cDNA-AFLP analysis of seed germination in Arabidopsis thaliana identifies transposons and new genomic sequences

A cDNA-AFLP experiment was designed to identify and clone nucleotide sequences induced during seed germination in Arabidopsis thaliana. Sequences corresponding to known genes involved in processes important for germination, such as mitochondrial biogenesis, protein synthesis and cell cycle progression, were isolated. Other sequences correspond to Arabidopsis BAC clones in regions where genes have not been annotated. Notably, a number of the sequences cloned did not correspond to available sequences in the databases from the Arabidopsis genome, but instead present significant similarity with DNA from other organisms, for example fish species; among them, some may encode transposons. A number of the sequences isolated showed no significant similarity with any sequences in the public databases. Oligonucleotides derived from these new sequences were used to amplify genomic DNA of Arabidopsis. Expression analysis of representative sequences is presented. This work suggests that, during germination, there may be a massive transposon mobilization that may be useful in the annotation of new genome sequences and identification of regulatory mechanisms.     

Nitrate promotes biological oxidation of sulfide in wastewaters: experiment at plant-scale

Biogenic production of sulfide in wastewater treatment plants involves odors, toxicity and corrosion problems. The production of sulfide is a consequence of bacterial activity, mainly sulfate-reducing bacteria (SRB). To prevent this production, the efficiency of nitrate addition to wastewater was tested at plant-scale by dosing concentrated calcium nitrate (Nutriox) in the works inlet. Nutriox dosing resulted in a sharp decrease of sulfide, both in the air and in the bulk water, reaching maximum decreases of 98.7% and 94.7%, respectively. Quantitative molecular microbiology techniques indicated that the involved mechanism is the development of the nitrate-reducing, sulfide-oxidizing bacterium Thiomicrospira denitrificans instead of the direct inhibition of the SRB community. Denitrification rate in primary sedimentation tanks was enhanced by nitrate, being this almost completely consumed. No significant increase of inorganic nitrogen was found in the discharged effluent, thus reducing potential environmental hazards to receiving waters. This study demonstrates the effectiveness of nitrate addition in controlling sulfide generation at plant-scale, provides the mechanism and supports the environmental adequacy of this strategy.     

Production of penicillin acylase by a recombinant Escherichia coli using cheese whey as substrate and inducer

Cheese whey (CW) is the major subproduct from cheese manufacturing and it is considered as a waste pollutant since its high content of lactose. In this work a fermentation process for the production of penicillin acylase (PA) by a recombinant Escherichia coli and using CW as unique carbon source and inducer was developed. A design factorial 3(2) was used to evaluate the influence of independent variables (dissolved oxygen and CW concentration) on the ability of E. coli W3110/pPA102 to produce PA. Maximum specific PA activity of 781 U g(-1) was attained at 5 g L(-1) of CW and 3% dissolved oxygen. The results showed that CW can be used successfully as unique carbon source and inducer for the production of recombinant proteins using constructions driven by the lac promoter and this way reducing the discharges of that pollutant to the environment.     

The interface between medically assisted reproduction and genetics: technical, social, ethical and legal issues*

¹⁹ To whom correspondence should be addressed at: Department of Medical Genetics, University of Turku, Kiinamyllykatu 10, FIN-20520 Turku, Finland. E-mail: hkaaria{at}utu.fi^* Reprinted from European Journal of Human Genetics (2006) 1–58 with permission. The views expressed in this study do not necessarily reflect those of the European Commission (EC). The interface between assisted reproductive technologies (ART)and genetics comprises several sensitive and important issuesthat affect infertile couples, families with severe geneticdiseases, potential children, professionals in ART and genetics,health care, researchers and the society in general. Geneticcauses have a considerable involvement in infertility. Geneticconditions may also be transmitted to the offspring and hencecreate transgenerational infertility or other serious healthproblems. Several studies also suggest a slightly elevated riskof birth defects in children born following ART. PGD has becomewidely practiced throughout the world for various medical indications,but its limits are being debated. The attitudes towards ARTand PGD vary substantially within Europe. The purpose of thisarticle was to outline a framework for development of guidelinesto be issued jointly by European Society of Human Genetics (ESHG)and European Society of Human Reproduction and Embryology (ESHRE)for the interface between genetics and ART. Technical, social,ethical and legal issues of ART and genetics will be reviewed.     

Enzymatic polymerization of phenolic compounds using laccase and tyrosinase from Ustilago maydis

Flavonoids are a big group of polyphenols of low molecular weight with in vitro antioxidant properties. In this study, the laccase and tyrosinase from Ustilago maydis were partially characterized and their effect on the antioxidant activity of some phenolic compounds was investigated. Since enzymatic polymerization of the phenolic compounds was detected, the size of the aggregates was determined and related to their antioxidant activity. Morphology of the polymers was analyzed by atomic force microscopy. The results showed that the laccase- and tyrosinase-catalyzed polymerization of quercetin produced aggregates with relatively low molecular weight and higher antioxidant activity than the monomeric quercetin. In the case of kaempferol, the aggregates reached higher sizes in the first 2 h of reaction and their antioxidant activity was increased. In the last case, the aggregates adopted fractal-ordered shapes similar to coral in the case of the kaempferol-laccase system and to fern in the case of the kaempferol-tyrosinase system. The kaempferol and quercetin polymers at low concentration had strong scavenging effect on Reactive oxygen species (ROS) and inhibition of lipoperoxidation in human hepatic cell line WRL-68.     

How behavioral constraints may determine optimal sensory representations

The sensory-triggered activity of a neuron is typically characterized in terms of a tuning curve, which describes the neuron's average response as a function of a parameter that characterizes a physical stimulus. What determines the shapes of tuning curves in a neuronal population? Previous theoretical studies and related experiments suggest that many response characteristics of sensory neurons are optimal for encoding stimulus-related information. This notion, however, does not explain the two general types of tuning profiles that are commonly observed: unimodal and monotonic. Here I quantify the efficacy of a set of tuning curves according to the possible downstream motor responses that can be constructed from them. Curves that are optimal in this sense may have monotonic or nonmonotonic profiles, where the proportion of monotonic curves and the optimal tuning-curve width depend on the general properties of the target downstream functions. This dependence explains intriguing features of visual cells that are sensitive to binocular disparity and of neurons tuned to echo delay in bats. The numerical results suggest that optimal sensory tuning curves are shaped not only by stimulus statistics and signal-to-noise properties but also according to their impact on downstream neural circuits and, ultimately, on behavior.     

Highly diastereoselective synthesis of enantiopure naphthylaminoalcohols with analgesic properties

The diastereoselective synthesis via Grignard reaction of enantiopure analgesic naphthylaminoalcohols has been performed. The chiral racemic key intermediate 3-dimethylamino-2-methyl-1-(naphthalen-2-yl)propan-1-one and enantiomers were prepared and transformed into the desired compounds by addition of the organometallic reagent. The chemical characterization of all diastereoisomers was accomplished by 1H NMR and HPLC analyses and the absolute configuration assigned by CD spectroscopy. The in vitro and in vivo profile has also been evaluated.     

Nucleotide specificity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase Kinetics, fluorescence spectroscopy, and molecular simulation studies

Phosphoenolpyruvate carboxykinases, depending on the enzyme origin, preferentially use adenine or guanine nucleotides as substrates. In this work, analyses of the substrate specificity of the Saccharomyces cerevisiae ATP-dependent enzyme have been carried out. Kinetics studies gave relative values of k(cat)/K(m) for the nucleoside triphosphate complexes in the order ATP>GTP>ITP>UTP>CTP. For the nucleoside diphosphate complexes the order is ADP>GDP>IDP congruent withUDP>CDP. This shows that the enzyme has a strong preference for ADP (or ATP) over other nucleotides, being this preference about an order of magnitude higher for the diphosphorylated than for the triphosphorylated nucleosides. The calculated binding free energies (kcalmol(-1)) at 25 degrees C are 7.39 and 6.51 for ATP and ADP, respectively. These values decrease with the nucleotide structure in the same order than the kinetic specificity. The binding energy for any triphosphorylated nucleoside is more favourable than for the corresponding diphosphorylated compound, showing the relevance of the P(gamma) for nucleotide binding. Homology models of the adenine and guanine nucleotides in complex with the enzyme show that the base adopts a similar conformation in the diphosphorylated nucleosides while in the triphosphorylated nucleosides the sugar-base torsion angle is 61 degrees for ATP and -53 degrees for GTP. Differences are also noted in the distance between P(beta) and Mn2+ at site 1. This distance is almost the same in the ATP, GTP, and UTP complexes, however in the ADP, GDP and UDP complexes it is 2.9, 5.1, and 7A, respectively. Experimental data obtained with a Thr463Ala mutant enzyme agree with molecular simulation predictions. The results here presented are discussed in terms of the proposed interactions of the nucleotides with the protein.     

In Silico Vaccine Design Based on Molecular Simulations of Rhinovirus Chimeras Presenting HIV-1 gp41 Epitopes

A cluster of promising epitopes for the development of human immunodeficiency virus (HIV) vaccines is located in the membrane-proximal external region (MPER) of the gp41 subunit of the HIV envelope spike structure. The crystal structure of the peptide corresponding to the so-called ELDKWA epitope (HIV-1 HxB2 gp41 residues 662-668), in complex with the corresponding broadly neutralizing human monoclonal antibody 2F5, provides a target for structure-based vaccine design strategies aimed at finding macromolecular carriers that are able to present this MPER-derived epitope with optimal antigenic activity. To this end, a series of replica exchange molecular dynamics computer simulations was conducted to characterize the distributions of conformations of ELDKWA-based epitopes inserted into a rhinovirus carrier and to identify those with the highest fraction of conformations that are able to bind 2F5. The length, hydrophobic character, and precise site of insertion were found to be critical for achieving structural similarity to the target crystal structure. A construct with a high degree of complementarity to the corresponding determinant region of 2F5 was obtained. This construct was employed to build a high-resolution structural model of the complex between the 2F5 antibody and the chimeric human rhinovirus type 14:HIV-1 ELDKWA virus particle. Additional simulations, which were conducted to study the conformational propensities of the ELDKWA region in solution, confirm the hypothesis that the ELDKWA region of gp41 is highly flexible and capable of assuming helical conformations (as in the postfusion helical bundle structure) and β-turn conformations (as in the complex with the 2F5 antibody). These results also suggest that the ELDKWA epitope can be involved in intramolecular—and likely intermolecular—hydrophobic interactions. This tendency offers an explanation for the observation that mutations decreasing the hydrophobic character of the MPER in many cases result in conformational changes that increase the affinity of this region for the 2F5 antibody.