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

Trail Marking by Caterpillars of the Silverspot Butterfly Dione Juno Huascuma

A pheromone is implicated in the trail marking behavior of caterpillars of the nymphalid silverspot butterfly, Dione juno huascuma (Reakirt) (Lepidoptera: Heliconiinae) that feed gregariously on Passiflora (Malpighiales: Passifloraceae) vines in Mexico. Although they mark pathways leading from one feeding site to another with silk, this study shows that the silk was neither adequate nor necessary to elicit trail following behavior. Caterpillars marked trails with a long-lived pheromone that was deposited when they brushed the ventral surfaces of the tips of their abdomens along branch pathways. The caterpillars distinguished between pathways deposited by different numbers of siblings and between trails of different ages. Caterpillars also preferentially followed the trails of conspecifics over those of another nymphalid, Nymphalis antiopa L., the mourning cloak butterfly

The resolution of acute inflammation induced by cyclic AMP is dependent on annexin A1

Annexin A1 (AnxA1) is a glucocorticoid-regulated protein known for its anti-inflammatory and pro-resolving effects. We have shown previously that the cAMP-enhancing compounds rolipram (ROL; a PDE4 inhibitor) and Bt2cAMP (a cAMP mimetic) drive caspase-dependent resolution of neutrophilic inflammation. In this follow-up study, we investigated whether AnxA1 could be involved in the pro-resolving properties of these compounds using a model of LPS-induced inflammation in BALB/c mice. The treatment with ROL or Bt2cAMP at the peak of inflammation shortened resolution intervals, improved resolution indices, and increased AnxA1 expression. In vitro studies showed that ROL and Bt2cAMP induced AnxA1 expression and phosphorylation, and this effect was prevented by PKA inhibitors, suggesting the involvement of PKA in ROL-induced AnxA1 expression. Akin to these in vitro findings, H89 prevented ROL- and Bt2cAMP-induced resolution of inflammation, and it was associated with decreased levels of intact AnxA1. Moreover, two different strategies to block the AnxA1 pathway (by using N-t-Boc-Met-Leu-Phe, a nonselective AnxA1 receptor antagonist, or by using an anti-AnxA1 neutralizing antiserum) prevented ROL- and Bt2cAMP-induced resolution and neutrophil apoptosis. Likewise, the ability of ROL or Bt2cAMP to induce neutrophil apoptosis was impaired in AnxA-knock-out mice. Finally, in in vitro settings, ROL and Bt2cAMP overrode the survival-inducing effect of LPS in human neutrophils in an AnxA1-dependent manner. Our results show that AnxA1 is at least one of the endogenous determinants mediating the pro-resolving properties of cAMP-elevating agents and cAMP-mimetic drug

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

Lepton flavour violation in the MSSM

We derive new constraints on the quantities delta_{XY}^{ij}, X,Y=L,R, which parametrise the flavour-off-diagonal terms of the charged slepton mass matrix in the MSSM. Considering mass and anomalous magnetic moment of the electron we obtain the bound |delta^{13}_{LL} delta^{13}_{RR}|<0.1 for tan beta=50, which involves the poorly constrained element delta^{13}_{RR}. We improve the predictions for the decays tau -> mu gamma, tau -> e gamma and mu -> e gamma by including two-loop corrections which are enhanced if tan beta is large. The finite renormalisation of the PMNS matrix from soft SUSY-breaking terms is derived and applied to the charged-Higgs-lepton vertex. We find that the experimental bound on BR(tau -> e gamma) severely limits the size of the MSSM loop correction to the PMNS element U_{e3}, which is important for the proper interpretation of a future U_{e3} measurement. Subsequently we confront our new values for delta^{ij}_{LL} with a GUT analysis. Further, we include the effects of dimension-5 Yukawa terms, which are needed to fix the Yukawa unification of the first two generations. If universal supersymmetry breaking occurs above the GUT scale, we find the flavour structure of the dimension-5 Yukawa couplings tightly constrained by mu -> e gamma.Comment: 37 pages, 15 figures; typo in Equation (35) and (49) correcte