Nucleic acid-binding properties of the RRM-containing protein RDM1.

RDM1 (RAD52 Motif 1) is a vertebrate protein involved in the cellular response to the anti-cancer drug cisplatin. In addition to an RNA recognition motif, RDM1 contains a small amino acid motif, named RD motif, which it shares with the recombination and repair protein, RAD52. RDM1 binds to single- and double-stranded DNA, and recognizes DNA distortions induced by cisplatin adducts in vitro. Here, we have performed an in-depth analysis of the nucleic acid-binding properties of RDM1 using gel-shift assays and electron microscopy. We show that RDM1 possesses acidic pH-dependent DNA-binding activity and that it binds RNA as well as DNA, and we present evidence from competition gel-shift experiments that RDM1 may be capable of discrimination between the two nucleic acids. Based on reported studies of RAD52, we have generated an RDM1 variant mutated in its RD motif. We find that the L119GF --> AAA mutation affects the mode of RDM1 binding to single-stranded DNA.

In vivo measurement of tissue oxygenation by time-resolved luminescence spectroscopy: advantageous properties of dichlorotris(1, 10-phenanthroline)-ruthenium(II) hydrate.

Measuring tissue oxygenation in vivo is of interest in fundamental biological as well as medical applications. One minimally invasive approach to assess the oxygen partial pressure in tissue (pO2) is to measure the oxygen-dependent luminescence lifetime of molecular probes. The relation between tissue pO2 and the probes' luminescence lifetime is governed by the Stern-Volmer equation. Unfortunately, virtually all oxygen-sensitive probes based on this principle induce some degree of phototoxicity. For that reason, we studied the oxygen sensitivity and phototoxicity of dichlorotris(1, 10-phenanthroline)-ruthenium(II) hydrate [Ru(Phen)] using a dedicated optical fiber-based, time-resolved spectrometer in the chicken embryo chorioallantoic membrane. We demonstrated that, after intravenous injection, Ru(Phen)'s luminescence lifetime presents an easily detectable pO2 dependence at a low drug dose (1 mg∕kg) and low fluence (120 mJ∕cm2 at 470 nm). The phototoxic threshold was found to be at 10 J∕cm2 with the same wavelength and drug dose, i.e., about two orders of magnitude larger than the fluence necessary to perform a pO2 measurement. Finally, an illustrative application of this pO2 measurement approach in a hypoxic tumor environment is presented.

Direct Determination of mechanical properties in shallow formations by (ultra) sonic methods

For several decades mechanical properties of shallow formations (soil) obtained by sonic to ultrasonic wave testing were reported to be greater than those based on mechanical tests. The present article relying on a statistical analysis of more than 300 tests shows that elastic moduli of the soil can indeed be obtained from (ultra)sonic tests and that they are identical to those resulting from mechanical tests.

Determination of chemical composition and its relationship with optical properties of Ti-N and Ti-V-N sputtered thin films

In the investigation of thin films of transition metal nitrides, an essential role is played by the accurate determination of their chemical composition. Actually the chemical composition depends on the deposition parameters and influences the optical properties. These relations are illustrated in thin films of TiNx and (Ti1-yVy)N-x deposited by reactive magnetron sputtering from composite targets of the elements. By variation of the nitrogen partial pressure and the target composition, different samples have been obtained. The chemical composition has been measured by electron probe microanalysis at low irradiation voltages. The optical properties are evaluated by ex-situ ellipsometry. Using the screened Drude model, they are correlated with the differences in composition. Adding vanadium or nitrogen in Ti-N is shown to have the same effect on the optical properties.

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.

DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA-DNA crowding DNA molecules with reduced supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes.

Immunological and protective properties of novel malaria blood stage peptide antigens

ABSTRACT Malaria is a major worldwide public health problem, with transmission occurring throughout Africa, Asia, Oceania and Latin America. Over two billion people live in malarious areas of the world and it is estimated that 300-500 million cases and 1.5-2.7 million deaths occur annually. The increase in multi-drug resistant parasites and insecticide-resistant vectors has made the development of malaria vaccine a public health priority. The published genome offers tremendous opportunity for the identification of new antigens that can befast-tracked for vaccine development. We identified potential protein antigens present on the surface of asexual malaria blood stages through bioinformatics and published transcriptome and proteorné analysis. Amongst the proteins identified, we selected those that contain predicted a-helical coiled-coil regions, which are generally short and structurally stable as isolated fragments. Peptides were synthesized and used to immunize mice. Most peptides tested were immunogenic as demonstrated in ELISA assays, and induced antibodies of varying titres. In immunofluorescence assays, anti-sera from immunized mice reacted with native proteins expressed at different intraerythrocytic developmental stages of the parasite's cycle. In parallel in vitro ADCI functional studies, human antibodies affinity purified on some of these peptides inhibited parasite growth in association with monocytes in magnitudes similar to that seen in semiimmune African adults. Siudies using human immune sera taken from different malaria endemic regions, demonstrated that majority of peptides were recognized at high prevalence. 73 peptides were next tested in longitudinal studies in two cohorts separated in space and time in coastal Kenya. In these longitudinal analyses, antibody responses to peptides were sequentially examined in two cohorts of children at risk of clinical malaria in order to characterize the level of peptide recognition by age, and the role of anti-peptide antibodies in protection from clinical malaria. Ten peptides were associated ?with a significantly reduced odds ratio for an episode of clinical malaria in the first cohort of children and two of these peptides (LR146 and ÁS202.11) were associated with a significantly reduced odds ratio in both cohorts. This study has identified proteins PFB0145c and MAL6P1.37 among others as likely targets of protective antibodies. Our findings support further studies to systematically assess immunogenicity of peptides of interest in order to establish clear criteria for optimal design of potential vaccine constructs to be tested in clinical trials. RESUME La malaria est un problème de santé publique mondial principalement en Afrique, en Asie, en Océanie et en Amérique latine. Plus de 2 milliards de personnes vivent dans des régions endémiques et le nombre de cas par année est estimé entre 300 et 500 millions. 1.5 à 2.7 millions de décès surviennent annuellement dans ces zones. L'augmentation de la résistance aux médicaments et aux insecticides fait du développement d'un vaccin une priorité. Le séquençage complet du génome du parasite offre l'opportunité d'identifier de nouveaux antigènes qui peuvent rapidement mener au développement d'un vaccin. Des protéines antigéniques potentielles présentes à la surface des globules rouges infectés ont été identifiées par bioinformatique et par l'analyse du protéome et du transcriptome. Nous avons sélectionné, parmi ces protéines, celles contenant des motifs dits "a helical coiled-coil" qui sont généralement courts et structurellement stables. Ces régions ont été obtenues par synthèse peptidique et utilisées pour immuniser des souris. La plupart des peptides testés sont immunogéniques et induisent un titre variable d'anticorps déterminé par ELISA. Les résultats de tests d'immunofluorescence indiquent que les sera produits chez la souris reconnaissent les protéines natives exprimées aux différents stades de développement du parasite. En parallèle, des études d'ADCI in vitro montrent qué des anticorps humains purifiés à partir de ces peptides associés à des monocytes inhibent la croissance du parasite aussi bien que celle observée chez des adultes africains protégés. Des études d'antigénicité utilisant des sera de personnes protégées de différents âges vivant dans des régions endémiques montrent que la majorité des peptides sont reconnus avec une haute prévalence. 73 peptides ont été testés dans une étude longitudinale avec 2 cohortes de la côte du Kenya. Ces 2 groupes viennent de zones bien distinctes et les prélèvements n'ont pas été effectués pendant la même période. Dans cette étude, la réponse anticorps contre les peptides synthétiques a été testée dans les 2 cohortes d'enfants à risque de développer un épisode de malaria afin de caractériser le niveau de reconnaissance des peptides en fonction de l'âge et de déterminer le rôle des anticorps anti-peptides dans la protection contre la malaria. Parmi ces peptides, 10 sont associés à une réduction significative des risques de développer un épisode de malaria dans la première cohorte alors qu'un seul (LR146 et AS202.11) l'est dans les 2 cohortes. Cette étude a identifié, parmi d'autres, les protéines PFB0145c et MAL6P1.37 comme pouvant être la cible d'anticorps. Ces résultats sont en faveur de futures études qui évalueraient systématiquement l'immunogénicité des peptides d'intérêt dans le but d'établir des critères de sélection clairs pour le développement d'un vaccin. Résumé pour un large public La malaria est un problème de santé publique mondial principalement en Afrique, en Asie, en Océanie et en Amérique latine. Plus de 2 milliards de personnes vivent dans des régions endémiques et le nombre de cas par année est estimé entre 300 et 500 millions. 1.5 à 2.7 millions de décès surviennent annuellement dans ces zones. La résistance aux médicaments et aux insecticides augmente de plus en plus d'où la nécessité de développer un vaccin. Le séquençage complet du génome (ensemble des gènes) de P. falciparum a conduit au développement de nouvelles .études à large échelle dans le domaine des protéines du parasite (protéome) ; dans l'utilisation d'algorithmes, de techniques informatiques et statistiques pour l'analyse de données biologiques (bioinformatique) et dans les technologies de transcription et de profiles d'expression (transcriptome). Nous avons identifié, en utilisant les outils ci-dessus, des nouvelles protéines antigéniques qui sont présentes au stade sanguin de la malaria. Nous avons sélectionné, parmi ces protéines, celles contenant un motif dit "a-helical coiled-coil" qui sont des domaines impliqués dans un large éventail de fonctions biologiques. Des peptides représentant ces régions structurellement stables ont été synthétisés et utilisés pour immuniser des souris. La plupart des peptides testés sont immunogéniques et induisent un titre variable d'anticorps déterminé par ELISA. Les résultats de tests d'immunofluorescence indiquent que plusieurs sera de souris immunisées avec ces peptides reconnaissent les protéines natives exprimées à la surface des globules rouges infectés. En parallèle, des études d'ADCI in vitro montrent que des anticorps humains purifiés à partir de ces peptides en présence de monocytes inhibent la croissance du parasite de manière similaire à celle observée chez des adultes africains protégés. Des études d'antigénicité utilisant des sera de personnes immunes de différents âges (adultes et enfants) vivant dans des régions endémiques montrent que la majorité des peptides sont reconnus avec une haute prévalence. 73 peptides ont été testés dans des études épidémiologiques dans 2 villages côtiers du Kenya Ces 2 groupes vivent dans des zones bien distinctes et les prélèvements n'ont pas été effectués pendant la même période. Dans ces études, la réponse anticorps dirigée contre les peptides synthétiques a été testée en utilisant 467 échantillons sanguins d'enfants à risque de développer un épisode de malaria afin de caractériser le niveau de reconnaissance des peptides en fonction de l'âge et de déterminer le rôle des anticorps anti-peptides dans la protection contre la malaria cérébrale. Parmi ces peptides, 10 sont associés à une protection contre un épisode de malaria dans le premier village alors qu'un seul l'est dans les 2 villages. Ces résultats sont en faveur de futures études qui évalueraient systématiquement l'immunogénicité des peptides intéressants dans le but d'établir des critères de sélection clairs pour le développement d'un vaccin.

The composition of mineral waters sourced from Europe and North America in respect to bone health: composition of mineral water optimal for bone.

The consumption of mineral waters is increasing in industrialised countries. High intakes of Ca and other alkalising cations as well as a low acid intake are beneficial to bone. We examined which components of mineral waters are conditioning their Ca content and their alkalinising power, in order to define the optimal profile. European mineral waters were randomly selected on the Internet: 100 waters with less than 200 mg Ca/l (9.98 mEq/l) and fifty with more than 200 mg/l, all with complete data for SO4, P, Cl, Na, K, Mg and Ca, and most also for HCO3. For comparison, forty North American mineral waters were randomly chosen. The potential renal acid load (PRAL) was calculated for each mineral water. North American waters did not reveal significant results because of their low mineralisation. We performed correlations between all eight components in order to explore the properties of the mineral waters. In the European waters, twenty-six out of twenty-eight correlations showed a P value of <or= 0.01. In waters with PRAL >0 (acidifying waters), PRAL was positively correlated with SO4, Ca, K and Mg (P < 0.001). In those with PRAL < 0 (alkalinising waters), PRAL was negatively correlated with HCO3, Na, Mg, Ca, K, Cl and SO4 (P < 0.001). SO4 and HCO3 were not found together in high quantities in the same water for geochemical reasons. A high Ca content is associated with either a high SO4 or a high HCO3 content. SO4 theoretically increases Ca excretion, while HCO3 and low PRAL values are associated with positive effects on bone. Therefore, the best waters for bone health are rich in both HCO3 and Ca, and by consequence low in SO4.

Arabidopsis NPH1: a flavoprotein with the properties of a photoreceptor for phototropism.

The NPH1 gene of Arabidopsis thaliana encodes a 120-kilodalton serine-threonine protein kinase hypothesized to function as a photoreceptor for phototropism. When expressed in insect cells, the NPH1 protein is phosphorylated in response to blue light irradiation. The biochemical and photochemical properties of the photosensitive protein reflect those of the native protein in microsomal membranes. Recombinant NPH1 noncovalently binds flavin mononucleotide, a likely chromophore for light-dependent autophosphorylation. The fluorescence excitation spectrum of the recombinant protein is similar to the action spectrum for phototropism, consistent with the conclusion that NPH1 is an autophosphorylating flavoprotein photoreceptor mediating phototropic responses in higher plants.

Validation of an adapted falls efficacy scale in older rehabilitation patients.

OBJECTIVE: To determine the psychometric properties of an adapted version of the Falls Efficacy Scale (FES) in older rehabilitation patients. DESIGN: Cross-sectional survey. SETTING: Postacute rehabilitation facility in Switzerland. PARTICIPANTS: Seventy elderly persons aged 65 years and older receiving postacute, inpatient rehabilitation. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: FES questions asked about subject's confidence (range, 0 [none]-10 [full]) in performing 12 activities of daily living (ADLs) without falling. Construct validity was assessed using correlation with measures of physical (basic ADLs [BADLs]), cognitive (Mini-Mental State Examination [MMSE]), affective (15-item Geriatric Depression Scale [GDS]), and mobility (Performance Oriented Mobility Assessment [POMA]) performance. Predictive validity was assessed using the length of rehabilitation stay as the outcome. To determine test-retest reliability, FES administration was repeated in a random subsample (n=20) within 72 hours. RESULTS: FES scores ranged from 10 to 120 (mean, 88.7+/-26.5). Internal consistency was optimal (Cronbach alpha=.90), and item-to-total correlations were all significant, ranging from .56 (toilet use) to .82 (reaching into closets). Test-retest reliability was high (intraclass correlation coefficient, .97; 95% confidence interval, .95-.99; P<.001). Subjects reporting a fall in the previous year had lower FES scores than nonfallers (85.0+/-25.2 vs 94.4+/-27.9, P=.054). The FES correlated with POMA (Spearman rho=.40, P<.001), MMSE (rho=.37, P=.001), BADL (rho=.43, P<.001), and GDS (rho=-.53, P<.001) scores. These relationships remained significant in multivariable analysis for BADLs and GDS, confirming FES construct validity. There was a significant inverse relationship between FES score and the length of rehabilitation stay, independent of sociodemographic, functional, cognitive, and fall status. CONCLUSIONS: This adapted FES is reliable and valid in older patients undergoing postacute rehabilitation. The independent association between poor falls efficacy and increased length of stay has not been previously described and needs further investigations.

Specific mutations in the estrogen receptor change the properties of antiestrogens to full agonists.

The estrogen receptor (ER) stimulates transcription of target genes by means of its two transcriptional activation domains, AF-1 in the N-terminal part of the receptor and AF-2 in its ligand-binding domain. AF-2 activity is dependent upon a putative amphipathic alpha-helix between residues 538 and 552 in the mouse ER. Point mutagenesis of conserved hydrophobic residues within this region reduces estrogen-dependent transcriptional activation without affecting hormone and DNA binding significantly. Here we show that these mutations dramatically alter the pharmacology of estrogen antagonists. Both tamoxifen and ICI 164,384 behave as strong agonists in HeLa cells expressing the ER mutants. In contrast to the wild-type ER, the mutant receptors maintain nuclear localization and DNA-binding activity after ICI 164,384 treatment. Structural alterations in AF-2 caused by gene mutations such as those described herein or by estrogen-independent signaling pathways may account for the insensitivity of some breast cancers to tamoxifen treatment.

Quantifying network properties in multi-electrode recordings: spatiotemporal characterization and inter-trial variation of evoked gamma oscillations in mouse somatosensory cortex in vitro.

Linking the structural connectivity of brain circuits to their cooperative dynamics and emergent functions is a central aim of neuroscience research. Graph theory has recently been applied to study the structure-function relationship of networks, where dynamical similarity of different nodes has been turned into a "static" functional connection. However, the capability of the brain to adapt, learn and process external stimuli requires a constant dynamical functional rewiring between circuitries and cell assemblies. Hence, we must capture the changes of network functional connectivity over time. Multi-electrode array data present a unique challenge within this framework. We study the dynamics of gamma oscillations in acute slices of the somatosensory cortex from juvenile mice recorded by planar multi-electrode arrays. Bursts of gamma oscillatory activity lasting a few hundred milliseconds could be initiated only by brief trains of electrical stimulations applied at the deepest cortical layers and simultaneously delivered at multiple locations. Local field potentials were used to study the spatio-temporal properties and the instantaneous synchronization profile of the gamma oscillatory activity, combined with current source density (CSD) analysis. Pair-wise differences in the oscillation phase were used to determine the presence of instantaneous synchronization between the different sites of the circuitry during the oscillatory period. Despite variation in the duration of the oscillatory response over successive trials, they showed a constant average power, suggesting that the rate of expenditure of energy during the gamma bursts is consistent across repeated stimulations. Within each gamma burst, the functional connectivity map reflected the columnar organization of the neocortex. Over successive trials, an apparently random rearrangement of the functional connectivity was observed, with a more stable columnar than horizontal organization. This work reveals new features of evoked gamma oscillations in developing cortex.

Arterial properties in relation to genetic variations in the adducin subunits in a white population.

BACKGROUND: Adducin is a membrane skeleton protein, which consists of either alpha- and beta- or alpha- and gamma-subunits. We investigated whether arterial characteristics might be related to the genes encoding ADD1 (Gly460Trp-rs4961), ADD2 (C1797T-rs4984), and ADD3 (IVS11+386A>G-rs3731566). METHODS: We randomly recruited 1,126 Flemish subjects (mean age, 43.8 years; 50.3% women). Using a wall-tracking ultrasound system, we measured the properties of the carotid, femoral, and brachial arteries. We studied multivariate-adjusted phenotype-genotype associations, using a population- and family-based approach. RESULTS: In single-gene analyses, brachial diameter was 0.15 mm (P = 0.0022) larger, and brachial distensibility and cross-sectional compliance were 1.55 x 10(-3)/kPa (P = 0.013) and 0.017 mm(2)/kPa (P = 0.0029) lower in ADD3 AA than ADD3 GG homozygotes with an additive effect of the G allele. In multiple-gene analyses, the association of brachial diameter and distensibility with the ADD3 G allele occurred only in ADD1 GlyGly homozygotes. Otherwise, the associations between the arterial phenotypes in the three vascular beds and the ADD1 or ADD2 polymorphisms were not significant. In family-based analyses, the multivariate-adjusted heritability was 0.52, 0.38, and 0.30 for brachial diameter, distensibility, and cross-sectional compliance, respectively (P < 0.001). There was no evidence for population stratification (0.07 < or = P < or = 0.96). Transmission of the mutated ADD3 G allele was associated with smaller brachial diameter in 342 informative offspring (-0.12 +/- 0.04 mm; P = 0.0085) and in 209 offspring, who were ADD1 GlyGly homozygotes (-0.14 +/- 0.06 mm; P = 0.018). CONCLUSIONS: In ADD1 GlyGly homozygotes, the properties of the brachial artery are related to the ADD3 (A386G) polymorphism, but the underlying mechanism needs further clarification.