorhyncs, polychaetes, gastrotrichs and turbellarians were more abundant in vegetated sediments. Regarding the nematode assemblages, 32.4% of the species were restricted to Z. capricorni and 25% only occurred in unvegetated sediments, this suggests that each habitat is characterized by a particular suite of species. Epistrate feeding nematodes were more abundant in seagrass beds, and it is suggested that they graze on the microphytobenthos which accumulates underneath the seagrass. Most of the genera that characterized these estuarine unvegetated sediments are also commonly found on exposed sandy beaches. This may be explained by the fact that Australian estuaries have very little input of freshwater and experience marine conditions for most of the year. This study demonstrates that the seagrass and unvegetated sediments have discrete meiofaunal communities, with little overlap in species composition. (C) 2010 Elsevier Ltd. All rights reserved.

Characterization of feather-degrading bacteria from Brazilian soils

Studies on keratinolytic microorganisms have been mainly related to their biotechnological applications and association with animal pathologies. However, these organisms have an ecological relevance to recycling keratinous residues in nature. This work aimed to select and identify new culturable feather-degrading bacteria isolated from soils of Brazilian Amazon forest and Atlantic forest. Bacteria that were isolated from temperate soils and bacteria from Amazonian basin soil were tested for their capability to grow on feather meal agar (FMA). Proteolytic bacteria were tested for feather degradation and were further identified according to their morphological and biochemical characteristics. Also, molecular identification based on 165 rDNA gene sequencing was carried out. A total of 24 proteolytic and 20 feather-degrading isolates were selected; Most of the isolates were from the Bacillus genus (division Firmicutes), but one Aeromonas, two Serratia (gamma-Proteobacteria), and one Chryseobacterium (Cytophaga-Flavobacterium group). (C) 2010 Elsevier Ltd. All rights reserved.

Evaluation of laser induced breakdown spectroscopy for cadmium determination in soils

Cadmium is known to be a toxic agent that accumulates in the living organisms and present high toxicity potential over lifetime. Efforts towards the development of methods for microanalysis of environmental samples, including the determination of this element by graphite furnace atomic absorption spectrometry (GFAAS). inductively coupled plasma optical emission spectrometry (ICP OES), and inductively coupled plasma-mass spectrometry (ICP-MS) techniques, have been increasing. Laser induced breakdown spectroscopy (UBS) is an emerging technique dedicated to microanalysis and there is a lack of information dealing with the determination of cadmium. The aim of this work is to demonstrate the feasibility of LIBS for cadmium detection in soils. The experimental setup was designed using a laser Q-switched (Nd:YAG, 10 Hz, lambda = 1064 nm) and the emission signals were collimated by lenses into an optical fiber Coupled to a high-resolution intensified charge-coupled device (ICCD)-echelle spectrometer. Samples were cryogenically ground and thereafter pelletized before LIBS analysis. Best results were achieved by exploring a test portion (i.e. sampling spots) with larger surface area, which contributes to diminish the uncertainty due to element specific microheterogeneity. Calibration curves for cadmium determination were achieved using certified reference materials. The metrological figures of merit indicate that LIBS can be recommended for screening of cadmium contamination in soils. (C) 2009 Elsevier B.V. All rights reserved.

Chemical changes in bromeliad leaves at different vegetative stages

Studies concerning the accumulating capacity of native epiphytic bromeliads are of utmost relevance, due to the continuous incorporation of chemical elements provided by these organisms in the ecosystems. Bromeliad species from diverse So Paulo State conservation units, Brazil, were sampled for young, mature and old leaves using a sustainable sampling method. By applying INAA, the accumulation of ten chemical elements, i.e. Br, Ca, Co, Fe, K, Na, Rb, Sc, Sr and Zn, was investigated in different leaf vegetative stages. The bromeliads showed divergent chemical element distribution patterns, demonstrating a real complexity in the accumulation and translocation mechanisms utilized by these plants.

Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove

Mangrove sediments are anaerobic ecosystems rich in organic matter. This environment is optimal for anaerobic microorganisms, such as sulphate-reducing bacteria and methanogenic archaea, which are responsible for nutrient cycling. In this study, the diversity of these two functional guilds was evaluated in a pristine mangrove forest using denaturing gradient gel electrophoresis (DGGE) and clone library sequencing in a 50 cm vertical profile sampled every 5.0 cm. DGGE profiles indicated that both groups presented higher richness in shallow samples (0-30 cm) with a steep decrease in richness beyond that depth. According to redundancy analysis, this alteration significantly correlated with a decrease in the amount of organic matter. Clone library sequencing indicated that depth had a strong effect on the selection of dissimilatory sulphate reductase (dsrB) operational taxonomic units (OTUs), as indicated by the small number of shared OTUs found in shallow (0.0 cm) and deep (40.0 cm) libraries. On the other hand, methyl coenzyme-M reductase (mcrA) libraries indicated that most of the OTUs found in the shallow library were present in the deep library. These results show that these two guilds co-exist in these mangrove sediments and indicate important roles for these organisms in nutrient cycling within this ecosystem.

FATTY ACID COMPOSITION OF ACID, BIOLOGICAL AND ENZYMATIC FISH SILAGE

The use of the fish silage as an ingredient in feed for aquatic organisms is an alternative to solve sanitary and environmental problems caused by the lack of an adequate destination for the residues generated by the fishing industry. It would also lower the costs with feed, and consequently the fish production costs, since the expenses with the feed account for approximately 60% of the total cost. The objective of this study was to evaluate the fatty acid composition of the acid silage (AS), biological silage (BS) and enzymatic silage (ES) produced from discardings of the culture and from processing residues of the Nile tilapia (Oreochromis niloticus). The values found for lipids (dry matter basis) were: 12.45; 12.25 and 12.17 g 100 g(-1) for BS, AS, and ES, respectively. The fatty acids present in the lipid fraction of the silages are predominantly unsaturated. Oleic acid was present in larger amounts (30.49, 28.60 and 30.60 g 100 g(-1) of lipids for BS, AS and ES, respectively). Among saturated fatty acids, palmitic and stearic acids were present in larger amounts. Only traces of eicosapentaenoic (EPA) and docosahexaenoic (DHA) fatty acids were found. The silages produced from discardings of the culture and processing residues of the Nile tilapia are not a good source of EPA and DHA for fish feeds.

Land planarians (Platyhelminthes) as a model organism for fine-scale phylogeographic studies: understanding patterns of biodiversity in the Brazilian Atlantic Forest hotspot

The Brazilian Atlantic Forest is one of the richest biodiversity hotspots of the world. Paleoclimatic models have predicted two large stability regions in its northern and central parts, whereas southern regions might have suffered strong instability during Pleistocene glaciations. Molecular phylogeographic and endemism studies show, nevertheless, contradictory results: although some results validate these predictions, other data suggest that paleoclimatic models fail to predict stable rainforest areas in the south. Most studies, however, have surveyed species with relatively high dispersal rates whereas taxa with lower dispersion capabilities should be better predictors of habitat stability. Here, we have used two land planarian species as model organisms to analyse the patterns and levels of nucleotide diversity on a locality within the Southern Atlantic Forest. We find that both species harbour high levels of genetic variability without exhibiting the molecular footprint of recent colonization or population expansions, suggesting a long-term stability scenario. The results reflect, therefore, that paleoclimatic models may fail to detect refugia in the Southern Atlantic Forest, and that model organisms with low dispersal capability can improve the resolution of these models.

TOXICITY EVALUATION AS A TOOL TO ASSES THE PERFORMANCE OF AN ANAEROBIC IMMOBILIZED BIOMASS REACTOR

Effluents from pulp mill are usually toxic and mutagenic. This characteristic is mainly a consequence of xenobiotic compounds that are formed during the process. Global parameters such as chemical oxidation demand, total organic carbon and others, do not permit identify whether the toxic potential was remedied by the treatments or not. The objective of this research was to evaluate the performance of an horizontal-flow anaerobic immobilized biomass reactor (HAIB) treating the bleaching effluent from a Kraft pulp mill using toxicological (Daphnia similis - Ceriodaphnia sdvestrii) mutagenicity and citotoxicological assays (Allium cepa L). The results showed high sensibility of the test-organisms and capability of the anaerobic reactor to remove compounds that are exerting toxic and mutagenic effects. The bioassays represented an attractive alternative to water quality analyzes and the performance evaluation of treatments.

Microbial processes and bacterial populations associated to anaerobic treatment of sulfate-rich wastewater

A pilot-scale (1.2 m(3)) anaerobic sequencing batch biofilm reactor (ASBBR) containing mineral coal for biomass attachment was fed with sulfate-rich wastewater at increasing sulfate concentrations. Ethanol was used as the main organic source. Tested COD/sulfate ratios were of 1.8 and 1.5 for sulfate loading rates of 0.65-1.90 kgSO(4)(2-)/cycle (48 h-cycle) or of 1.0 in the trial with 3.0 gSO(4)(2-) l(-1). Sulfate removal efficiencies observed in all trials were as high as 99%. Molecular inventories indicated a shift on the microbial composition and a decrease on species diversity with the increase of sulfate concentration. Beta-proteobacteria species affiliated with Aminomonas spp. and Thermanaerovibrio spp. predominated at 1.0 gSO(4)(2-) l(-1). At higher sulfate concentrations the predominant bacterial group was Delta-proteobacteria mainly Desulfovibrio spp. and Desulfomicrobium spp. at 2.0 gSO(4)(2-) l(-1), whereas Desulfurella spp. and Coprothermobacter spp. predominated at 3.0 gSO(4)(2-) l(-1). These organisms have been commonly associated with sulfate reduction producing acetate, sulfide and sulfur. Methanogenic archaea(Methanosaeta spp.)was found at 1.0 and 2.0 gSO(4)(2-) l(-1). Additionally, a simplified mathematical model was used to infer on metabolic pathways of the biomass involved in sulfate reduction. (C) 2009 Elsevier Ltd. All rights reserved.

Advanced process of microbiological control of wastewater in combined system of disinfection with UV radiation

The purpose of this study was to present a methodology with superior efficiency for inactivating pathogenic indicators commonly found in domestic sewage. The adopted method was based on synergistic effect resulting from the introduction of a UV radiation pre-disinfection stage of sewage followed by secondary treatment. A pilot unit was installed in the sewage treatment plant of the University of Sao Paulo to simulate the combined system in full-scale operational conditions. Its performance was evaluated through microbiological examinations for determining Escherichia coli, total coliforms and coliphages. The application of UV radiation at 5.1mW/cm(2) for 10 s of exposure in the first disinfection stage was enough to reduce the surviving number of E. coli around 100 times, in comparison to the conventional method. Therefore, based on experimental data, it is possible to conclude that combining treatment and pre-disinfection stage is an effective potential technique to produce effluents with lower degree of contamination by pathogenic organisms.

Do Larvae and Ovipositing Chironomus riparius (Diptera: Chironomidae) Females Avoid Copper-Contaminated Environments?

Studies on the avoidance behavior of aquatic organisms to contaminants have confirmed that such behavior can be relevant in field situations. However, almost all toxicity tests involve the forced exposure of organisms to toxicants. In particular, despite the importance of Chironomus riparius Meigen larvae in sediment toxicity testing, only a few studies on avoidance behavior have been performed. This study investigated the ability of different life stages of C. riparius, including ovipositing females, first-, second-, and fourth-instar larvae, to avoid copper-contaminated environments. Ovipositing females were given a choice between a control and copper solution (1.3 mg Cu l(-1)). First-instar larvae were provided with a choice between a control and a copper (2.0 mg Cu l(-1))-spiked sediment. Both second- and fourth-instars were exposed to a copper gradient (0.38-3.4 mg Cu l(-1)) in a flow-through system. None of the life stages avoided copper, even though the highest concentrations caused lethal effects on midges. The avoidance behavior of C. riparius is not a sensitive endpoint to assess copper sublethal toxicity.

Effects of bed materials on the performance of an anaerobic sequencing batch biofilm reactor treating domestic sewage

The objective of this study was to determine the best performance of an anaerobic sequencing batch biofilm reactor (AnSBBR) based on the use of four different bed materials as support for biomass immobilization. The bed materials utilized were Polyurethane foam (PU), vegetal carbon (VC), synthetic pumice (SP), and recycled low-density polyethylene (PE). The AnSBBR. with I total volume Of 7.2 L, was operated in 8-h batch cycles over 10 months, and fed with domestic sewage with an average influent chemical oxygen demand (COD) of 358 +/- 110 mg/L. The average effluent COD values were 121 +/- 31, 208 +/- 54, 233 +/- 52, and 227 +/- 51 mg/L. for PU, VC, SP, and PE, respectively. A modified first-order kinetic model was adjusted to temporal profiles of COD during a batch cycle, and the apparent kinetic constants were 0.52 +/- 0.05, 0.37 +/- 0.05, 0.80 +/- 0.04, and 0.30 +/- 0.021h(-1) for PU, VC, SP, and PE, respectively. Specific substrate utilization rates of 1.08, 0.11, and 0.86 mg COD/mg VS day were obtained for PU, VC, and PE, respectively. Although SP yielded the highest kinetic coefficient, PU was considered the best support, since SP presented loss of chemical constituents during the reactor`s operational phase. In addition, findings oil the microbial community were associated with the reactor`s performance data. Although PE did not show a satisfactory performance, an interesting microbial diversity was found oil its surface. Based oil the morphology and denaturing gradient gel electrophoresis (DGGE) results, PE showed the best capacity for promoting the attachment of methanogenic organisms, and is therefore a material that merits further analysis. PU was considered the Most suitable material showing the best performance in terms of efficiency of solids and COD removal. (C) 2007 Elsevier Ltd. All rights reserved.

Specific methanogenic activity in an anaerobic-aerobic reactor applied to the treatment of domestic residual water

The specific methanogenic activity (SMA) test is an important tool for the monitoring of anaerobic digestion. This paper presents the behavior of the methanogenic archaea of an anaerobic sludge under different conditions of oxygenation in a fixed-bed anaerobic-aerobic reactor treating domestic sewage. The reactor was operated in a continuous manner under different liquid recycle ratios from aerobic to anaerobic zones in order to remove carbon and nitrogen. The application of the SMA test was adapted from several authors and the measurement of the accumulated methane in the reactor was carried out by means of gas chromatography. Methanogenic organisms were not inhibited by the presence of oxygen. In contrast, the values of CH, production rate by sludge exposed to oxygen were greater than those obtained for strictly anaerobic sludge.