Microbial population response to changes of the operating conditions in a dynamic nutrient-removal sequencing batch reactor

A nutrient-removal sequencing batch reactor operated with short anaerobic/aerobic cycles was subjected to different operating conditions, namely, cycle length, feeding pattern and feed composition. The changes in microbial population, as well as the contribution of microbial groups to the total nutrient removal, were estimated using the kinetic parameters obtained in this study. Denitrifying polyphosphate-accumulating organisms (DPAOs) were detected in the system, representing a fraction of 23% of phosphorus-accumulating organisms (PAOs). The results suggest that DPAOs and non-DPAOs are different microorganisms. The presence of nitrate in the feed stimulated DPAOs to predominate over non-DPAOs. Feeding the reactor with a mixture of organic substrates also stimulated DPAOs. Glycogen-accumulating organisms (GAOs) were likely to be present in the system and their development over PAOs was apparently favoured by increasing the aeration time and feeding during the aerobic phase. In contrast, the presence of propanoate in the feed apparently favoured PAOs over GAOs.     

Release of IL-1beta via IL-1beta-converting enzyme in a skin dendritic cell line exposed to 2,4-dinitrofluorobenzene

We used a mouse fetal skin dendritic cell line (FSDC) to study the effect of the strong allergen 2,4-dinitrofluorobenzene (DNFB) on interleukin (IL)-1beta release and IL-1beta receptor immunoreactivity. Stimulation with DNFB (30 minutes) increased IL-1 release without changing the mRNA levels of the protein. Furthermore, DNFB increased transiently the interleukin-1beta-converting enzyme (ICE) activity, as measured with its fluorogenic substrate Z-Tyr-Val-Ala-Asp-AFC. The ICE inhibitor Z-YVAD-FMK prevented the release of IL-1beta evoked by DNFB. Incubation of the cells with DNFB (30 minutes) strongly increased IL-1beta receptor immunoreactivity. The rapid effect of DNFB on the release of mature IL-1beta, without inducing an increase of IL-1beta mRNA in FSDC, suggests a posttranslational modification of pro-IL-1beta by ICE activity.     

The Gō model revisited: Native structure and the geometric coupling between local and long-range contacts

Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modeled by the Gō potential. For three target structures with different native geometries we found a sharp increase in the folding time when the relative contribution of the long-range interactions to the native state's energy is decreased from approximately 50% towards zero. However, the dispersion of the simulated folding times is strongly dependent on native geometry and Gō polymers folding to one of the target structures exhibits folding times spanning three orders of magnitude. We have also found that, depending on the target geometry, a strong geometric coupling may exist between local and long-range contacts, which means that, when this coupling exists, the formation of long-range contacts is forced by the previous formation of local contacts. The absence of a strong geometric coupling results in a kinetics that is more sensitive to the interaction energy parameters; in this case, the formation of local contacts is not capable of promoting the establishment of long-range ones when the latter are strongly penalized energetically and this results in longer folding times.     

The Drosophila gene brainiac encodes a glycosyltransferase putatively involved in glycosphingolipid synthesis

The Drosophila genes fringe and brainiac exhibit sequence similarities to glycosyltransferases. Drosophila and mammalian fringe homologs encode UDP-N-acetylglucosamine:fucose-O-Ser beta1,3-N-acetylglucosaminyltransferases that modulate the function of Notch family receptors. The biological function of brainiac is less well understood. brainiac is a member of a large homologous mammalian beta3-glycosyltransferase family with diverse functions. Eleven distinct mammalian homologs have been demonstrated to encode functional enzymes forming beta1-3 glycosidic linkages with different UDP donor sugars and acceptor sugars. The putative mammalian homologs with highest sequence similarity to brainiac encode UDP-N-acetylglucosamine:beta1,3-N-acetylglucosaminyltransferases (beta3GlcNAc-transferases), and in the present study we show that brainiac also encodes a beta3GlcNAc-transferase that uses beta-linked mannose as well as beta-linked galactose as acceptor sugars. The inner disaccharide core structures of glycosphingolipids in mammals (Galbeta1-4Glcbeta1-Cer) and insects (Manbeta1-4Glcbeta1-Cer) are different. Both disaccharide glycolipids served as substrates for brainiac, but glycolipids of insect cells have so far only been found to be based on the GlcNAcbeta1-3Manbeta1-4Glcbeta1-Cer core structure. Infection of High Five(TM) cells with baculovirus containing full coding brainiac cDNA markedly increased the ratio of GlcNAcbeta1-3Manbeta1-4Glcbeta1-Cer glycolipids compared with Galbeta1-4Manbeta1-4Glcbeta1-Cer found in wild type cells. We suggest that brainiac exerts its biological functions by regulating biosynthesis of glycosphingolipids.     

Structure at 1.3 A resolution of Rhodothermus marinus caa(3) cytochrome c domain

The cytochrome c domain of subunit II from the Rhodothermus marinus caa(3) HiPIP:oxygen oxidoreductase, a member of the superfamily of heme-copper-containing terminal oxidases, was produced in Escherichia coli and characterised. The recombinant protein, which shows the same optical absorption and redox properties as the corresponding domain in the holo enzyme, was crystallized and its structure was determined to a resolution of 1.3 A by the multiwavelength anomalous dispersion (MAD) technique using the anomalous dispersion of the heme iron atom. The model was refined to final R(cryst) and R(free) values of 13.9% and 16.7%, respectively. The structure reveals the insertion of two short antiparallel beta-strands forming a small beta-sheet, an interesting variation of the classical all alpha-helical cytochrome c fold. This modification appears to be common to all known caa(3)-type terminal oxidases, as judged by comparative modelling and by analyses of the available amino acid sequences for these enzymes. This is the first high-resolution crystal structure reported for a cytochrome c domain of a caa(3)-type terminal oxidase. The R.marinus caa(3) uses HiPIP as the redox partner. The calculation of the electrostatic potential at the molecular surface of this extra C-terminal domain provides insights into the binding to its redox partner on one side and its interaction with the remaining subunit II on the other side.     

The distribution of ticks (Acari: Ixodidae) of domestic livestock in Portugal

This paper introduces the first countrywide faunistic study of the tick parasites on ruminants in Portugal. The aim of this study was to map accurately the distribution of the ticks Dermacentor marginatus, Rhipicephalus (Boophilus) annulatus, R. bursa, Hyalomma m. marginatum, H. lusitanicum and Ixodes ricinus in Portugal. Additional information about the abiotic preferences of these species has been obtained through the use of abiotic (temperature- and vegetation-derived) variables have been recorded from remotely sensed information at a nominal resolution of 1.1 km². A further aim was the development of predictive models of distribution using Classification and Regression Trees (CART) methodologies. Four species (R. annulatus, R. bursa, D. marginatus and H. m. marginatum) are mostly restricted to south-eastern parts of the country, under hot and dry climate conditions of Mediterranean type. H. lusitanicum has been collected almost only in the southern half of Portugal. I. ricinus has a very patchy distribution and is mainly associated with vegetation of Quercus spp., found in southern zones of the country, but it is present also in the more humid western part. A variable number of abiotic variables, mainly temperature derived, are able to describe the preferences of the tick species. It is remarkable that variables derived from maximum values of the Normalized Derived Vegetation Index (yearly or summer-derived) only apply to discriminate areas where I. ricinus has been collected. CART models are able to map the distribution of these ticks with accuracy ranging within 75.3 and 96.4% of actual positive sites.     

Role of oxidative stress in ERK and p38 MAPK activation induced by the chemical sensitizer DNFB in a fetal skin dendritic cell line

The intracellular mechanisms involved in the early phase of dendritic cell (DC) activation upon contact with chemical sensitizers are not well known. The strong skin sensitizer 2,4-dinitrofluorobenzene (DNFB) was shown to induce the activation of mitogen-activated protein kinases (MAPK) in DC. In the present study, we investigated a putative role for oxidative stress in DNFB-induced MAPK activation and upregulation of the costimulatory molecule CD40. In a DC line generated from fetal mouse skin, DNFB induced a significant increase in protein oxidation, measured by the formation of carbonyl groups, while it had almost no effect on lipid peroxidation. The antioxidants glutathione and vitamin E, which inhibit protein and lipid oxidation, respectively, were used to assess the role of oxidative stress in DNFB-induced MAPK activation. Glutathione, but not vitamin E, inhibited DNFB-induced p38 MAPK and ERK1/2 phosphorylation, whereas none of the antioxidants interfered significantly with the DNFB-induced upregulation of CD40 protein levels. Taken together, these results indicate that DNFB activates p38 MAPK and ERK1/2 via production of reactive oxygen species, and that protein oxidation plays an important role in MAPK activation.     

Custom microarray for glycobiologists: considerations for glycosyltransferase gene expression profiling

The development of microarray technology offers the unprecedented possibility of studying the expression of thousands of genes in one experiment. Its exploitation in the glycobiology field will eventually allow the parallel investigation of the expression of many glycosyltransferases, which will ultimately lead to an understanding of the regulation of glycoconjugate synthesis. While numerous gene arrays are available on the market, e.g. the Affymetrix GeneChip arrays, glycosyltransferases are not adequately represented, which makes comprehensive surveys of their gene expression difficult. This chapter describes the main issues related to the establishment of a custom glycogenes array.     

Hairy root cultures of Anethum graveolens (dill): establishment, growth, time-course study of their essential oil and its comparison with parent plant oils

Transformed root cultures of Anethum graveolens were induced by inoculation of aseptically grown seedlings with Agrobacterium rhizogenes carrying plasmid pRi 1855. The main component of the essential oils from the fruits and from the roots of the parent plant was carvone, whereas -phellandrene and apiole were dominant in the oil from, respectively, the aerial parts and the hairy roots. The essential oils from the fruits, aerial parts and roots of the parent plant were at 2%, 0.3% and 0.06% (v/w), respectively, but only 0.02% (v/w) in the hairy root cultures. Growth of the hairy root cultures reached 600 mg dry wt/50 ml medium after 50 days. The essential oil composition did not change significantly during their growth.     

Susceptibility of Prevotella intermedia/Prevotella nigrescens (and Porphyromonas gingivalis) to propolis (bee glue) and other antimicrobial agents

Black-pigmented gram-negative anaerobes such as Porphyromonas gingivalis and Prevotella intermedia are suspected pathogens in adult periodontitis, whereas Prevotella nigrescens has been associated with health. Antimicrobial resistance among bacteria from this group has been reported in the past decade. This research aimed to evaluate and compare the susceptibility profile of 17 P. intermedia/P. nigrescens isolates recovered from patients with periodontitis and three reference strains to six antimicrobials, prescribed in dentistry in Brazil, and propolis (bee glue). The antimicrobial agents tested were tetracycline, penicillin, clindamycin, erythromycin, metronidazole, meropenem and six ethanolic extracts of propolis (EEPs) from Brazil. The reference strains P. gingivalis ATCC 33277 and P. intermedia ATCC 25611 were used for determination of minimum bactericidal concentration (MBC) and for time-kill assay to the EEPs. All of the strains were susceptible to penicillin, erythromycin, meropenem, metronidazole and 95% of them (n=19) to tetracycline. Thirty six percent (n=7) of the P. intermedia/P. nigrescens strains tested were resistant to clindamycin. As for propolis activity, all strains were susceptible and the minimum inhibitory concentration values ranged from 64 to 256 microg/mL. For the reference strains P. gingivalis ATCC 33277 and Prevotella intermedia ATCC 25611 the MBC was 256 microg/mL and death was observed within 3 h of incubation for P. gingivalis and within 6 h for P. intermedia. The action of propolis (bee glue) against suspected periodontal pathogens suggests that it may be of clinical value.