Comparison of pattern detection methods in microarray time series of the segmentation clock.

While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data (tens of thousands of profiles) associated with a certain level of noise remains a challenge. A microarray time series was recently generated to study the transcriptional program of the mouse segmentation clock, a biological oscillator associated with the periodic formation of the segments of the body axis. A method related to Fourier analysis, the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset, leading to the identification of a novel set of cyclic genes associated with the segmentation clock. Here, we applied to the same microarray time series dataset four distinct mathematical methods to identify significant patterns in gene expression profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron test and Stable persistence, and are based on different conceptual frameworks that are either hypothesis- or data-driven. Some of the methods, unlike Fourier transforms, are not dependent on the assumption of periodicity of the pattern of interest. Remarkably, these methods identified blindly the expression profiles of known cyclic genes as the most significant patterns in the dataset. Many candidate genes predicted by more than one approach appeared to be true positive cyclic genes and will be of particular interest for future research. In addition, these methods predicted novel candidate cyclic genes that were consistent with previous biological knowledge and experimental validation in mouse embryos. Our results demonstrate the utility of these novel pattern detection strategies, notably for detection of periodic profiles, and suggest that combining several distinct mathematical approaches to analyze microarray datasets is a valuable strategy for identifying genes that exhibit novel, interesting transcriptional patterns.

Basic components in the scienctific didactical training of the secondary school mathematics teachers

Secondary mathematics teacher training in Spain is currently the subject of a heated revision debate. The speed of social, cultural, scientific and economic changes have left a hundred years old teacher training model well behind. However, academical inertia and professional interests are impeding a real new training of the mathematics teacher as an autonomous mathematical educator. Teachers of Didactic of Mathematics and the Spanish Associations of mathematics teachers have recently been discussing the issue. Their conclusions are included here.

Decrease in diatom palatability contributes to bloom formation in the Western English Channel

The aim of this paper is to investigate the role of phytoplankton nutritional status in the formation of the spring bloom regularly observed at the station L4 in the Western English Channel. Using a modelling approach, we tested the hypothesis that the increase in light from winter to spring induces a decrease in diatom nutritional status (i.e., an increase in the C:N and C:P ratios), thereby reducing their palatability and allowing them to bloom. To this end, a formulation describing the Stoichiometric Modulation of Predation (SMP) has been implemented in a simplified version of the European Regional Seas Ecosystem Model (ERSEM). The model was coupled with the General Ocean Turbulence Model (GOTM), implemented at the station L4 and run for 10 years (2000-.2009). Simulated carbon to nutrient ratios in diatoms were analysed in relation to microzooplankton biomass, grazing and assimilation efficiency. The model reproduced in situ data evolutions and showed the importance of microzooplankton grazing in controlling the early onset of the bloom. Simulation results supported our hypothesis and provided a conceptual model explaining the formation of the diatom spring bloom in the investigated area. However, additional data describing the microzooplankton grazing impact and the variation of carbon to nutrient ratios inside phytoplanktonic cells are required to further validate the proposed mechanisms.

Exploration of the Kuiper Belt by High-Precision Photometric Stellar Occultations: First Results

We report here the first detection of hectometer-size objects by the method of serendipitous stellar occultation. This method consists of recording the diffraction shadow created when an object crosses the observer's line of sight and occults the disk of a background star. One of our detections is most consistent with an object between Saturn and Uranus. The two other diffraction patterns detected are caused by Kuiper Belt objects beyond 100 AU from the Sun and hence are the farthest known objects in the solar system. These detections show that the Kuiper Belt is much more extended than previously believed and that the outer part of the disk could be composed of smaller objects than the inner part. This gives critical clues to understanding the problem of the formation of the outer planets of the solar system.

Mutational analysis of the active centre of coronavirus 3C-like proteases.

Formation of the coronavirus replication-transcription complex involves the synthesis of large polyprotein precursors that are extensively processed by virus-encoded cysteine proteases. In this study, the coding sequence of the feline infectious peritonitis virus (FIPV) main protease, 3CL(pro), was determined. Comparative sequence analyses revealed that FIPV 3CL(pro) and other coronavirus main proteases are related most closely to the 3C-like proteases of potyviruses. The predicted active centre of the coronavirus enzymes has accepted unique replacements that were probed by extensive mutational analysis. The wild-type FIPV 3CL(pro) domain and 25 mutants were expressed in Escherichia coli and tested for proteolytic activity in a peptide-based assay. The data strongly suggest that, first, the FIPV 3CL(pro) catalytic system employs His(41) and Cys(144) as the principal catalytic residues. Second, the amino acids Tyr(160) and His(162), which are part of the conserved sequence signature Tyr(160)-Met(161)-His(162) and are believed to be involved in substrate recognition, were found to be indispensable for proteolytic activity. Third, replacements of Gly(83) and Asn(64), which were candidates to occupy the position spatially equivalent to that of the catalytic Asp residue of chymotrypsin-like proteases, resulted in proteolytically active proteins. Surprisingly, some of the Asn(64) mutants even exhibited strongly increased activities. Similar results were obtained for human coronavirus (HCoV) 3CL(pro) mutants in which the equivalent Asn residue (HCoV 3CL(pro) Asn(64)) was substituted. These data lead us to conclude that both the catalytic systems and substrate-binding pockets of coronavirus main proteases differ from those of other RNA virus 3C and 3C-like proteases.

Unusual voltammetry of the reduction of O-2 in [C(4)dmim][N(Tf)(2)] reveals a strong interaction of O-2(center dot-) with the [C(4)dmim](+) cation

Voltammetric studies of the reduction of oxygen in the room temperature ionic liquid [C(4)dmim][N(Tf)(2)] have revealed a significant positive shift in the back peak potential, relative to that expected for a simple electron transfer. This shift is thought to be due to the strong association of the electrogenerated superoxide anion with the solvent cation. In this work we quantitatively simulate the microdisc electrode voltammetry using a model based upon a one-electron reduction followed by a reversible chemical step, involving the formation of the [C(4)dmim](+)center dot center dot center dot O-2(center dot-) ion-pair, and in doing so we extract a set of parameters completely describing the system. We have simulated the voltammetry in the absence of a following chemical step and have shown that it is impossible to simultaneously fit both the forward and reverse peaks. To further support the parameters extracted from fitting the experimental voltammetry, we have used these parameters to independently simulate the double step chronoamperometric response and found excellent agreement. The parameters used to describe the association of the O-2(center dot-) with the [C(4)dmim](+) were k(f) = 1.4 x 10(3) s(-1) for the first-order rate constant and K-eq = 25 for the equilibrium constant.

Formation of Novel Di-Nuclear Lanthanide Luminescent Sm(III), Eu(III) and Tb(III) Triple Stranded Helicates from a C2 Symmetrically 2,6-Dicarboxylic Amide based 1,3-Xylene Ligand in CH3CN

The synthesis of the C2-symmetrical ligand 1 consisting of two naphthalene units connected to two pyridine-2,6-dicarboxamide moieties linked by a xylene spacer and the formation of LnIII-based (Ln1/4 Sm, Eu, Tb, and Lu) dimetallic helicates [Ln2 · 13] in MeCN by means of a metal-directed synthesis is described. By analyzing the metal-induced changes in the absorption and the fluorescence of 1, the formation of the helicates, and the presence of a second species [Ln2 · 12] was confirmed by nonlinear- regression analysis. While significant changes were observed in the photophysical properties of 1, the most dramatic changes were observed in the metal-centred lanthanide emissions, upon excitation of the naphthalene antennae. From the changes in the lanthanide emission, we were able to demonstrate that these helicates were formed in high yields (ca. 90% after the addition of 0.6 equiv. of LnIII), with high binding constants, which matched well with that determined from the changes in the absorption spectra. The formation of the LuIII helicate, [ Lu2 · 13 ] , was also investigated for comparison purposes, as we were unable to obtain accurate binding constants from the changes in the fluorescence emission upon formation of [Sm2 · 13], [Eu2 · 13], and [Tb2 · 13].

Investigating the Mechanism and Electrode Kinetics of the Oxygen vertical bar Superoxide (O-2 vertical bar O-2(center dot-)) Couple in Various Room-Temperature Ionic Liquids at Gold and Platinum Electrodes in the Temperature Range 298-318 K

The reduction of oxygen was studied over a range of temperatures (298-318 K) in n-hexyltriethylammonium bis(trifluoromethanesulfonyl)imide, [N-6,N-2,N-2,N-2][NTf2], and 1-butyl-2,3-methylimidazolium bis(trifluoromethanesulfonyl)imide, [C(4)dmim][NTf2] on both gold and platinum microdisk electrodes, and the mechanism and electrode kinetics of the reaction investigated. Three different models were used to simulate the CVs, based on a simple electron transfer ('E'), an electron transfer coupled with a reversible homogeneous chemical step ('ECrev') and an electron transfer followed by adsorption of the reduction product ('EC(ads)'), and where appropriate, best fit parameters deduced, including the heterogeneous rate constant, formal electrode potential, transfer coefficient, and homogeneous rate constants for the ECrev mechanism, and adsorption/desorption rate constants for the EC(ads) mechanism. It was concluded from the good simulation fits on gold that a simple E process operates for the reduction of oxygen in [N-6,N-2,N-2,N-2][NTf2], and an ECrev process for [C(4)dmim][NTf2], with the chemical step involving the reversible formation of the O-2(center dot-)center dot center dot center dot [C(4)dmim](+) ion-pair. The E mechanism was found to loosely describe the reduction of oxygen in [N-6,N-2,N-2,N-2][NTf2] on platinum as the simulation fits were reasonable although not perfect, especially for the reverse wave. The electrochemical kinetics are slower on Pt, and observed broadening of the oxidation peak is likely due to the adsorption of superoxide on the electrode surface in a process more complex than simple Langmuirian. In [C(4)dmim][NTf2] the O-2(center dot-) predominantly ion-pairs with the solvent rather than adsorbs on the surface, and an ECrev quantitatively describes the reduction of oxygen on Pt also.

The electrochemical reduction of the purines guanine and adenine at platinum electrodes in several room temperature ionic liquids

The reduction of guanine was studied by microelectrode voltammetry in the room temperature ionic liquids (RTILs) N-hexyltriethylammonium his (trifluoromethanesulfonyl) imide [N-6.2.2.2][N(Tf)(2)], 1-butyl-3-methylimidazolium hexafluorosphosphate [C(4)mim] [PF6], N-butyl-N-methyl-pyrrolidinium bis(trifluoromethanesulfonyl)imide [C(4)mpyrr][N(Tf)(2)], 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [C-4mim][N(TF)(2)], N-butyl-N-methyl-pyrrolidinium dicyanamide [C(4)mpyrr][N(NC)(2)] and tris(P-hexyl)-tetradecylphosphonium trifluorotris(pentafluoroethyl)phosphate [P-14,P-6,(6,6)][FAP] on a platinum microelectrode. In [N-6,N-2,N-2,N-2][NTf2] and [P-14,P-6,P-6.6][FAP], but not in the other ionic liquids studied, guanine reduction involves a one-electron, diffusion-controlled process at very negative potential to produce an unstable radical anion. which is thought to undergo a dimerization reaction, probably after proton abstraction from the cation of the ionic liquid. The rate of this subsequent reaction depends on the nature of the ionic liquid, and it is faster in the ionic liquid [P-14,P-6,P-6.6[FAP], in which the formation of the resulting dimer can be voltammetrically monitored at less negative potentials than required for the reduction of the parent molecule. Adenine showed similar behaviour to guanine but the pyrimidines thymine and cytosine did not; thymine was not reduced at potentials less negative than required for solvent (RTIL) decomposition while only a poorly defined wave was seen for cytosine. The possibility for proton abstraction from the cation in [N-6,N-2,N-2,N-2],[NTF2] and [P-14,P-6,P-6.6][FAP] is noted and this is thought to aid the electrochemical dimerization process. The resulting rapid reaction is thought to shift the reduction potentials for guanine and adenine to lower values than observed in RTILs where the scope for proton abstraction is not present. Such shifts are characteristic of so-called EC processes where reversible electron transfer is followed by a chemical reaction. (C) 2009 Elsevier B.V. All rights reserved.

Development of a high-throughput enzyme-linked immunosorbent assay for the routine detection of the carcinogen acrylamide in food, via rapid derivatisation pre-analysis

The spontaneous formation of the neurotoxic carcinogen acrylamide in a wide range of cooked foods has recently been discovered. These foods include bread and other bakery products, crisps, chips, breakfast cereals, and coffee. To date, the diminutive size of acrylamide (71.08Da) has prevented the development of screening immunoassays for this chemical. In this study, a polyclonal antibody capable of binding the carcinogen was produced by the synthesis of an immunogen comprising acrylamide derivatised with 3-mercaptobenzoic acid (3-MBA), and its conjugation to the carrier protein bovine thyroglobulin. Antiserum from the immunised rabbit was harvested and fully characterised. it displayed no binding affinity for acrylamide or 3-MBA but had a high affinity for 3-MBA-derivitised acrylamide. The antisera produced was utilised in the development of an ELISA based detection system for acrylamide. Spiked water samples were assayed for acrylamide content using a previously published extraction method validated for coffee, crispbread, potato, milk chocolate and potato crisp matrices. Extracted acrylamide was then subjected to a rapid 1-h derivatisation with 3-MBA, pre-analysis. The ELISA was shown to have a high specificity for acrylamide, with a limit of detection in water samples of 65.7 mu g kg(-1), i.e. potentially suitable for acrylamide detection in a wide range of food commodities. Future development of this assay will increase sensitivity further. This is the first report of an immunoassay capable of detecting the carcinogen, as its small size has necessitated current analytical detection via expensive, slower, physico-chemical techniques such as Gas or Liquid Chromatography coupled to Mass Spectrometry. (c) 2007 Elsevier B.V. All rights reserved.

Early Results of the 3mm Spectral Line Survey toward the L1157 B1 Shocked Region

We have conducted a sensitive 3mm observation toward the shocked region, Lynds 1157 B1, which is an interaction spot between a molecular outflow and its ambient gas. We have successfully detected the CH3CHO, HCOOCH3, and HCOOH lines, as well as the CH2DOH line. The abundances of these molecules relative to CH3OH are found to be lower than those in the low-mass star-forming core, IRAS 16293-2422. Since these molecules are thought to evaporate from grain mantles, the observational results mean that complex molecules are less abundant in grain mantles residing in the ambient cloud surrounding a prestellar/protostellar core. Instead, efficient formation of the complex organic species and deuterated species should take place in a prestellar/protostellar core. The present result verifies the importance of an unbiased line survey of this source.

Development of the nervous system in Dugesia tigrina during regeneration after fission and decapitation

In the present study of Dugesia tigrina the development of the nervous system is followed and compared during regeneration after fission and after decapitation. Immunocytochemistry was used, with antisera raised against the biogenic amine, 5-hydroxytryptamine (5-HT) and the two neuropeptides, neuropeptide F (NPF), and FMRF amide. The results indicate that two processes are involved in the formation of the new cerebral ganglion. First, new processes sprouting from the original main longitudinal nerve cords bend transversely, indicating the position of the developing horseshoe-shaped anterior cerebral commissure. Then new nerve cells in front of the commissure differentiate from neoblasts and their growth cones fasciculate with the fibres from the old main longitudinal nerve cords. In the cerebral ganglion, 5-HT-IR cells appear before NPF-IR cells, in contrast to the pharynx where NPF-IR cells differentiate before the 5-HT-IR cells. In the peripheral nervous system, NPF-IR fibres and cells appear at a very early stage and dominate the whole regeneration process. A role for the PNS in early pattern formation is suggested.

Identification, expression, and DNA sequence of the GDP-mannose biosynthesis genes encoded by the O7 rfb gene cluster of strain VW187 (Escherichia coli O7:K1)

The O7-specific lipopolysaccharide (LPS) in strains of Escherichia coli consists of a repeating unit made of galactose, mannose, rhamnose, 4-acetamido-2,6-dideoxyglucose, and N-acetylglucosamine. We have recently cloned and characterized genetically the O7-specific LPS biosynthesis region (rfbEcO7) of the E. coli O7:K1 strain VW187 (C. L. Marolda, J. Welsh, L. Dafoe, and M. A. Valvano, J. Bacteriol. 172:3590-3599, 1990). In this study, we localized the gnd gene encoding gluconate-6-phosphate dehydrogenase at one end of the rfbEcO7 gene cluster and sequenced that end of the cluster. Three open reading frames (ORF) encoding polypeptides of 275, 464, and 453 amino acids were identified upstream of gndEcO7, all transcribed toward the gnd gene. ORF275 had 45% similarity at the protein level with ORF16.5, which occupies a similar position in the Salmonella enterica LT2 rfb region, and presumably encodes a nucleotide sugar transferase. The polypeptides encoded by ORFs 464 and 453 were expressed under the control of the ptac promoter and visualized in Coomassie blue-stained sodium dodecyl sulfate-polyacrylamide gels and by maxicell analysis. ORF464 expressed GDP-mannose pyrophosphorylase and ORF453 encoded a phosphomannomutase, the enzymes for the biosynthesis pathway of GDP-mannose, one of the nucleotide sugar precursors for the formation of the O7 repeating unit. They were designated rfbMEcO7 and rfbKEcO7, respectively. The RfbMEcO7 polypeptide was homologous to the corresponding protein in S. enterica LT2, XanB of Xanthomonas campestris, and AlgA of Pseudomonas aeruginosa, all GDP-mannose pyrophosphorylases. RfbKEcO7 was very similar to CpsG of S. enterica LT2, an enzyme presumably involved in the biosynthesis of the capsular polysaccharide colanic acid, but quite different from the corresponding RfbK protein of S. enterica LT2.

Expression of the NF-κB inhibitor A20 is altered in the Cystic Fibrosis epithelium

Research Question: A20 is an LPS-inducible, cytoplasmic zinc finger protein, that inhibits TLR-activated NF-?B signalling by deubiquitinating TRAF6. A20 action is facilitated by complex formation with RNF11, Itch and TAX1BP1. This study investigates if the expression of A20 is altered in the chronically inflamed Cystic Fibrosis (CF) airway epithelium.

Methods: Nasal epithelial cells from CF patients (F508del homozygous), non-CF controls and immortalised epithelial cells (16HBE14o- and CFBE41o-) were stimulated with LPS. Cytoplasmic expression of A20 and expression of NF-?B subunits was analysed. Formation of the A20 ubiquitin editing complex was also investigated.

Results: In CFBE41o-, peak LPS-induced A20 expression was delayed compared with 16HBE14o- and fell significantly below basal levels 12-24 h after LPS stimulation. This was confirmed in primary CF airway cells. Additionally, a significant inverse relationship between A20 and p65 expression was observed. Inhibitor studies showed that A20 does not undergo proteasomal degradation in CFBE41o-. A20 interacted with TAX1BP1, RNF11 and TRAF6 in 16HBE14o- cells, but these interactions were not observed in CFBE41o-.

Conclusion: he expression of A20 is significantly altered in CF and important interactions with complex members and target proteins are lost, which may contribute to the state of chronic NF-?B-driven inflammation.

Proteomic analysis of the excretory-secretory proteins of the Trichinella spiralis L1 larva, a nematode parasite of skeletal muscle

Trichinella spiralis is an intracellular nematode parasite of mammalian skeletal muscle. Infection of the muscle cell leads to the formation of a host-parasite complex that results in profound alterations to the host cell and a re-alignment of muscle-specific gene expression. The role of parasite excretory-secretory (ES) proteins in mediating these effects is currently unknown, largely due to the difficulty in identifying and assigning function to individual proteins. In this study, a global proteomics approach was used to analyse the ES proteins from T. spiralis muscle larvae. Following 2-DE of ES proteins,MALDI-TOF-MS and LC-MS/MS were used to identify the peptide spots. Specific Trichinella EST databases were assembled and used to analyse the data. Despite the current absence of a Trichinella genome-sequencing project, 43 out of 52 protein spots analysed were identified and included the major secreted glycoproteins. Other novel proteins were identified from matches with sequences in the T. spiralis database. Our results demonstrate the value of proteomics as a tool for the identification of Trichinella ES proteins and in the study of the molecular mechanism underpinning the formation of the host-parasite complex during Trichinella infections.