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Structure and function of human fibrinogen inferred from dysfibrinogens.

Fibrinogen is a 340-kDa plasma protein that is composed of two identical molecular halves, each consisting of three non-identical subunit polypeptides designated as A alpha, B beta- and gamma-chains held together by multiple disulfide bonds. Fibrinogen has a trinodular structure, i.e., one central E domain comprizing the amino-terminal regions of paired individual three polypeptides, and two identical outer D domains. These three nodules are linked by two coiled-coil regions [1,2]. After activation with thrombin, a tripeptide segment consisting of Gly-Pro-Arg is exposed at the amino-terminus of each alpha-chain residing at the center of the E domain and combines with its complementary binding site, called the 'a' site, residing in the carboxyl-terminal region of the gamma-chain in the outer D domain of another molecule. By crystallographic analysis [3], the alpha-amino group of alpha Gly-1 is shown to be juxtaposed between the carboxyl group of gamma Asp-364 and the carboxyamide of Gln-329 in the 'a' site. Half molecule-staggered, double-stranded fibrin protofibrils are thus formed [4,5]. Upon abutment of two adjacent D domains on the same strand, D-D self association takes place involving Arg-275, Tyr-280 and Ser-300 of the gamma-chain on the surface of the abutting two D domains [3]. Thereafter, carboxyl-terminal regions of the fibrin a-chains are thought to be untethered and interact with those of other protofibrils leading to the formation of thick fibrin bundles and interwoven networks after appropriate branching [6-9]. Although many enigmas still remain regarding the mechanisms of these molecular interactions, fibrin assembly proceeds in a highly ordered fashion. In my talk, I would like to discuss these molecular interactions of fibrinogen and fibrin based on the up-date data provided by analyses of normal as well as hereditary dysfibrinogens, particularly in the latter by introducing representative molecules at each step of fibrin clot formation.

Binding Sites↗

A gateway-compatible yeast one-hybrid system.

Since the advent of microarrays, vast amounts of gene expression data have been generated. However, these microarray data fail to reveal the transcription regulatory mechanisms that underlie differential gene expression, because the identity of the responsible transcription factors (TFs) often cannot be directly inferred from such data sets. Regulatory TFs activate or repress transcription of their target genes by binding to cis-regulatory elements that are frequently located in a gene's promoter. To understand the mechanisms underlying differential gene expression, it is necessary to identify physical interactions between regulatory TFs and their target genes. We developed a Gateway-compatible yeast one-hybrid (Y1H) system that enables the rapid, large-scale identification of protein-DNA interactions using both small (i.e., DNA elements of interest) and large (i.e., gene promoters) DNA fragments. We used four well-characterized Caenorhabditis elegans promoters as DNA baits to test the functionality of this Y1H system. We could detect approximately 40% of previously reported TF-promoter interactions. By performing screens using two complementary libraries, we found novel potentially interacting TFs for each promoter. We recapitulated several of the Y1H-based protein-DNA interactions using luciferase reporter assays in mammalian cells. Taken together, the Gateway-compatible Y1H system will allow the high-throughput identification of protein-DNA interactions and may be a valuable tool to decipher transcription regulatory networks.

Animals↗

Perturbation of red blood cell membrane rigidity by extracellular ligands.

It is known that binding of extracellular antibodies against the major sialoglycoprotein, glycophorin A, reduced the deformability of the red blood cell membrane. This has been taken to result from new or altered interactions between the glycophorin A and the membrane skeleton. We have shown by means of the micropipette aspiration technique that antibodies against the preponderant transmembrane protein, band 3, induce similar effects. A definite but much smaller reduction in elasticity of the membrane is engendered by univalent Fab fragments of the anti-band 3 antibodies. By examining cells genetically devoid of glycophorin A or containing a variant of this constituent, truncated at the inner membrane surface, we have shown that the anti-band 3 antibodies do not act through the band 3-associated glycophorin A. We examined the effect of anti-glycophorin A antibodies on homozygous Wr(a+b-) cells, in which an amino acid replacement in band 3 annihilates the Wright b (Wrb) epitope (comprising sequence elements of glycophorin A and band 3) and thus, by implication disrupts or perturbs the band 3-glycophorin A interaction; these cells show a much smaller response to an anti-glycophorin A antibody than do normal controls. We infer that in this case anti-glycophorin A antibodies exert their rigidifying effect through the associated band 3. Another anti-glycophorin A antibody, directed against an epitope remote from the membrane surface, however, increases the rigidity of both Wr(a+b-) and normal cells. This implies that not all antibodies act in the same manner in modifying the membrane mechanical properties. The effect exerted by anti-band 3 antibodies appears not to be transmitted through the band 3-ankyrin-spectrin pathway because the rigidifying effect of the intact antibody persists at alkaline pH, at which there is evidence that the ankyrin-band 3 link is largely dissociated. The large difference between the effects of saturating concentrations of the divalent and univalent anti-band 3 antibodies implies the existence of an overriding effect on rigidity, resulting from the bifunctionality of the intact antigen. Freeze-fracture electron microscopy shows that the anti-band 3 promotes the formation of small clusters of intra-membrane proteins. Extracellular ligands may in general act by promoting strong or transient interactions between integral membrane proteins, thereby impeding local distortion of the membrane skeletal network in response to shear.

Anion Exchange Protein 1, Erythrocyte↗

[Asthma attacks in general practice--epidemiologic markers and seasonal patterns in longitudinal observation].

The continuous registration of asthmatic attacks by the Swiss Sentinel Network "Sentinella" since November 1988 has been preceded by a pilot study which tested the methods of data collection and analysis. The original aim was (a) to use the incidence of asthmatic attacks as a possible indicator for the adverse effects of rising concentrations of air pollutants, and (b) to create a set of baseline data for future research in this field, i.e. data of asthmatic attacks for retrospective analysis of periods with increased levels of air pollution. Here, morbidity characteristics and seasonal patterns of asthmatic attacks as registered from November 1988 to May 1991, will be presented only. With regard to age and sex the data show that more than half of all asthmatic attacks occurred in children 0-14 years of age. Males outweigh females by roughly two to one, but the distribution becomes more even after adolescence. These results are in accordance with the literature (Table 1). Whereas hospital beds (hospitalisations) are occupied by a growing number of patients suffering from asthma, especially in children hospitals, the referral rate of children with asthmatic attacks by primary car physicians has remained relatively steady over the past three years (Table 2). Thus, it can be inferred that asthma, while a major problem in the hospital, is dealt with successfully by practitioners in the primary care setting. This is to the contrary of international trends which show an increasing referral rate for asthma. A differential analysis of workload from asthmatic attacks for general practitioners, internists and paediatricians is directing toward a rising incidence of asthma.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗

Adaptive neuro-fuzzy modeling of poorly soluble drug formulations.

PURPOSE: The purpose of this study was to evaluate the efficiency of a neuro-fuzzy logic-based methodology to model poorly soluble drug formulations and predict the development of the particle size that has been proven to be an important factor for long-term stability. METHODS: An adaptive neuro-fuzzy inference system was used to model the natural structures within the data and construct a set of fuzzy rules that can subsequently used as a predictive tool. The model was implemented in Matlab 6.5 and trained using 75% of an experimental data set. Subsequently, the model was evaluated and tested using the remaining 25%, and the predicted values of the particle size were compared to the ones from the experimental data. The produced adaptive neuro-fuzzy inference system-based model consisted of four inputs, i.e., acetone, propylene glycol, POE-5 phytosterol (BPS-5), and hydroxypropylmethylcellulose 90SH-50, with four membership functions each. Moreover, 256 fuzzy rules were employed in the model structure. RESULTS: Model training resulted in a root mean square error of 4.5 x 10(-3), whereas model testing proved its highly predictive efficiency, achieving a correlation coefficient of 0.99 between the actual and the predicted values of the particle size (mean diameter). CONCLUSIONS: Neuro-fuzzy modeling has been proven to be a realistic and promising tool for predicting the particle size of drug formulations with an easy and fast way, after proper training and testing.

Acetone↗

On-line analysis of gap junctions reveals more efficient electrical than dye coupling between islet cells.

Pancreatic beta-cells constitute a well-communicating multicellular network that permits a coordinated and synchronized signal transmission within the islet of Langerhans that is necessary for proper insulin release. Gap junctions are the molecular keys that mediate functional cellular connections, which are responsible for electrical and metabolic coupling in the majority of cell types. Although the role of gap junctions in beta-cell electrical coupling is well documented, metabolic communication is still a matter of discussion. Here, we have addressed this issue by use of a fluorescence recovery after photobleaching (FRAP) approach. This technique has been validated as a reliable and noninvasive approach to monitor functional gap junctions in real time. We show that control pancreatic islet cells did not exchange a gap junction-permeant molecule in either clustered cells or intact islets of Langerhans under conditions that allowed cell-to-cell exchange of current-carrying ions. Conversely, we have detected that the same probe was extensively transferred between islet cells of transgenic mice expressing connexin 32 (Cx32) that have enhanced junctional coupling properties. The results indicate that the electrical coupling of native islet cells is more extensive than dye communication. Dye-coupling domains in islet cells appear more restricted than previously inferred with other methods.

Animals↗

Is there tonic activity in the endogenous opioid systems? A c-Fos study in the rat central nervous system after intravenous injection of naloxone or naloxone-methiodide.

This study examined the possibility that a tonic activity in the endogenous opioid systems (EO systems) exists in animals under normal conditions. In a first set of experiments, concurrent changes in behavioral responses and in the numbers of c-Fos-like immunoreactive (Fos-LI) neurons in 58 structures of the brain and lumbosacral spinal cord were analyzed in rats after systemic administration of the opioid antagonist naloxone (NAL; 2 mg/kg). Possible roles of the EO systems were inferred from changes in the numbers of Fos-LI neurons between normal rats that received either NAL or the same volume of saline. Free-floating sections were processed immunohistochemically for c-Fos protein using standard avidin-biotin complex methods. After NAL, the numbers of Fos-LI neurons were significantly increased in the area postrema; in the caudal, intermediate, and rostral parts of the nucleus tractus solitarii; in the rostral ventrolateral medulla; in the Kölliker-Fuse nucleus; in the supramammillary nucleus; and in the central nucleus of the amygdala. In a second set of experiments examining changes in c-Fos expression in the latter structures, similar increases were found after NAL but not after an equimolar dose of NAL-methiodide, a preferential, peripherally acting opioid receptor antagonist. Therefore, Fos-LI was likely triggered after blockade of central opioid receptors, but not peripheral opioid receptors, releasing neurons from EO system-mediated inhibition. The results of this study suggest the existence of a tonic activity of the EO systems exerted on a restricted number of brain regions in normal rats. This tonic activity of the EO systems may control part of the neural networks involved in cardiorespiratory functions and in emotional and learning processes.

Animals↗

Identification of functional links between genes using phylogenetic profiles.

MOTIVATION: Genes with identical patterns of occurrence across the phyla tend to function together in the same protein complexes or participate in the same biochemical pathway. However, the requirement that the profiles be identical (i) severely restricts the number of functional links that can be established by such phylogenetic profiling; (ii) limits detection to very strong functional links, failing to capture relations between genes that are not in the same pathway, but nevertheless subserve a common function and (iii) misses relations between analogous genes. Here we present and apply a method for relaxing the restriction, based on the probability that a given arbitrary degree of similarity between two profiles would occur by chance, with no biological pressure. Function is then inferred at any desired level of confidence. RESULTS: We derive an expression for the probability distribution of a given number of chance co-occurrences of a pair of non-homologous orthologs across a set of genomes. The method is applied to 2905 clusters of orthologous genes (COGs) from 44 fully sequenced microbial genomes representing all three domains of life. Among the results are the following. (1) Of the 51 000 annotated intrapathway gene pairs, 8935 are linked at a level of significance of 0.01. This is over 30-fold greater than the 271 intrapathway pairs obtained at the same confidence level when identical profiles are used. (2) Of the 540 000 interpathway genes pairs, some 65 000 are linked at the 0.01 level of significance, some 12 standard deviations beyond the number expected by chance at this confidence level. We speculate that many of these links involve nearest-neighbor path, and discuss some examples. (3) The difference in the percentage of linked interpathway and intrapathway genes is highly significant, consistent with the intuitive expectation that genes in the same pathway are generally under greater selective pressure than those that are not. (4) The method appears to recover well metabolic networks. This is illustrated by the TCA cycle which is recovered as a highly connected, weighted edge network of 30 of its 31 COGs. (5) The fraction of pairs having a common pathway is a symmetric function of the Hamming distance between their profiles. This finding, that the functional correlation between profiles with near maximum Hamming distance is as large as between profiles with near zero Hamming distance, and as statistically significant, is plausibly explained if the former group represents analogous genes.

Algorithms↗

Identification of distributed metabolic objectives in the hypermetabolic liver by flux and energy balance analysis.

A methodology for inferring distributed metabolic objectives from time series flux data is developed by combining metabolic flux analysis, pathway identification, free energy balances, and nested optimization. This methodology is used to investigate the metabolic response of the rat liver to burn injury-induced whole body inflammation. Gibbs free energy changes were computed for stoichiometrically balanced sequences of reactions, or pathways, rather than individual reactions, to account for energetic coupling between reactions. Systematic enumeration of pathways proceeded by elementary flux mode (EFM) analysis. Together with stoichiometric balances and external metabolite flux measurements, the DeltaG(PATH)(o) criterion provided sufficient constraints to solve a series of nested optimization problems on the metabolic goal functions and associated flux distributions of fasted livers during the first-week time course of burn injury. The optimization results suggest that there is a consistent metabolic goal function for the liver that is insensitive to the changing metabolic burdens experienced by the liver during the first-week time course. As defined by the goal function coefficients, the global metabolic objective was to distribute the metabolic resources between amino acid metabolism and ketone body synthesis. These findings point to a role for the time-invariant structure of the metabolic reaction network, expressed as stoichiometric and thermodynamic constraints, in shaping the cellular metabolic objective.

Animals↗

Manhattan world: orientation and outlier detection by Bayesian inference.

This letter argues that many visual scenes are based on a "Manhattan" three-dimensional grid that imposes regularities on the image statistics. We construct a Bayesian model that implements this assumption and estimates the viewer orientation relative to the Manhattan grid. For many images, these estimates are good approximations to the viewer orientation (as estimated manually by the authors). These estimates also make it easy to detect outlier structures that are unaligned to the grid. To determine the applicability of the Manhattan world model, we implement a null hypothesis model that assumes that the image statistics are independent of any three-dimensional scene structure. We then use the log-likelihood ratio test to determine whether an image satisfies the Manhattan world assumption. Our results show that if an image is estimated to be Manhattan, then the Bayesian model's estimates of viewer direction are almost always accurate (according to our manual estimates), and vice versa.

Artificial Intelligence↗

Stochastic reasoning, free energy, and information geometry.

Belief propagation (BP) is a universal method of stochastic reasoning. It gives exact inference for stochastic models with tree interactions and works surprisingly well even if the models have loopy interactions. Its performance has been analyzed separately in many fields, such as AI, statistical physics, information theory, and information geometry. This article gives a unified framework for understanding BP and related methods and summarizes the results obtained in many fields. In particular, BP and its variants, including tree reparameterization and concave-convex procedure, are reformulated with information-geometrical terms, and their relations to the free energy function are elucidated from an information-geometrical viewpoint. We then propose a family of new algorithms. The stabilities of the algorithms are analyzed, and methods to accelerate them are investigated.

Algorithms↗

Protein flexibility and rigidity predicted from sequence.

Structural flexibility has been associated with various biological processes such as molecular recognition and catalytic activity. In silico studies of protein flexibility have attempted to characterize and predict flexible regions based on simple principles. B-values derived from experimental data are widely used to measure residue flexibility. Here, we present the most comprehensive large-scale analysis of B-values. We used this analysis to develop a neural network-based method that predicts flexible-rigid residues from amino acid sequence. The system uses both global and local information (i.e., features from the entire protein such as secondary structure composition, protein length, and fraction of surface residues, and features from a local window of sequence-consecutive residues). The most important local feature was the evolutionary exchange profile reflecting sequence conservation in a family of related proteins. To illustrate its potential, we applied our method to 4 different case studies, each of which related our predictions to aspects of function. The first 2 were the prediction of regions that undergo conformational switches upon environmental changes (switch II region in Ras) and the prediction of surface regions, the rigidity of which is crucial for their function (tunnel in propeller folds). Both were correctly captured by our method. The third study established that residues in active sites of enzymes are predicted by our method to have unexpectedly low B-values. The final study demonstrated how well our predictions correlated with NMR order parameters to reflect motion. Our method had not been set up to address any of the tasks in those 4 case studies. Therefore, we expect that this method will assist in many attempts at inferring aspects of function.

Amino Acid Sequence↗

[The analysis of physicians' work: announcing the end of attempts at in vitro fertilization].

The purpose of this empirical study is to analyze modalities of announcing the end of attempts at in vitro ferti-lization to women who, for various reasons, were not able to have a child after several trials. What are the problems physicians face when, in the course of their work, they make these announcements? How do they give (or not give) support to these women who have placed so much hope in this technique? These are some of the questions that led the authors to conduct this empirical study within the framework of a clinical and qualitative approach to work psychology. Within this framework, work is conceptualised as a complex activity that involves the subject, both bodily and through his various modes of socialisation. The field of clinical and quali-tative approach to work psychology situations focuses on different ways of expressing distress related to contradictory work demands, as the activity is being performed; it also focuses on those creative processes used by the subject to cope with those internal and external conflicts that hinder task performance. A review of the literature and preliminary observations led us to postulate that the problems physicians are faced with when they announce the end of attempts at in vitro fertilisation (IVF) are linked to several conflicts between work values (that are specific to the medical world) and the recognition of work failure: termination of attempts at IVF. The popu-lation that participated in this research project belongs to a network of private practitioners who work with the in-house team of a Parisian clinic. But the group is not uniform and some physicians perform IVFs more frequently than others. Our qualitative study involved 10 semi-directive interviews of approximately 1 1/2 hours each, which were recorded and transcribed. Initial instructions focused on a concrete description of situations of abandonment of attempts at IVF, in terms of their preparation, development, and the way they are experienced . Interviews therefore centred on specific and limited practitioner activity. Each transcription was submitted to a Qualitative Analysis of Discourse, followed by a comparative analysis of the 10 transcriptions. We propose an original method of Qualitative Analysis of Discourse, to be applied to semi-structured clinical interviews. This method seeks to analyse the structure of the resulting egocentric monologue in research si-tuations of semi-directive interviewing. The method of Quali-tative Analysis of Discourse involves three steps, but only the first two were applied in this work: a) identification of sequences of discourse; b) analysis of relationships between statements; c) stylistic analysis of figures of speech. Our first set of analyses showed that seve-ral markers increase in physicians' discourse when they describe difficult and/or conflict-laden consultation situations: logical connectors, impersonal pronouns, reported discourse, anti-cipations regarding the interviewer's judgement. The logical balance of the discourse therefore appears threatened when pro-blems inherent in the work demands involved in ending IVF attempts are mentioned. As a whole, these markers underscore the importance of the implicit dimension of discourse (inferences, presuppositions, hints, allusions, etc.), thus reflecting complex speech that attempts to negotiate between subjective positions and shared cultural values. A comparative analysis of the markers identified in the 10 interviews revealed four areas, each involving nervous tension poles, that are suggestive of cognitive-emotional dissonance in the task to be performed. Some factors increase professional distress while others temper it. They act upon the work situation itself on the one hand, and on the working relationship between physician and patient on the other. 1. Areas of tension relating to the task to be performed. The first area contrasts individual with collective decision-making. The independent status which characterises private medical practice increases self-esteem in cases of success but weakens it when IVF attempts fail. In addition, it goes against collective involvement in the work situation, yet such involvement may act as a strong moderating factor for the experience of distress. The second area contrasts work that is well done with recognition by peers. Indeed, in the hierarchy of medical values, recognition by peers that work has been well performed is anchored in successful healing (in the broad sense of the term), whereas in situations of abandonment of IVF attempts, ending the attempt is considered by everyone to be a failure, even if it has been well conducted . The third area opposes objective medical practice to a necessarily subjective medical involvement. The scientific and ideal values which characterise medicine reflect its objective and scientific orientation, but IVF situations are a reminder that medicine is not an exact science and that it can make mistakes. There are numerous special individual cases which reduce certainty that a decision to terminate IVF is well-founded. The fourth area distinguishes between work that is considered to be well done and work considered to be well conducted . Personal estimation of work that is well done is based on the impression that the maximum feasible has been done . But in IVF situations, constant uncertainty leads to professional over-involvement (examinations, verifications, changes of protocols). Work that is poorly done is work that does not cure or that brings no relief. As a result, work that consists in ending IVF attempts, even if it is well conducted , remains a subjective failure for everyone since it does not bring a cure (pregnancy). 2. Areas of tension in the physician-patient relationship. The first area contrasts women's irrational desire with possible support from their husbands, when the time has come to announce the end of the attempts. But this voice/presence of husbands is consi-dered desirable and important only when attempts have failed, so that husbands are not encouraged to participate in the protocols except to help restrain their wives' over reactions . The second area opposes respect for the patient role with demands made by women. Lack of respect for the patient role, by making demands or by refusing to follow advice, particularly when IVF attempts are abandoned, crystallises all the resentment experienced by physicians in difficult work situations. Two cognitive-emotional worlds, more or less tuned to one another over the course of the IVF, start to clash and lose all mutual understanding: the medical world and the patient's subjective world. The third area results from the second one. It contrasts a listening physician with a powerful one. Physicians are very concerned that their relationship with their patients be one of partnership. But this (idealised) equilibrium is abruptly disrupted by the end of the attempts, inasmuch as it is the physician who has the power to stop these attempts and who decides to do so. The unveiling of this reality of a power relationship becomes a source of suffering and contradicts expressed surface values. The fourth area contrasts an attitude of ongoing patient support based on a belief in success with an attitude of patient support based on the prediction of a possible failure. Indeed, for a patient to be supported in a way physicians would consider right and adequate , the abandonment of IVF attempts should be anticipated in advance so that the physician can prepare both himself and the patients for the high risk of failure. But physicians insist on the fact that medical work can only succeed if they believe in it . As a result, the more energy the physician puts into launching the initial phase of IVF, the greater the feeling of self-accomplishment during the first phase of IVF; but conversely, the weaker the efficacy of the process of seeing the patient through the end of the attempts, the stronger the fee-ling of subjective distress at work will be. Overall, it is a para-doxical work situation for physicians to have to anticipate the interruption of IVF attempts and to have to prepare for seeing the patient through this abandonment. This situation creates conflicts of representations and values within their very practice and generates distress at work. It is worth noting that some moderating factors could alleviate their sense of suffering and contribute to improving their work experience: a) the deve-lopment of a protocol for seeing patients through the end of IVF attempts, which would make abandonment part of a job well done for physicians; b) regular participation by the spouse in these protocols; c) making all decisions to end IVF attempts a collective process, in order to avoid placing exclusive responsibility on the treating physician. The limitations of this study are inherent both in the qualitative nature of the data that involve a small number of physicians, and in the specificity of this population that works within a poorly structured network. On the other hand, our method of Qualitative Analysis of Discourse can be applied to all types of discourse obtained in research situations, provided the discourse is produced through semi-directive or non-directive interviews.

Affect↗

Performance and diagnostic evaluation of ozone predictions by the Eta-Community Multiscale Air Quality Forecast System during the 2002 New England Air Quality Study.

A real-time air quality forecasting system (Eta-Community Multiscale Air Quality [CMAQ] model suite) has been developed by linking the National Centers for Environmental Estimation Eta model to the U.S. Environmental Protection Agency (EPA) CMAQ model. This work presents results from the application of the Eta-CMAQ modeling system for forecasting ozone (O3) over the Northeastern United States during the 2002 New England Air Quality Study (NEAQS). Spatial and temporal performance of the Eta-CMAQ model for O3 was evaluated by comparison with observations from the EPA Air Quality System (AQS) network. This study also examines the ability of the model to simulate the processes governing the distributions of tropospheric O3 on the basis of the intensive datasets obtained at the four Atmospheric Investigation, Regional Modeling, Analysis, and Estimation (AIRMAP) and Harvard Forest (HF) surface sites. The episode analysis reveals that the model captured the buildup of O3 concentrations over the northeastern domain from August 11 and reproduced the spatial distributions of observed O3 very well for the daytime (8:00 p.m.) of both August 8 and 12 with most of normalized mean bias (NMB) within +/- 20%. The model reproduced 53.3% of the observed hourly O3 within a factor of 1.5 with NMB of 29.7% and normalized mean error of 46.9% at the 342 AQS sites. The comparison of modeled and observed lidar O3 vertical profiles shows that whereas the model reproduced the observed vertical structure, it tended to overestimate at higher altitude. The model reproduced 64-77% of observed NO2 photolysis rate values within a factor of 1.5 at the AIRMAP sites. At the HF site, comparison of modeled and observed O3/nitrogen oxide (NOx) ratios suggests that the site is mainly under strongly NOx-sensitive conditions (>53%). It was found that the modeled lower limits of the O3 production efficiency values (inferred from O3-CO correlation) are close to the observations.

Air Pollutants↗

The maintenance of reproductive isolation in a mosaic hybrid zone between the fire-bellied toads Bombina bombina and B. variegata.

Mosaic hybrid zones arise when ecologically differentiated taxa hybridize across a network of habitat patches. Frequent interbreeding across a small-scale patchwork can erode species differences that might have been preserved in a clinal hybrid zone. In particular, the rapid breakdown of neutral divergence sets an upper limit to the time for which differences at marker loci can persist. We present here a case study of a mosaic hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae) near Apahida in Romania. In our 20 x 20 km study area, we detected no evidence of a clinal transition but found a strong association between aquatic habitat and mean allele frequencies at four molecular markers. In particular, pure populations of B. bombina in ponds appear to cause massive introgression into the surrounding B. variegata gene pool found in temporary aquatic sites. Nevertheless, the genetic structure of these hybrid populations was remarkably similar to those of a previously studied transect near Pescenica (Croatia), which had both clinal and mosaic features: estimates of heterozygote deficit and linkage disequilibrium in each country are similar. In Apahida, the observed strong linkage disequilibria should stem from an imperfect habitat preference that guides most (but not all) adults into the habitats to which they are adapted. In the absence of a clinal structure, the inferred migration rate between habitats implies that associations between selected loci and neutral markers should break down rapidly. Although plausible selection strengths can maintain differentiation at those loci adapting the toads to either permanent or temporary breeding sites, the divergence at neutral markers must be transient. The hybrid zone may be approaching a state in which the gene pools are homogenized at all but the selected loci, not dissimilar from an early stage of sympatric divergence.

Animal Migration↗

LRP and H-NS--cooperative partners for transcription regulation at Escherichia coli rRNA promoters.

The synthesis of ribosomal RNAs in bacteria is tightly coupled to changes in the environment. This rapid adaptation is the result of several intertwined regulatory networks. The two proteins FIS and H-NS have previously been described to act as antagonistic transcription factors for rRNA synthesis. Here we provide evidence for another player, the regulatory protein LRP, which binds with high specificity to all seven Escherichia coli rRNA P1 promoter upstream regions (UAS). Comparison of the binding properties of LRP and H-NS, and characterization of the stabilities of the various complexes formed with the rRNA UAS regions revealed different binding modes. Binding studies with LRP and H-NS in combination demonstrated that the two proteins interacted with obvious synergism. The efficiency of LRP binding to the rRNA regulatory region is modified by the presence of the effector amino acid leucine, as has been shown for several other operons regulated by this transcription factor. The effect of LRP on the binding of RNA polymerase to the rrnB P1 promoter and in vitro transcription experiments indicated that LRP acts as a transcriptional repressor, thus resembling the activity of H-NS described previously. The results show for the first time that LRP binds to the regulatory region of bacterial rRNA promoters, and very likely contributes in combination with H-NS to the control of rRNA synthesis. From the known properties of LRP a mechanism can be inferred that couples rRNA synthesis to changes in nutritional quality.

Bacterial Proteins↗

Network formation of catanionic vesicles and oppositely charged polyelectrolytes. Effect of polymer charge density and hydrophobic modification.

In nonequimolar solutions of a cationic and an anionic surfactant, vesicles bearing a net charge can be spontaneously formed and apparently exist as thermodynamically stable aggregates. These vesicles can associate strongly with polymers in solution by means of hydrophobic and/or electrostatic interactions. In the current work, we have investigated the rheological and microstructural properties of mixtures of cationic polyelectrolytes and net anionic sodium dodecyl sulfate/didodecyldimethylammonium bromide vesicles. The polyelectrolytes consist of two cationic cellulose derivatives with different charge densities; the lowest charge density polymer contains also hydrophobic grafts, with the number of charges equal to the number of grafts. For both systems, polymer-vesicle association leads to a major increase in viscosity and to gel-like behavior, but the viscosity effects are more pronounced for the less charged, hydrophobically modified polymer. Evaluation of the frequency dependence of the storage and loss moduli for the two systems shows further differences in behavior: while the more long-lived cross-links occur for the more highly charged hydrophilic polymer, the number of cross-links is higher for the hydrophobically modified polymer. Microstructure studies by cryogenic transmission electron microscopy indicate that the two polymers affect the vesicle stability in different ways. With the hydrophobically modified polymer, the aggregates remain largely in the form of globular vesicles and faceted vesicles (polygon-shaped vesicles with largely planar regions). For the hydrophilic polycation, on the other hand, the surfactant aggregate structure is more extensively modified: first, the vesicles change from a globular to a faceted shape; second, there is opening of the bilayers leading to holey vesicles and ultimately to considerable vesicle disruption leading to planar bilayer, disklike aggregates. The faceted shape is tentatively attributed to a crystallization of the surfactant film in the vesicles. It is inferred that a hydrophobically modified polyion with relatively low charge density can better stabilize vesicles due to formation of molecularly mixed aggregates, while a hydrophilic polyion with relatively high charge density associates so strongly to the surfactant films, due to strong electrostatic interactions, that the vesicles are more perturbed and even disrupted.

Journal Article↗

ret receptor tyrosine kinase immunoreactivity is altered in glial cell line-derived neurotrophic factor-responsive neurons following lesions of the nigrostriatal and septohippocampal pathways.

Glial cell line-derived neurotrophic factor was initially identified as a survival factor for developing midbrain dopamine neurons (for reviews, see Refs 17 and 19). Subsequent studies have demonstrated a more wide-spread role for glial cell line-derived neurotrophic factor in the developing and adult CNS. In the adult rat brain, for instance, prior administration of glial cell line-derived neurotrophic factor protects nigrostriatal dopamine neurons from 6-hydroxydopamine-induced damage. When given several weeks after 6-hydroxydopamine injection, glial cell line-derived neurotrophic factor also restores the function of these neurons. Glial cell line-derived neurotrophic factor attenuates excitotoxin-induced cell death in the striatum and hippocampal formation and protective effects of glial cell line-derived neurotrophic factor following axotomy have been reported for spinal motor neurons and basal forebrain cholinergic neurons. These findings suggest that glial cell line-derived neurotrophic factor may be a protective/restorative agent for a diverse population of neurons and imply that it may be a useful therapeutic tool for a variety of neurodegenerative diseases including Parkinson's, Huntington's and Alzheimer's diseases. The potential receptor mediating the pleiotropic effects of glial cell line-derived neurotrophic factor has been characterized only recently as a novel glycosyl-phosphatidylinositol-linked protein, GDNFR-alpha. Because GDNFR-alpha is a cell surface receptor, an additional protein(s) was thought to be involved in the glial cell line-derived neurotrophic factor signalling cascade. The identity of the likely candidate, ret, was inferred initially from indirect evidence. Not only were there remarkable similarities in the distribution of glial cell line-derived neurotrophic factor and the proto-oncogene ret in the developing rat and mouse brain, but also in the phenotype of glial cell line-derived neurotrophic factor knockout mice and mice with ret mutations. Mice with either mutation exhibited pronounced renal and enteric abnormalities, implicating the receptor tyrosine kinase protein product of the ret proto-oncogene as the glial cell line-derived neurotrophic factor signalling protein. More conclusive evidence showing that activation of GDNFR-alpha by glial cell line-derived neurotrophic factor induces phosphorylation of ret has confirmed ret as a signalling protein for glial cell line-derived neurotrophic factor. Preliminary results showing that 6-hydroxydopamine lesions of the substantia nigra markedly reduced ret messenger RNA expression, established its localization to presumably glial cell line-derived neurotrophic factor-responsive dopamine neurons in the nigrostriatal pathway. In contrast, it is not clear whether other glial cell line-derived neurotrophic factor-responsive neurons in the CNS, such as the basal forebrain cholinergic neurons and striatal neurons, also express ret, nor is it evident whether levels of the protein are regulated by disruption of the respective pathways. The present study shows that dense networks of ret immunoreactivity are distributed throughout the nigrostriatal pathway, with lower densities of staining in other brain regions, including the septohippocampal pathway. Following extensive unilateral 6-hydroxydopamine lesions of the medial forebrain bundle, ret immunoreactivity in the substantia nigra and striatum was reduced significantly, to a similar extent as tyrosine hydroxylase immunoreactivity. In contrast, excitotoxic lesions of the striatum, achieved by intrastriatal quinolinic acid injections, resulted in increased ret staining in this brain region. In addition, marked decrements in septal ret immunoreactivity were consequent to complete transections of the fimbria-fornix.

Animals↗