DGGE with genomic DNA: Suitable for detection of numerically important organisms but not for identification of the most abundant organisms

Identification of all important community members as well as of the numerically dominant members of a community are key aspects of microbial community analysis of bioreactor samples. A systematic study was conducted with artificial consortia to test whether denaturing gradient gel electrophoresis (DGCE) is a reliable technique to obtain such community data under conditions where results would not be affected by differences in DNA extraction efficiency from cells. A total of 27 consortia were established by mixing DNA extracted from Escherichia coli K12, Burkholderia cepacia and Stenotrophomonas maltophilia in different proportions. Concentrations of DNA of single organisms in the consortia were either 0.04, 0.4 or 4 ng/mu l. DGGE-PCR of genomic DNA with primer sets targeted at the V3 and V6-V8 regions of the 16S rDNA failed to detect the three community members in only 7% of consortia, but provided incorrect information about dominance or co-dominance for 85% and 89% of consortia with the primer sets for the V6-V8 and V3 regions, respectively. The high failure rate in detection of dominant B. cepacia with the primers for the V6-V8 region was attributable to a single nucleoticle primer mismatch in the target sequences of both, the forward and reverse primer. Amplification bias in PCR of E. coli and S. maltophilia for the V6-V8 region and for all three organisms for the V3 region occurred due to interference of genomic DNA in PCR-DGGE, since a nested PCR approach, where PCR-DGGE was started from mixtures of 16S rRNA genes of the organisms, provided correct information about the relative abundance of original DNA in the sample. Multiple bands were not observed in pure culture amplicons produced with the V6-V8 primer pair, but pure culture V3 DGGE profiles of E. coli, S. maltophilia and B. cepacia contained 5, 3 and 3 bands, respectively. These results demonstrate DGGE was suitable for identification of all important community members in the three-membered artificial consortium, but not for identification of the dominant organisms in this small community. Multiple DGGE bands obtained for single organisms with the V3 primer pair could greatly confound interpretation of DGGE profiles. (C) 2008 Elsevier Ltd. All rights reserved.

Quantitative analysis of indexed publications on seventeen model organisms in nine countries, from 1974 to 2006

Developed countries have an even distribution of published papers on the seventeen model organisms. Developing countries have biased preferences for a few model organisms which are associated with endemic human diseases. A variant of the Hirsch-index, that we call the mean (mo)h-index (""model organism h-index""), shows an exponential relationship with the amount of papers published in each country on the selected model organisms. Developing countries cluster together with low mean (mo)h-indexes, even those with high number of publications. The growth curves of publications on the recent model Caenorhabditis elegans in developed countries shows different formats. We also analyzed the growth curves of indexed publications originating from developing countries. Brazil and South Korea were selected for this comparison. The most prevalent model organisms in those countries show different growth curves when compared to a global analysis, reflecting the size and composition of their research communities.

A quasispecies approach to the evolution of sexual replication in unicellular organisms

This study develops a simplified model describing the evolutionary dynamics of a population composed of obligate sexually and asexually reproducing, unicellular organisms. The model assumes that the organisms have diploid genomes consisting of two chromosomes, and that the sexual organisms replicate by first dividing into haploid intermediates, which then combine with other haploids, followed by the normal mitotic division of the resulting diploid into two new daughter cells. We assume that the fitness landscape of the diploids is analogous to the single-fitness-peak approach often used in single-chromosome studies. That is, we assume a master chromosome that becomes defective with just one point mutation. The diploid fitness then depends on whether the genome has zero, one, or two copies of the master chromosome. We also assume that only pairs of haploids with a master chromosome are capable of combining so as to produce sexual diploid cells, and that this process is described by second-order kinetics. We find that, in a range of intermediate values of the replication fidelity, sexually reproducing cells can outcompete asexual ones, provided the initial abundance of sexual cells is above some threshold value. The range of values where sexual reproduction outcompetes asexual reproduction increases with decreasing replication rate and increasing population density. We critically evaluate a common approach, based on a group selection perspective, used to study the competition between populations and show its flaws in addressing the evolution of sex problem.

Chemoselective screening for the reduction of a chiral functionalised (+/-)-2-(phenylthio)cyclohexanone by whole cells of Brazilian micro-organisms

The use of whole cells of micro-organisms to bring about the biotransformation of an organic compound offers a number of advantages, but problems caused by enzymatic Promiscuity may be encountered upon With Substrates hearing more than one functional group. A one-pot screening method, in which whole fungal cells were incubated with a Mixture of 4-rnethylcyclohexanone I and phenyl methyl Sulfide 2, has been employed to determine the chemoselectivity of various biocatalysts. The hyphomycetes, Aspergillus terreus CCT 3320 and A. terreus URM 3571, catalysed the oxidation of 2 accompanied by the reduction of I to 4-methylcyclohexanol 1a and, for strain A. terreus CCT 3320, the Baeyer-Villiger oxidation of 1. The Basidomycetes, Trametes versicolor CCB 202, Pycnoporus sanguineus CCB 501 and Trichaptum byssogenum CCB 203, catalysed the oxidation of 2 and the reduction 1, but no Baeyer-Villiger reaction products were detected. In contrast. Trametes rigida CCB 285 catalysed the biotransformation of 1 to 1a, exclusively, in the absence of any detectable Sulfide oxidation reactions. The chemoselective reduction Of (+/-)-2-(phenylthio)cyclohexanone 3 by T. rigida CCB 285 afforded exclusively the (+)-cis-(1R,2S) and (+)-trans-(1S,2S) diastereoisomers of 2-(phenylthio)cyclohexan-1-ol 3a in moderate yields (13% and 27%, respectively) and high enantiomeric excesses (>98%). Chemoselective screening for the reduction of a ketone and/or the oxidation Of a Sulfide group in one pot by whole cells of micro-organisms represents an attractive technique with applications in the development of synthesis of complex molecule hearing different functional groups. (C) 2008 Published by Elsevier Ltd.

International civil society actors in Genetically Modificied Organisms as a field of struggle: a neo-gramscian study in Brazil and the United Kingdom

Since the international financial and food crisis that started in 2008, strong emphasis has been made on the importance of Genetically Modified Organisms (GMOs) (or “transgenics”) under the claim that they could contribute to increase food productivity at a global level, as the world population is predicted to reach 9.1 billion in the year 2050 and food demand is predicted to increase by as much as 50% by 2030. GMOs are now at the forefront of the debates and struggles of different actors. Within civil society actors, it is possible to observe multiple, and sometime, conflicting roles. The role of international social movements and international NGOs in the GMO field of struggle is increasingly relevant. However, while many of these international civil society actors oppose this type of technological developments (alleging, for instance, environmental, health and even social harms), others have been reportedly cooperating with multinational corporations, retailers, and the biotechnology industry to promote GMOs. In this thesis research, I focus on analysing the role of “international civil society” in the GMO field of struggle by asking: “what are the organizing strategies of international civil society actors, such as NGOs and social movements, in GMO governance as a field of struggle?” To do so, I adopt a neo-Gramscian discourse approach based on the studies of Laclau and Mouffe. This theoretical approach affirms that in a particular hegemonic regime there are contingent alliances and forces that overpass the spheres of the state and the economy, while civil society actors can be seen as a “glue” to the way hegemony functions. Civil society is then the site where hegemony is consented, reproduced, sustained, channelled, but also where counter-hegemonic and emancipatory forces can emerge. Considering the importance of civil society actors in the construction of hegemony, I also discuss some important theories around them. The research combines, on the one hand, 36 in-depth interviews with a range of key civil society actors and scientists representing the GMO field of struggle in Brazil (19) and the UK (17), and, on the other hand, direct observations of two events: Rio+20 in Rio de Janeiro in 2012, and the first March Against Monsanto in London in 2013. A brief overview of the GMO field of struggle, from its beginning and especially focusing in the 1990s when the process of hegemonic formation became clearer, serves as the basis to map who are the main actors in this field, how resource mobilization works, how political opportunities (“historical contingencies”) are discovered and exploited, which are the main discourses (“science” and “sustainability” - articulated by “biodiversity preservation”, “food security” and “ecological agriculture”) articulated among the actors to construct a collective identity in order to attract new potential allies around “GMOs” (“nodal point”), and which are the institutions and international regulations within these processes that enable hegemony to emerge in meaningful and durable hegemonic links. This mapping indicates that that the main strategies applied by the international civil society actors are influenced by two central historical contingencies in the GMO field of struggle: 1) First Multi-stakeholder Historical Contingency; and 2) “Supposed” Hegemony Stability. These two types of historical contingency in the GMO field of struggle encompass deeper hegemonic articulations and, because of that, they induce international civil society actors to rethink the way they articulate and position themselves within the field. Therefore, depending on one of those moments, they will apply one specific strategy of discourse articulation, such as: introducing a new discourse in hegemony articulation to capture the attention of the public and of institutions; endorsing new plural demands; increasing collective visibility; facilitating material articulations; sharing a common enemy identity; or spreading new ideological elements among the actors in the field of struggle.

Ecotoxicology of Nano-TiO2 An Evaluation of its Toxicity to Organisms of Aquatic Ecosystems

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Abundance of sedentary consumers and sessile organisms along the wave exposure gradient of subtropical rocky shores of the south-west Atlantic

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

Toxicity of the therapeutic potassium permanganate to tilapia Oreochromis niloticus and to non-target organisms Ceriodaphnia dubia (microcrustacean cladocera) and Pseudokirchneriella subcapitata (green microalgae)

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

Molecular diagnosis of Anaplasmataceae organisms in dogs with clinical and microscopical signs of ehrlichiosis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Colonisation of soft lining materials by micro-organisms

Objective:This study evaluated the in vitro adherence of pathogenic micro-organisms, Candida albicans, Staphylococcus aureus and Pseudomonas aeruginosa, to soft lining materials and their inhibitory effect on these micro-organisms.Materials and Methods:To measure adherence, specimens of Molloplast B and Ufi Gel P were inoculated [107 colony-forming units per millimetre (cfu/ml)] with TSB media containing the micro-organisms. To determine the number of micro-organisms in the 10-2-10-5 dilutions, 25 mu l of the suspension were transferred to plates of selective media. Colony counts of each specimen were quantified (cfu/ml). The surface roughness was measured with a perfilometer to assess the relationship between the adherence of micro-organisms and surface roughness of each material. For the inhibition test, specimens of materials were placed in agar plates inoculated individually with the micro-organisms. After 48 h, the inhibition zones around the specimens were measured.Results:None of the materials exhibited inhibition zones. The number of cfu/ml of S. aureus and P. aeruginosa were significantly greater than C. albicans for both materials. The Ufi Gel P exhibited greater adherence of C. albicans than Molloplast B. No correlation was observed between the adherence of micro-organisms and surface roughness.Conclusion:The surface roughness of the materials is not the only factor governing micro-organism adherence.

Cyanobacteria from coastal lagoons in southern Brazil: non-heterocytous filamentous organisms

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Cyanobacteria from coastal lagoons of Southern Brazil: coccoid organisms

Considering the great ecological importance of the cyanobacteria and the need for more detailed information about these organisms in Brazilian waters, this paper provides taxonomic information about the unicellular cyanobacteria flora in lagoon systems along the coastal plains of Rio Grande do Sul State. Sampling was performed in different freshwater bodies along the eastern (Casamento Lake area) and western (near the city of Tapes) banks of the Patos Lagoon (30º40' S-30º10' S and 50º30' W-51º30' W). The samples were collected once in the rainy season and once in the dry season (from May 2003 to December 2003) using a plankton net (25 µm mesh) in pelagic and littoral zones, and by squeezing the submerged parts of aquatic macrophytes. Thirty one species belonging to the families Synechoccocaceae (7 taxa), Merismopediaceae (12 taxa), Chamaesiphonaceae (1 taxon), Microcystaceae (4) and Chroococcaceae (7 taxa) were identified. Among these species, five are reported for the first time in Rio Grande do Sul State: Chamaesiphon amethystinus (Rostafinski) Lemmermann, Chroococcus minimus (Keissler) Lemmermann, Coelomoron pusillum (Van Goor) Komárek, Coelosphaerium kuetzingeanum Naegeli, and Cyanodictyon tubiforme Cronberg.

Presence of wall-devoid micro-organisms in hypopharyngeal glands of forager bees (Hymenoptera, Apidae)

The occurrence of mycoplasma-like bodies in the axial duct and intracellular canaliculli from hypopharyngeal glands of bees (Meliponinae and Apinae) is described. Since they are not found within cells and due to the absence of cellular alterations in the infected glands it is suggested that micro-organisms are not pathogenic to the bees.

The in vitro antimicrobial activity of natural infant fluoride-free toothpastes on oral micro-organisms

Purpose: The objective of this study was to evaluate the antimicrobial activity of six toothpastes for infants: 3 fluoride-free experimental toothpastes - cashew-based, mango-based and without plant extract and fluoride compared with 2 commercially fluoride-free toothpastes and 1 fluoridated toothpastes. Methods: Six toothpastes for infants were evaluated in this study: (1) experimental cashew-based toothpaste; (2) experimental mango-based toothpaste; (3) experimental toothpaste without plant extract and fluoride (negative control); (4) First Teeth brand toothpaste; (5) Weleda brand toothpaste; and (6) Tandy brand toothpaste (positive control). The antimicrobial activity was recorded against Streptococcus mutans, Streptococcus sobrinus, Lactobacillus acidophilus, and Candida albicans using the agar plate diffusion test. Results: First Teeth, Weleda, mango-based toothpaste, and toothpaste without plant extract presented no antimicrobial effect against any of the tested micro-organisms. Cashew toothpaste had antimicrobial activity against S mutans, S sobrinus, and L acidophilus, but it showed no antimicrobial activity against C albicans. There was no statistical difference between the inhibition halo of cashew and Tandy toothpastes against S mutans and L acidophilus. Conclusions: Cashew fluoride-free toothpaste had inhibitory activity against Streptococcus mutans and Lactobacillus acidophilus, and these results were similar to those obtained for fluoridated toothpaste.

Evaluation of Three Formulations of Culture Media for Isolation of Brucella spp. regarding Their Ability to Inhibit the Growth of Contaminating Organisms

Three culture media (Brucella agar, Farrell medium, and CITA) were compared for their effectiveness in inhibiting contamination and for isolating Brucella spp. One hundred lymph nodes from pigs (n = 50) and wild boars (n = 50) with lymphadenitis were collected in slaughterhouses in the State of Sao Paulo and were assessed on these three selective media for Brucella spp. All of the samples were negative for Brucella spp. on the three culture media. On the agar medium, fungal (70 plates) and Gram-positive bacterial (59 plates) contaminants were observed; in the CITA medium, the absence of fungal and Gram-positive bacteria on 15 plates was observed; no bacterial or fungal growth was observed on the Farrell media. The results demonstrated that the CITA and Farrell media inhibited the growth of contaminants better than the Brucella agar.