Promoter recognition and activation by the global response regulator CbrB in Pseudomonas aeruginosa.

In Pseudomonas aeruginosa, the CbrA/CbrB two-component system is instrumental in the maintenance of the carbon-nitrogen balance and for growth on carbon sources that are energetically less favorable than the preferred dicarboxylate substrates. The CbrA/CbrB system drives the expression of the small RNA CrcZ, which antagonizes the repressing effects of the catabolite repression control protein Crc, an RNA-binding protein. Dicarboxylates appear to cause carbon catabolite repression by inhibiting the activity of the CbrA/CbrB system, resulting in reduced crcZ expression. Here we have identified a conserved palindromic nucleotide sequence that is present in upstream activating sequences (UASs) of promoters under positive control by CbrB and σ(54) RNA polymerase, especially in the UAS of the crcZ promoter. Evidence for recognition of this palindromic sequence by CbrB was obtained in vivo from mutational analysis of the crcZ promoter and in vitro from electrophoretic mobility shift assays using crcZ promoter fragments and purified CbrB protein truncated at the N terminus. Integration host factor (IHF) was required for crcZ expression. CbrB also activated the lipA (lipase) promoter, albeit less effectively, apparently by interacting with a similar but less conserved palindromic sequence in the UAS of lipA. As expected, succinate caused CbrB-dependent catabolite repression of the lipA promoter. Based on these results and previously published data, a consensus CbrB recognition sequence is proposed. This sequence has similarity to the consensus NtrC recognition sequence, which is relevant for nitrogen control.

Dynamics of turing patterns under spatiotemporal forcing

We study, both theoretically and experimentally, the dynamical response of Turing patterns to a spatiotemporal forcing in the form of a traveling-wave modulation of a control parameter. We show that from strictly spatial resonance, it is possible to induce new, generic dynamical behaviors, including temporally modulated traveling waves and localized traveling solitonlike solutions. The latter make contact with the soliton solutions of Coullet [Phys. Rev. Lett. 56, 724 (1986)] and generalize them. The stability diagram for the different propagating modes in the Lengyel-Epstein model is determined numerically. Direct observations of the predicted solutions in experiments carried out with light modulations in the photosensitive chlorine dioxide-iodine-malonic acid reaction are also reported.

Mechanisms and evolutionary patterns of mammalian and avian dosage compensation.

As a result of sex chromosome differentiation from ancestral autosomes, male mammalian cells only contain one X chromosome. It has long been hypothesized that X-linked gene expression levels have become doubled in males to restore the original transcriptional output, and that the resulting X overexpression in females then drove the evolution of X inactivation (XCI). However, this model has never been directly tested and patterns and mechanisms of dosage compensation across different mammals and birds generally remain little understood. Here we trace the evolution of dosage compensation using extensive transcriptome data from males and females representing all major mammalian lineages and birds. Our analyses suggest that the X has become globally upregulated in marsupials, whereas we do not detect a global upregulation of this chromosome in placental mammals. However, we find that a subset of autosomal genes interacting with X-linked genes have become downregulated in placentals upon the emergence of sex chromosomes. Thus, different driving forces may underlie the evolution of XCI and the highly efficient equilibration of X expression levels between the sexes observed for both of these lineages. In the egg-laying monotremes and birds, which have partially homologous sex chromosome systems, partial upregulation of the X (Z in birds) evolved but is largely restricted to the heterogametic sex, which provides an explanation for the partially sex-biased X (Z) expression and lack of global inactivation mechanisms in these lineages. Our findings suggest that dosage reductions imposed by sex chromosome differentiation events in amniotes were resolved in strikingly different ways.

Travelling-stripe forcing generates hexagonal patterns

We study the response of Turing stripe patterns to a simple spatiotemporal forcing. This forcing has the form of a traveling wave and is spatially resonant with the characteristic Turing wavelength. Experiments conducted with the photosensitive chlorine dioxide-iodine-malonic acid reaction reveal a striking symmetry-breaking phenomenon of the intrinsic striped patterns giving rise to hexagonal lattices for intermediate values of the forcing velocity. The phenomenon is understood in the framework of the corresponding amplitude equations, which unveils a complex scenario of dynamical behaviors.

Relevance of dynamic wetting in viscous fingering patterns

We demonstrate that wetting effects at moving contact lines have a strong impact in viscous fingering patterns. Experiments in a rotating Hele-Shaw (HS) cell, dry or prewetted, show consistent morphological differences. When the wetting fluid invades a dry region, contact angle dynamics yield a kinetic contribution to the interface pressure drop that scales with capillary number as Ca2¿3 but is significantly larger than the Park-Homsy kinetic correction. Numerical results are in very good agreement with experiments and show that standard HS equations work best for prewetted cells.

Surface tension and dynamics of fingering patterns

We study the minimal class of exact solutions of the Saffman-Taylor problem with zero surface tension, which contains the physical fixed points of the regularized (nonzero surface tension) problem. New fixed points are found and the basin of attraction of the Saffman-Taylor finger is determined within that class. Specific features of the physics of finger competition are identified and quantitatively defined, which are absent in the zero surface tension case. This has dramatic consequences for the long-time asymptotics, revealing a fundamental role of surface tension in the dynamics of the problem. A multifinger extension of microscopic solvability theory is proposed to elucidate the interplay between finger widths, screening and surface tension.

Covalent binding of C3b to monoclonal antibodies selectively up-regulates heavy chain epitope recognition by T cells.

Protein C3 of the complement system is known for its role in the nonspecific immune response. Covalent binding of C3b to antigen upon complement activation also plays a significant role in specific T cell immune response. C3b-antigen complexes can bind to complement receptors on the antigen-presenting cell, and the C3b antigen link (most often an ester link) remains fairly stable inside the cells. In this study, IgG1,kappa and IgG2a,kappa murine monoclonal antibodies (mAb) were used as antigens; covalent complexes between mAb and C3b were produced and purified in vitro from purified proteins; human B cell lines and T cell clones were raised from tumor patients who received mAb injections for cancer therapy or diagnosis. Recognition of epitopes of these mAb by T cell clones when the mAb were processed alone or bound to C3b was compared. IgG or IgG-C3b complexes presented by B cell lines were able to stimulate proliferation of kappa light chain-specific T cell clones at similar concentrations. In contrast, IgG-C3b complex recognition by heavy chain-specific T cell clones required 100-fold less IgG-C3b than uncomplexed IgG. As C3b was shown to be covalently bound only to the IgG heavy chains in the complexes, C3b chaperoning is restricted to only the IgG heavy chain and selectively influences intracellular steps of IgG heavy chain processing. This differential modulation of C3b suggests an early dissociation of IgG heavy and light chains in antigen-presenting cells.

Soil losses from typic cambisols and red latosol as related to three erosive rainfall patterns

Rainfall erosivity is one of the main factors related to water erosion in the tropics. This work focused on relating soil loss from a typic dystrophic Tb Haplic Cambisol (CXbd) and a typic dystrophic Red Latosol (LVdf) to different patterns of natural erosive rainfall. The experimental plots of approximately 26 m² (3 x 8.67 m) consisted of a CXbd area with a 0.15 m m-1 slope and a LVdf area with 0.12 m m-1 slope, both delimited by galvanized plates. Drainpipes were installed at the lower part of these plots to collect runoff, interconnected with a Geib or multislot divisor. To calculate erosivity (EI30), rainfall data, recorded continuously at a weather station in Lavras, were used. The data of erosive rainfall events were measured (10 mm precipitation intervals, accuracy 0.2 mm, 24 h period, 20 min intervals), characterized as rainfall events with more than 10 mm precipitation, maximum intensity > 24 mm h-1 within 15 min, or kinetic energy > 3.6 MJ, which were used in this study to calculate the rainfall erosivity parameter, were classified according to the moment of peak precipitation intensity in advanced, intermediate and delayed patterns. Among the 139 erosive rainfall events with CXbd soil loss, 60 % were attributed to the advanced pattern, with a loss of 415.9 Mg ha-1, and total losses of 776.0 Mg ha-1. As for the LVdf, of the 93 erosive rainfall events with soil loss, 58 % were listed in the advanced pattern, with 37.8 Mg ha-1 soil loss and 50.9 Mg ha-1 of total soil loss. The greatest soil losses were observed in the advanced rain pattern, especially for the CXbd. From the Cambisol, the soil loss per rainfall event was greatest for the advanced pattern, being influenced by the low soil permeability.

Early dyadic patterns of mother-infant interactions and outcomes of prematurity at 18 months.

OBJECTIVE: With the increased survival of very preterm infants, there is a growing concern for their developmental and socioemotional outcomes. The quality of the early mother-infant relationship has been noted as 1 of the factors that may exacerbate or soften the potentially adverse impact of preterm birth, particularly concerning the infant's later competencies and development. The first purpose of the study was to identify at 6 months of corrected age whether there were specific dyadic mother-infant patterns of interaction in preterm as compared with term mother-infant dyads. The second purpose was to examine the potential impact of these dyadic patterns on the infant's behavioral and developmental outcomes at 18 months of corrected age. METHODS: During a 12-month period (January-December 1998), all preterm infants who were <34 weeks of gestational age and hospitalized at the NICU of the Lausanne University Hospital were considered for inclusion in this longitudinal prospective follow-up study. Control healthy term infants were recruited during the same period from the maternity ward of our hospital. Mother-infant dyads with preterm infants (n = 47) and term infants (n = 25) were assessed at 6 months of corrected age during a mother-infant play interaction and coded according to the Care Index. This instrument evaluates the mother's interactional behavior according to 3 scales (sensitivity, control, and unresponsiveness) and the child's interactional behavior according to 4 scales (cooperation, compliance, difficult, and passivity). At 18 months, behavioral outcomes of the children were assessed on the basis of a semistructured interview of the mother, the Symptom Check List. The Symptom Check List explores 4 groups of behavioral symptoms: sleeping problems, eating problems, psychosomatic symptoms, and behavioral and emotional disorders. At the same age, developmental outcomes were evaluated using the Griffiths Developmental Scales. Five areas were evaluated: locomotor, personal-social, hearing and speech, eye-hand coordination, and performance. RESULTS: Among the possible dyadic patterns of interaction, 2 patterns emerge recurrently in mother-infant preterm dyads: a "cooperative pattern" with a sensitive mother and a cooperative-responsive infant (28%) and a "controlling pattern" with a controlling mother and a compulsive-compliant infant (28%). The remaining 44% form a heterogeneous group that gathers all of the other preterm dyads and is composed of 1 sensitive mother-passive infant; 10 controlling mothers with a cooperative, difficult, or passive infant; and 10 unresponsive mothers with a cooperative, difficult, or passive infant. Among the term control subjects, 68% of the dyads are categorized as cooperative pattern dyads, 12% as controlling pattern dyads, and the 20% remaining as heterogeneous dyads. At 18 months, preterm infants of cooperative pattern dyads have similar outcomes as the term control infants. Preterm infants of controlling pattern dyads have significantly fewer positive outcomes as compared with preterm infants of cooperative pattern dyads, as well as compared with term control infants. They display significantly more behavioral symptoms than term infants, including more eating problems than term infants as well as infants from cooperative preterm dyads. Infants of the controlling preterm dyads do not differ significantly for the total development quotient but have worse personal-social development than term infants and worse hearing-speech development than infants from cooperative preterm dyads. The preterm infants of the heterogeneous group have outcomes that can be considered as intermediate with no significant differences compared with preterm infants from the cooperative pattern or the controlling pattern dyads. CONCLUSION: Among mother-preterm infant dyads, we identified 2 specific patterns of interaction that could play either a protective (cooperative pattern) or a risk-precipitating (controlling pattern) role on developmental and behavioral outcome, independent of perinatal risk factors and of the family's socioeconomic background. The controlling pattern is much more prevalent among preterm than term dyads and is related to a less favorable infant outcome. However, the cooperative pattern still represents almost 30% of the preterm dyads, with infants' outcome comparable to the ones of term infants. These results point out the impact of the quality of mother-infant relationship on the infant's outcome. The most important clinical implication should be to support a healthy parent-infant relationship already in the NICU but also in the first months of the infant's life. Early individualized family-based interventions during neonatal hospitalization and transition to home have been shown to reduce maternal stress and depression and increase maternal self-esteem and to improve positive early parent-preterm infant interactions.

New multiple matched filter: design and experimental realization

A method of making a multiple matched filter which allows the recognition of different characters in successive planes in simple conditions is proposed. The generation of the filter is based on recording on the same plate the Fourier transforms of the different patterns to be recognized, each of which is affected by different spherical phase factors because the patterns have been placed at different distances from the lens. This is proved by means of experiments with a triple filter which allows satisfactory recognition of three characters.

Application of fuzzy-rule-based postprocessing to correlation methods in pattern recognition

One of the most important problems in optical pattern recognition by correlation is the appearance of sidelobes in the correlation plane, which causes false alarms. We present a method that eliminate sidelobes of up to a given height if certain conditions are satisfied. The method can be applied to any generalized synthetic discriminant function filter and is capable of rejecting lateral peaks that are even higher than the central correlation. Satisfactory results were obtained in both computer simulations and optical implementation.

Correlation postprocessing-based method for the detection of de focused images

We present a method to detect patterns in defocused scenes by means of a joint transform correlator. We describe analytically the correlation plane, and we also introduce an original procedure to recognize the target by postprocessing the correlation plane. The performance of the methodology when the defocused images are corrupted by additive noise is also considered.

False recognition following frontal lobe damage: The role of encoding factors

This paper reports a series of experiments on patient JB, a man with memory difficulties following damage to the left frontal lobe. The primary characteristic of JB's recognition memory impairment is a high level of false recognition together with a normal hit rate. The hypothesis that JB's false recognition reflects an over-reliance on familiarity is considered, but discounted on the basis that the false alarm rate is not affected by increasing the similarity between distracters and targets, and remains high when nonword stimuli are used. It is suggested, instead, that JB relies on a poorly focused memory description, which lacks item-specific detail but contains more general, low-level properties of the target items-these properties being held by many distracter items as well. This deficit is considered to arise because of damage to frontally mediated control processes involved in the selection of elements for memory encoding. An encoding deficit is supported by the fact that JB's false recognition is significantly reduced by orienting instructions, and is eliminated when his remote memory is subjected to recognition testing. In contrast, it is shown that manipulations at the level of retrieval (e.g. restricting the number of "old" responses) have little effect on his false recognition.