Clonal relationships determined by multilocus sequence typing among enteropathogenic Escherichia coli isolated in Brazil

Enteropathogenic Escherichia coli (EPEC) infections are a leading cause of infantile diarrhea in developing nations. Multilocus sequence typing (MLST) characterizes bacterial strains based on the sequences of internal fragments in housekeeping genes. Little is known about strains of EPEC analyzed by MLST from Brazil. In this study, a diverse collection of 29 EPEC strains isolated from patients with diarrhea, admitted to the University Hospital of Ribeirao Preto, was characterized by MLST. Strain analysis demonstrated 22 different sequence types (STs), of which almost half (48%) were new, indicating a high genotype diversity. The 22 STs were divided by eBURST into 12 clonal complexes. It was not possible to correlate typical and atypical EPEC with other strains in the MLST database. This is the first study that analyzed EPEC strains from South America that are included in the E. coli MLST database. Nine (31%) out of 29 strains are part of the CC10 clonal complex, the major clonal complex in the database, which comprises 174 strains and 86 different STs, suggesting that these strains might be the most important intestinal pathogenic E. coli worldwide. Genetic relationships between typical and atypical EPEC, enterohemorrhagic E. coli, and enteroaggregative E. coli strains were not established by MLST.

Biomechanical consequences of impairment: A taxonomically valid basis for classification in a unified disability athletics system

Developing a unified classification system to replace four of the systems currently used in disability athletics (i.e., track and field) has been widely advocated. The diverse impairments to be included in a unified system require severed assessment methods, results of which cannot be meaningfully compared. Therefore, the taxonomic basis of current classification systems is invalid in a unified system. Biomechanical analysis establishes that force, a vector described in terms of magnitude and direction, is a key determinant of success in all athletic disciplines. It is posited that all impairments to be included in a unified system may be classified as either force magnitude impairments (FMI) or force control impairments (FCI). This framework would provide a valid taxonomic basis for a unified system, creating the opportunity to decrease the number of classes and enhance the viability of disability athletics.

Time-reversal test for stochastic quantum dynamics

The calculation of quantum dynamics is currently a central issue in theoretical physics, with diverse applications ranging from ultracold atomic Bose-Einstein condensates to condensed matter, biology, and even astrophysics. Here we demonstrate a conceptually simple method of determining the regime of validity of stochastic simulations of unitary quantum dynamics by employing a time-reversal test. We apply this test to a simulation of the evolution of a quantum anharmonic oscillator with up to 6.022×1023 (Avogadro's number) of particles. This system is realizable as a Bose-Einstein condensate in an optical lattice, for which the time-reversal procedure could be implemented experimentally.

Cloning and characterization of a gene encoding the major surface protein of the bacterial endosymbiont Wolbachia pipientis

The maternally inherited intracellular symbiont Wolbachia pipientis is well known for inducing a variety of reproductive abnormalities in the diverse arthropod hosts it infects. It has been implicated in causing cytoplasmic incompatibility, parthenogenesis, and the feminization of genetic males in different hosts. The molecular mechanisms by which this fastidious intracellular bacterium causes these reproductive and developmental abnormalities have not yet been determined. In this paper, we report on (i) the purification of one of the most abundantly expressed Wolbachia proteins from infected Drosophila eggs and (ii) the subsequent cloning and characterization of the gene (wsp) that encodes it. The functionality of the wsp promoter region was also successfully tested in Escherichia coli. Comparison of sequences of this gene from different strains of Wolbachia revealed a high level of variability. This sequence variation correlated with the ability of certain Wolbachia strains to induce or rescue the cytoplasmic incompatibility phenotype in infected insects. As such, this gene will be a very useful tool for Wolbachia strain typing and phylogenetic analysis, as well as understanding the molecular basis of the interaction of Wolbachia with its host.

Cytoplasmic incompatibility in Drosophila populations: influence of assortative mating on symbiont distribution

Cytoplasmic incompatibility is known to occur between strains of both Drosophila simulans and D. melanogaster. Incompatibility is associated with the infection of Drosophila with microorganismal endosymbionts. This paper reports survey work conducted on strains of D. simulans and D. melanogaster from diverse geographical locations finding that infected populations are relatively rare and scattered in their distribution. The distribution of infected populations of D. simulans appears to be at odds with deterministic models predicting the rapid spread of the infection through uninfected populations. Examination of isofemale lines from four localities in California where populations appear to be polymorphic for the infection failed to find evidence for consistent assortative mating preferences between infected and uninfected populations that may explain the basis for the observed polymorphism.

Preface and Acknowledgments

This volume is a joint project undertaken by three scholars from diverse backgrounds around the world. In the following, I trace the history of this project from a personal perspective and acknowledge the contributions of those who have been involved.

Regulation of photosynthetic pigments in micro-algae by multiple environmental factors: a dynamic balance hypothesis

Environmental effects on the concentration of photosynthetic pigments in micro-algae can be explained by dynamics of photosystem synthesis and deactivation. A model that couples photosystem losses to the relative cellular rates of energy harvesting (light absorption) and assimilation predicts optimal concentrations of light-harvesting pigments and balanced energy flow under environmental conditions that affect light availability and metabolic rates. Effects of light intensity, nutrient supply and temperature on growth rate and pigment levels were similar to general patterns observed across diverse micro-algal taxa. Results imply that dynamic behaviour associated with photophysical stress, and independent of gene regulation, might constitute one mechanism for photo-acclimation of photosynthesis.

The treatment of tardive dyskinesia: A systematic review and meta-analysis

This systematic review aimed to collate randomized controlled trials (RCTs) of various interventions used to treat tardive dyskinesia (TD) and, where appropriate, to combine the data for mete-analysis, Clinical trials were identified by electronic searches, handsearches and contact with principal investigators. Data were extracted independently by two reviewers, for outcomes related to improvement, deterioration, side-effects and drop out rates. Data were pooled using the Mantel-Haenzel Odds Ratio (fixed effect model). For treatments that had significant effects, the number needed to treat (NNT) was calculated. From 296 controlled clinical trials, data were extracted from 47 trials. For most interventions, we could identify no RCT-derived evidence of efficacy. A meta-analysis showed that baclofen, deanol and diazepam were no more effective than a placebo. Single RCTs demonstrated a lack of evidence of any effect for bromocriptine, ceruletide, clonidine, estrogen, gamma linolenic acid, hydergine, lecithin, lithium, progabide, seligiline and tetrahydroisoxazolopyridinol. The meta-analysis found that five interventions were effective: L-dopa, oxypertine, sodium valproate, tiapride and vitamin E; neuroleptic reduction was marginally significant. Data from single RCTs revealed that insulin, alpha methyl dopa and reserpine were more effective than a placebo. There was a significantly increased risk of adverse events associated with baclofen, deanol, L-dopa, oxypertine and reserpine. Metaanalysis of the impact of placebo (n=485) showed that 37.3% of participants showed an improvement. Interpretation of this systematic review requires caution as the individual trials identified tended to have small sample sizes. For many compounds, data from only one trial were available, and where meta-analyses were possible, these were based on a small number of trials. Despite these concerns, the review facilitated the interpretation of the large and diverse range of treatments used for TD. Clinical recommendations for the treatment of TD are made, based on the availability of RCT-derived evidence, the strength of that evidence and the presence of adverse effects. (C) 1999 Elsevier Science B.V. All rights reserved.

Improving wheat simulation capabilities in Australia from a cropping systems perspective - II. Testing simulation capabilities of wheat growth

To simulate cropping systems, crop models must not only give reliable predictions of yield across a wide range of environmental conditions, they must also quantify water and nutrient use well, so that the status of the soil at maturity is a good representation of the starting conditions for the next cropping sequence. To assess the suitability for this task a range of crop models, currently used in Australia, were tested. The models differed in their design objectives, complexity and structure and were (i) tested on diverse, independent data sets from a wide range of environments and (ii) model components were further evaluated with one detailed data set from a semi-arid environment. All models were coded into the cropping systems shell APSIM, which provides a common soil water and nitrogen balance. Crop development was input, thus differences between simulations were caused entirely by difference in simulating crop growth. Under nitrogen non-limiting conditions between 73 and 85% of the observed kernel yield variation across environments was explained by the models. This ranged from 51 to 77% under varying nitrogen supply. Water and nitrogen effects on leaf area index were predicted poorly by all models resulting in erroneous predictions of dry matter accumulation and water use. When measured light interception was used as input, most models improved in their prediction of dry matter and yield. This test highlighted a range of compensating errors in all modelling approaches. Time course and final amount of water extraction was simulated well by two models, while others left up to 25% of potentially available soil water in the profile. Kernel nitrogen percentage was predicted poorly by all models due to its sensitivity to small dry matter changes. Yield and dry matter could be estimated adequately for a range of environmental conditions using the general concepts of radiation use efficiency and transpiration efficiency. However, leaf area and kernel nitrogen dynamics need to be improved to achieve better estimates of water and nitrogen use if such models are to be use to evaluate cropping systems. (C) 1998 Elsevier Science B.V.

The Australian mortality decline: cause-specific mortality 1907-1990

This review describes the changes in composition of mortality by major attributed cause during the Australian mortality decline this century. The principal categories employed were: infectious diseases, nonrheumatic cardiovascular disease, external causes, cancer,'other' causes and ill-defined conditions. The data were age-adjusted. Besides registration problems (which also affect all-cause mortality) artefacts due to changes in diagnostic designation and coding-are evident. The most obvious trends over the period are the decline in infectious disease mortality (half the decline 1907-1990 occurs before 1949), and the epidemic of circulatory disease mortality which appears to commence around 1930, peaks during the 1950s and 1960s, and declines from 1970 to 1990 (to a rate half that at the peak). Mortality for cancer remains static for females after 1907, but increases steadily for males, reaching a plateau in the mid-1980s (owing to trends in lung cancer); trends in cancers of individual sites are diverse. External cause mortality declines after 1970. The decline in total mortality to 1930 is associated with decline in infection and 'other' causes, Stagnation of mortality decline in 1930-1940 and 1946-1970 for males is a consequence of contemporaneous movements in opposite directions of infection mortality (decrease) and circulatory disease and cancer mortality (increase). In females, declines in infections and 'other' causes of death exceed the increase in circulatory disease mortality until 1960, then stability in all major causes of death to 1970. The overall mortality decline since 1970 is a consequence of a reduction in circulatory disease,'other' cause, external cause and infection mortality, despite the increase in cancer mortality (for males).

Crystal structures of reduced and oxidized DsbA: investigation of domain motion and thiolate stabilization

Background: The redox proteins that incorporate a thioredoxin fold have diverse properties and functions. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyzes disulfide-bond formation during the folding of secreted proteins, The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilizing active-site interactions in the reduced form. In the domain motion model, hinge bending between the two domains of DsbA occurs as a result of redox-related conformational changes. Results: We have determined the crystal structures of reduced and oxidized DsbA in the same crystal form and at the same pH (5.6). The crystal structure of a lower pH form of oxidized DsbA has also been determined (pH 5.0). These new crystal structures of DsbA, and the previously determined structure of oxidized DsbA at pH 6.5, provide the foundation for analysis of structural changes that occur upon reduction of the active-site disulfide bond. Conclusions: The structures of reduced and oxidized DsbA reveal that hinge bending motions do occur between the two domains. These motions are independent of redox state, however, and therefore do not contribute to the energetic differences between the two redox states, instead, the observed domain motion is proposed to be a consequence of substrate binding. Furthermore, DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulfide at the active site.

Tetrachromacy, oil droplets and bird plumage colours

There is a growing body of data on avian eyes, including measurements of visual pigment and oil droplet spectral absorption, and of receptor densities and their distributions across the retina. These data are sufficient to predict psychophysical colour discrimination thresholds for light-adapted eyes, and hence provide a basis for relating eye design to visual needs. We examine the advantages of coloured oil droplets, UV vision and tetrachromacy for discriminating a diverse set of avian plumage spectra under natural illumination. Discriminability is enhanced both by tetrachromacy and coloured oil droplets. Oil droplets may also improve colour constancy. Comparison of the performance of a pigeon's eye, where the shortest wavelength receptor peak is at 410 nm, with that of the passerine Leiothrix, where the ultraviolet-sensitive peak is at 365 nm, generally shows a small advantage to the latter, but this advantage depends critically on the noise level in the sensitivity mechanism and on the set of spectra being viewed.

Subantarctic Macquarie Island - a model ecosystem for studying animal-derived nitrogen sources using N-15 natural abundance

Plants collected from diverse sites on subantarctic Macquarie Island varied by up to 30 parts per thousand in their leaf delta(15)N values. N-15 natural abundance of plants, soils, animal excrement and atmospheric ammonia suggest that the majority of nitrogen utilised by plants growing in the vicinity of animal colonies or burrows is animal-derived. Plants growing near scavengers and animal higher in the food chain had highly enriched delta(15)N values (mean = 12.9 parts per thousand), reflecting the highly enriched signature of these animals' excrement, while plants growing near nesting penguins and albatross, which have an intermediate food chain position, had less enriched delta(15)N values (> 6 parts per thousand). Vegetation in areas affected by rabbits had lower delta(15)N values (mean = 1.2 parts per thousand), while the highly depleted delta(15)N values (below -5 parts per thousand) of plants at upland plateau sites inland of penguin colonies, suggested that a portion of their nitrogen is derived from ammonia (mean N-15 = -10 parts per thousand) lost during the degradation of penguin guano. Vegetation in a remote area had delta(15)N values near -2 parts per thousand. These results contrast with arctic and subarctic studies that attribute large variations in plant N-15 values to nitrogen partitioning in nitrogen-limited environments. Here, plant N-15 reflects the N-15 Of the likely nitrogen sources utilised by plants.

Long-term clozapine treatment identifies significant improvements in clinical and functioning scales

The majority of clinical drug trials only cover a small number of variables over a short period of time on a small group of people. The objective of this study was to track a large group of people over a long period of time, using a diverse range of variables with a naturalistic design to assess the ‘real world’ use of clozapine. Fifty-three people with treatment-resistant schizophrenia were recruited into a 2-year study which assessed the subjects using the following scales: Positive and Negative Syndrome Scale (PANSS), Clinical Global Impression Scale (CGI), Life Skills Profile (LSP), and Role Functioning Scale (RFS). Discharge, leave, and ward movement rates were also monitored. All subjects were inpatients at a tertiary psychiatric facility. Thirty-three percent of the group was discharged. Seventythree percent moved to less cost-intensive wards, and the leave rate increased by 105”/0. Sixty-seven percent of the study group were identified as responders by the 24-month time point. Twenty-four percent of the group had their CGI scores reduced to 2 or better 0, =O.OOOl). Significant improvements were identified in the RFS (p = 0.02) and LSP (p = 0.0001). Long-term clozapine treatment has identified a significant group of responders on a variety of measures.

Crystal structure of human T cell leukemia virus type 1 gp21 ectodomain crystallized as a maltose-binding protein chimera reveals structural evolution of retroviral transmembrane proteins

Retroviral entry into cells depends on envelope glycoproteins, whereby receptor binding to the surface-exposed subunit triggers membrane fusion by the transmembrane protein (TM) subunit. We determined the crystal structure at 2.5-Angstrom resolution of the ectodomain of gp21, the TM from human T cell leukemia virus type 1. The gp21 fragment was crystallized as a maltose-binding protein chimera, and the maltose-binding protein domain was used to solve the initial phases by the method of molecular replacement. The structure of gp21 comprises an N-terminal trimeric coiled coil, an adjacent disulfide-bonded loop that stabilizes a chain reversal, and a C-terminal sequence structurally distinct from HIV type 1/simian immunodeficiency virus gp41 that packs against the coil in an extended antiparallel fashion. Comparison of the gp21 structure with the structures of other retroviral TMs contrasts the conserved nature of the coiled coil-forming region and adjacent disulfide-bonded loop with the variable nature of the C-terminal ectodomain segment. The structure points to these features having evolved to enable the dual roles of retroviral TMs: conserved fusion function and an ability to anchor diverse surface-exposed subunit structures to the virion envelope and infected cell surface. The structure of gp21 implies that the N-terminal fusion peptide is in close proximity to the C-terminal transmembrane domain and likely represents a postfusion conformation.