The protist Trichomonas vaginalis harbors multiple lineages of transcriptionally active Mutator-like elements

<p>Abstract</p> <p>Background</p> <p>For three decades the <it>Mutator </it>system was thought to be exclusive of plants, until the first homolog representatives were characterized in fungi and in early-diverging amoebas earlier in this decade.</p> <p>Results</p> <p>Here, we describe and characterize four families of <it>Mutator</it>-like elements in a new eukaryotic group, the Parabasalids. These <b><it>T</it></b><it>richomonas </it><b><it>v</it></b><it>aginalis </it><it><b>Mu</b>tator- <b>l</b>ike </it><it><b>e</b>lements</it>, or <it>TvMULEs</it>, are active in <it>T. vaginalis </it>and patchily distributed among 12 trichomonad species and isolates. Despite their relatively distinctive amino acid composition, the inclusion of the repeats <it>TvMULE1</it>, <it>TvMULE2</it>, <it>TvMULE3 </it>and <it>TvMULE4 </it>into the <it>Mutator </it>superfamily is justified by sequence, structural and phylogenetic analyses. In addition, we identified three new <it>TvMULE</it>-related sequences in the genome sequence of <it>Candida albicans</it>. While <it>TvMULE1 </it>is a member of the <it>MuDR </it>clade, predominantly from plants, the other three <it>TvMULEs</it>, together with the <it>C. albicans </it>elements, represent a new and quite distinct <it>Mutator </it>lineage, which we named <it>TvCaMULEs</it>. The finding of <it>TvMULE1 </it>sequence inserted into other putative repeat suggests the occurrence a novel TE family not yet described.</p> <p>Conclusion</p> <p>These findings expand the taxonomic distribution and the range of functional motif of <it>MULEs </it>among eukaryotes. The characterization of the dynamics of <it>TvMULEs </it>and other transposons in this organism is of particular interest because it is atypical for an asexual species to have such an extreme level of TE activity; this genetic landscape makes an interesting case study for causes and consequences of such activity. Finally, the extreme repetitiveness of the <it>T. vaginalis </it>genome and the remarkable degree of sequence identity within its repeat families highlights this species as an ideal system to characterize new transposable elements.</p

Phylogenetic and functional diversity of metagenomic libraries of phenol degrading sludge from petroleum refinery wastewater treatment system

In petrochemical refinery wastewater treatment plants (WWTP), different concentrations of pollutant compounds are received daily in the influent stream, including significant amounts of phenolic compounds, creating propitious conditions for the development of particular microorganisms that can rapidly adapt to such environment. In the present work, the microbial sludge from a refinery WWTP was enriched for phenol, cloned into fosmid vectors and pyrosequenced. The fosmid libraries yielded 13,200 clones and a comprehensive bioinformatic analysis of the sequence data set revealed a complex and diverse bacterial community in the phenol degrading sludge. The phylogenetic analyses using MEGAN in combination with RDP classifier showed a massive predominance of Proteobacteria, represented mostly by the genera Diaphorobacter, Pseudomonas, Thauera and Comamonas. The functional classification of phenol degrading sludge sequence data set generated by MG-RAST showed the wide metabolic diversity of the microbial sludge, with a high percentage of genes involved in the aerobic and anaerobic degradation of phenol and derivatives. In addition, genes related to the metabolism of many other organic and xenobiotic compounds, such as toluene, biphenyl, naphthalene and benzoate, were found. Results gathered herein demonstrated that the phenol degrading sludge has complex phylogenetic and functional diversities, showing the potential of such community to degrade several pollutant compounds. This microbiota is likely to represent a rich resource of versatile and unknown enzymes which may be exploited for biotechnological processes such as bioremediation

Transcriptome analysis of the oil-rich seed of the bioenergy crop Jatropha curcas L

<p>Abstract</p> <p>Background</p> <p>To date, oil-rich plants are the main source of biodiesel products. Because concerns have been voiced about the impact of oil-crop cultivation on the price of food commodities, the interest in oil plants not used for food production and amenable to cultivation on non-agricultural land has soared. As a non-food, drought-resistant and oil-rich crop, <it>Jatropha curcas </it>L. fulfils many of the requirements for biofuel production.</p> <p>Results</p> <p>We have generated 13,249 expressed sequence tags (ESTs) from developing and germinating <it>Jatropha </it>seeds. This strategy allowed us to detect most known genes related to lipid synthesis and degradation. We have also identified ESTs coding for proteins that may be involved in the toxicity of <it>Jatropha </it>seeds. Another unexpected finding is the high number of ESTs containing transposable element-related sequences in the developing seed library (800) when contrasted with those found in the germinating seed library (80).</p> <p>Conclusions</p> <p>The sequences generated in this work represent a considerable increase in the number of sequences deposited in public databases. These results can be used to produce genetically improved varieties of <it>Jatropha </it>with increased oil yields, different oil compositions and better agronomic characteristics.</p

The effect of pond dyes on oviposition and survival in wild UK Culex mosquitoes

British Culex pipiens complex [Culex pipiens sensu lato) mosquito distribution, abundance, and potential for disease transmission are intimately linked to their environment. Pond and lake dyes that block light to restrict algal photosynthesis are a relatively new product assumed to be an environmentally friendly since they are based on food dyes. Their use in urban garden ponds raises questions linked to mosquito oviposition, since coloured water can be an attractant. Culex (mostly pipiens) is commonly found in UK gardens and is a potential vector of viruses including the West Nile Virus (WNV). Any factors that significantly change the distribution and population of Cx pipiens could impact future risks of disease transmission. A gravid trap was used to catch female Cx pipiens mosquitoes for use in oviposition choice tests in laboratory and semi-field conditions. Two types of pond dye, blue and shadow (which looks slightly red), were tested for their impact on oviposition and survival of wild caught Cx pipiens. There were no significant differences in the number of egg batches laid when gravid mosquitoes were given a choice between either blue dye and clear water or shadow dye and clear water indicating that these dyes are not attractants. Larvae hatched from egg batches laid by wild-caught gravid females were used to measure survival to adulthood with or without dye, , in a habitat controlled to prevent further colonisation. The experiment was run twice, once in the summer and again in the autumn, whereas the dyes had no impact on emergence in the summer, there were highly significant reductions in emergence of adults in both dye treated habitats in the autumn. Containers with or without shadow dye were placed outside to colonise naturally and were sampled weekly for larvae and pupae over a 6 month period through summer and autumn. There was a significant negative effect of shadow dye on pupal abundance in a three week period over the summer, but otherwise there was no effect. It is likely that population abundance and food was a more powerful factor for mosquito survival than the dye

A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao

<p>Abstract</p> <p>Background</p> <p>The basidiomycete fungus <it>Moniliophthora perniciosa </it>is the causal agent of Witches' Broom Disease (WBD) in cacao (<it>Theobroma cacao</it>). It is a hemibiotrophic pathogen that colonizes the apoplast of cacao's meristematic tissues as a biotrophic pathogen, switching to a saprotrophic lifestyle during later stages of infection. <it>M. perniciosa</it>, together with the related species <it>M. roreri</it>, are pathogens of aerial parts of the plant, an uncommon characteristic in the order Agaricales. A genome survey (1.9× coverage) of <it>M. perniciosa </it>was analyzed to evaluate the overall gene content of this phytopathogen.</p> <p>Results</p> <p>Genes encoding proteins involved in retrotransposition, reactive oxygen species (ROS) resistance, drug efflux transport and cell wall degradation were identified. The great number of genes encoding cytochrome P450 monooxygenases (1.15% of gene models) indicates that <it>M. perniciosa </it>has a great potential for detoxification, production of toxins and hormones; which may confer a high adaptive ability to the fungus. We have also discovered new genes encoding putative secreted polypeptides rich in cysteine, as well as genes related to methylotrophy and plant hormone biosynthesis (gibberellin and auxin). Analysis of gene families indicated that <it>M. perniciosa </it>have similar amounts of carboxylesterases and repertoires of plant cell wall degrading enzymes as other hemibiotrophic fungi. In addition, an approach for normalization of gene family data using incomplete genome data was developed and applied in <it>M. perniciosa </it>genome survey.</p> <p>Conclusion</p> <p>This genome survey gives an overview of the <it>M. perniciosa </it>genome, and reveals that a significant portion is involved in stress adaptation and plant necrosis, two necessary characteristics for a hemibiotrophic fungus to fulfill its infection cycle. Our analysis provides new evidence revealing potential adaptive traits that may play major roles in the mechanisms of pathogenicity in the <it>M. perniciosa</it>/cacao pathosystem.</p

Toxicity of neem's oil, a potential biocide against the invasive mussel Limnoperna fortunei (Dunker 1857)

The golden mussel Limnoperna fortunei (Dunker 1857) is one of the most distributed Nuisance Invasive Species (NIS) in South America, and a threat of great concern for the industry of the area. In this study, we carried out toxicity tests made with a Neem's oil solution with L. fortunei larvae and benthonic adults (7, 13 and 19 ± 1 mm). Tests with non-target species (Daphnia magna, Lactuca sativa and Cnesterodon decemmculatus) were also made with the aim to evaluate the potential toxicity of the Neem's solution in the environment. The LC100 of Neem's solution obtained for larvae was 500 μl/L, a value much higher than the one obtained for D. magna and C. decemmaculatus. Thus, we recommend that it should not be used in open waters. However, since the adults were killed in 72 h and the larvae in 24 h, this product can be used in closed systems, in man-made facilities.Facultad de Ciencias Naturales y Muse

Control of Visceral Leishmaniasis in Latin America—A Systematic Review

Visceral leishmaniasis is a vector-borne disease characterized by fever, spleen and liver enlargement, and low blood cell counts. In the Americas VL is zoonotic, with domestic dogs as main animal reservoirs, and is caused by the intracellular parasite Leishmania infantum (syn. Leishmania chagasi). Humans acquire the infection through the bite of an infected sand fly. The disease is potentially lethal if untreated. VL is reported from Mexico to Argentina, with recent trends showing a rapid spread in Brazil. Control measures directed against the canine reservoir and insect vectors have been unsuccessful, and early detection and treatment of human cases remains as the most important strategy to reduce case fatality. Well-designed studies evaluating diagnosis, treatment, and prevention/control interventions are scarce. The available scientific evidence reasonably supports the use of rapid diagnostic tests for the diagnosis of human disease. Properly designed randomized controlled trials following good clinical practices are needed to inform drug policy. Routine control strategies against the canine reservoirs and insect vectors are based on weak and conflicting evidence, and vector control strategies and vaccine development should constitute research priorities

Prevalence and risk factors for Hepatitis C and HIV-1 infections among pregnant women in Central Brazil

<p>Abstract</p> <p>Background</p> <p>Hepatitis C (HCV) and human immunodeficiency virus (HIV) infections are a major burden to public health worldwide. Routine antenatal HIV-1 screening to prevent maternal-infant transmission is universally recommended. Our objectives were to evaluate the prevalence of and potential risk factors for HCV and HIV infection among pregnant women who attended prenatal care under the coverage of public health in Central Brazil.</p> <p>Methods</p> <p>Screening and counselling for HIV and HCV infections was offered free of charge to all pregnant women attending antenatal clinic (ANC) in the public health system, in Goiania city (~1.1 million inhabitants) during 2004–2005. Initial screening was performed on a dried blood spot collected onto standard filter paper; positive or indeterminate results were confirmed by a second blood sample. HCV infection was defined as a positive or indeterminate sample (EIA test) and confirmed HCV-RNA technique. HIV infection was defined according to standard criteria. Factors associated with HIV and HCV infections were identified with logistic regression. The number needed to screen (NNS) to prevent one case of infant HIV infection was calculated using the Monte Carlo simulation method.</p> <p>Results</p> <p>A total of 28,561 pregnant women were screened for HCV and HIV-1 in ANC. Mean maternal age was 23.9 years (SD = 5.6), with 45% of the women experiencing their first pregnancy. Prevalence of HCV infection was 0.15% (95% CI 0.11%–0.20%), and the risk increased with age (p < 0.01). The prevalence of anti-HIV infection was 0.09% (95% CI 0.06%–0.14%). Black women had a 4.9-fold (95% CI 1.42–16.95) greater risk of HIV-1 infection compared to non-black women. NNS to prevent one case of infant HIV infection ranged from 4,141 to 13,928.</p> <p>Conclusion</p> <p>The prevalence of HIV and HCV infections were low among pregnant women, with high acceptability rates in the opt-in strategy in primary care. Older maternal age was a risk factor for HCV and antenatal HCV testing does not fulfill the requirements for screening recommendation. The finding of higher risk of HIV-1 infection among black women despite being in consonance with the HIV-1 ethnic pattern in some American regions cannot be ruled out to be a surrogate marker of socio-economic condition.</p