Analysis of RNA-protein interactions by flow cytometry

Flow cytometry, in combination with advances in bead coding technologies, is maturing as a powerful high-throughput approach for analyzing molecular interactions. Applications of this technology include antibody assays and single nucleotide polymorphism mapping. This review describes the recent development of a microbead flow cytometric approach to analyze RNA-protein interactions and discusses emerging bead coding strategies that together will allow genome-wide identification of RNA-protein complexes. The microbead flow cytometric approach is flexible and provides new opportunities for functional genomic studies and small-molecule screening.

Chain scission and branching in irradiated poly(tetrafluoroethylene-co-hexafluoropropylene)

The radiation chemistry of poly(tetrafluoroethylene-co-hexafluoropropylene) (FEP) with a TFE mole fraction of 0.90 has been studied under vacuum using Co-60 gamma-radiation over a range of temperatures and absorbed doses. The radiolysis temperatures were 300, 363, 423, 523 and 543 K. New structure formation in the copolymers was analysed by solid-state F-19 NMR spectroscopy. The new structures formed in the copolymers have been identified and the G-values for the formation of new chemical structures have been investigated at 363 and 523 K. These two temperatures are just above and just below the polymer T-g and T-m, respectively. At the lower temperature, there was no evidence for any chain branching and an estimate of G(S) of 1.0 was obtained. A value of G(S) of 1.3 and a minimum value of G(X)(Y) of 1.3 were obtained at 523 K. (C) 2003 Society of Chemical Industry.

Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms

The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes generally code for proteins, and that proteins fulfil not only most structural and catalytic but also most regulatory functions, in all cells, from microbes to mammals. However, the latter may not be the case in complex organisms. A number of startling observations about the extent of non-protein-coding RNA (ncRNA) transcription in the higher eukaryotes and the range of genetic and epigenetic phenomena that are RNA-directed suggests that the traditional view of the structure of genetic regulatory systems in animals and plants may be incorrect. ncRNA dominates the genomic output of the higher organisms and has been shown to control chromosome architecture, mRNA turnover and the developmental timing of protein expression, and may also regulate transcription and alternative splicing. This paper re-examines the available evidence and suggests a new framework for considering and understanding the genomic programming of biological complexity, autopoletic development and phenotypic variation. BioEssays 25:930-939,2003. (C) 2003 Wiley Periodicals, Inc.

Young children's understanding of oddity: reducing complexity by simple oddity and "most different" strategies

Children aged between 3 and 7 years were taught simple and dimension-abstracted oddity discrimination using learning-set training techniques, in which isomorphic problems with varying content were presented with verbal explanation and feedback. Following the training phase, simple oddity (SO), dimension-abstracted oddity with one or two irrelevant dimensions, and non-oddity (NO) tasks were presented (without feedback) to determine the basis of solution. Although dimension-abstracted oddity requires discrimination based on a stimulus that is different from the others, which are all the same as each other on the relevant dimension, this was not the major strategy. The data were more consistent with use of a simple oddity strategy by 3- to 4-year-olds, and a most different strategy by 6- to 7-year-olds. These strategies are interpreted as reducing task complexity. (C) 2002 Elsevier Science Inc. All rights reserved.

External perturbation of the trunk in standing humans differentially activates components of the medial back muscles

During voluntary arm movements, the medial back muscles are differentially active. It is not known whether differential activity also occurs when the trunk is perturbed unpredictably, when the earliest responses are initiated by short-latency spinal mechanisms rather than voluntary commands. To assess this, in unpredictable and self-initiated conditions, a weight was dropped into a bucket that was held by the standing subject (n = 7). EMG activity was recorded from the deep (Deep MF), superficial (Sup MF) and lateral (Lat MF) lumbar multifidus, the thoracic erector spinae (ES) and the biceps brachii. With unpredictable perturbations, EMG activity was first noted in the biceps brachii, then the thoracic ES, followed synchronously in the components of the multifidus. During self-initiated perturbations, background EMG in the Deep MF increased two- to threefold, and the latency of the loading response decreased in six out of the seven subjects. In Sup MF and Lat MF, this increase in background EMG was not observed, and the latency of the loading response was increased. Short-latency reflex mechanisms do not cause differential action of the medial back muscles when the trunk is loaded. However, during voluntary tasks the central nervous system exerts a 'tuned response', which involves discrete activity in the deep and superficial components of the medial lumbar muscles in a way that varies according to the biomechanical action of the muscle component.

Theory of mind and relational complexity

Cognitive complexity and control theory and relational complexity theory attribute developmental changes in theory of mind (TOM) to complexity. In 3 studies, 3-, 4-, and 5-year-olds performed TOM tasks (false belief, appearance-reality), less complex connections (Level 1 perspective-taking) tasks, and transformations tasks (understanding the effects of location changes and colored filters) with content similar to TOM. There were also predictor tasks at binary-relational and ternary-relational complexity levels, with different content. Consistent with complexity theories: (a) connections and transformations were easier and mastered earlier than TOM; (b) predictor tasks accounted for more than 80% of age-related variance in TOM; and (c) ternary-relational items accounted for TOM variance, before and after controlling for age and binary-relational items. Prediction did not require hierarchically structured predictor tasks.

Delayed traveling ionospheric disturbances, especially in equatorial regions, following geomagnetic activity

For the Western-Pacific region spread-F has been found to occur with delays after geomagnetic activity (GA) ranging from 5 to 10 days as station groups are considered from low midlatitudes to equatorial regions. The statistical (superposed-epoch) analyses also indicate that at the equator the spread-F, and therefore associated medium-scale traveling ionospheric disturbances (MS-TIDs) occur with additional delays around 16, 22 and 28 days representing a 6-day modulation of the delay period. These results are compared with similar delays, including the modulation, for D-region enhanced hydroxyl emission (Shefov, 1969). It is proposed that this similarity may be explained by MS-TIDs influencing both the F and D regions as they travel. Long delays of over 20 days are also found near the equator for airglow-measured MS-TIDs (Sobral et al., 1997). These are recorded infrequently and have equatorward motions, while normally eastward motions are measured at the equator. Also in midlatitudes D-region absorption events have been shown (statistically) to have similar long delays after GA. It is suggested that atmospheric gravity waves and associated MS-TIDs may be generated by some of the precipitations responsible for the absorption. The recording of the delayed spread-F events depends on the GA being well below the average levels around sunset on the nights of recording. This implies that lower upper-atmosphere neutral particle densities are necessary.

Proteome analysis of extracellular proteins regulated by the las and rhl quorum sensing systems in Pseudomonas aeruginosa PAO1

The las and rhl quorum sensing (QS) systems regulate the expression of several genes in response to cell density changes in Pseudomonas aeruginosa. Many of these genes encode surface-associated or secreted virulence factors. Proteins from stationary phase culture supernatants were collected from wild-type and P. aeruginosa PAO1 mutants deficient in one or more of the lasRI, rhIRI and vfr genes and analysed using two-dimensional gel electrophoresis. All mutants released significantly lower amounts of protein than the wild-type. Protein spot patterns from each strain were compared using image analysis and visible spot differences were identified using mass spectrometry. Several previously unknown OS-regulated proteins were characterized, including an aminopeptidase (PA2939), an endoproteinase (PrpL) and a unique 'hypothetical' protein (PA0572), which could not be detected in the culture supernatants of Delta/as mutants, although they were unaffected in Deltarhl mutants. Chitin-binding protein (CbpD) and a hypothetical protein (PA4944) with similarity to host factor I (HF-1) could not be detected when any of the lasRI or rhIRI genes were disrupted. Fourteen proteins were present at significantly greater levels in the culture supernatants of OS mutants, suggesting that QS may also negatively control the expression of some genes. Increased levels of two-partner secretion exoproteins (PA0041 and PA4625) were observed and may be linked to increased stability of their cognate transporters in a CS-defective background. Known QS-regulated extracellular proteins, including elastase (lasB), LasA protease (lasA) and alkaline metalloproteinase (aprA) were also detected.

The threat of predictable and unpredictable pain: Differential effects on central nervous system processing?

Central nervous system performance is disrupted by pain and by the threat of pain. It is not known whether disruption caused by the threat of pain is dependent on the likelihood of pain occurring. We hypothesised that when a painful stimulus is possible but unpredictable central nervous system performance is reduced, but when the pain is predictable and unavoidable it is not. Sixteen healthy subjects performed a reaction time task during predictable and unpredictable conditions (100% and 50% probability of pain, respectively). Group data showed increased reaction time with the threat of pain by 50 ms (95% Cl 16 to 83 ms) for the predictable condition and 46 ms (95% CI 12 to 80 ms) for the unpredictable condition (p < 0.01 for both), but there was no difference between predictable and unpredictable conditions (p = 0.41). However, individual data showed that there was a differential effect in 75% of subjects (p < 0.05 for all) and that there was a greater effect of predictable pain for some subjects and a greater effect of unpredictable pain for others. Reaction time was related to reported anxiety (r = 0.49, p = 0.02 for both conditions). The predictability of a painful stimulus may have a differential effect on central nervous system performance within individuals, but anxiety about the impending pain appears to be important in determining this effect.

More maximal arcs in Desarguesian projective planes and their geometric structure

In a previous paper R. Mathon gave a new construction method for maximal arcs in finite Desarguesian projective planes via closed sets of conics, as well as giving many new examples of maximal arcs. In the current paper, new classes of maximal arcs are constructed, and it is shown that every maximal arc so constructed gives rise to an infinite class of maximal arcs. Apart from when they are of Denniston type or dual hyperovals, closed sets of conics are shown to give maximal arcs that are not isomorphic to the known constructions. An easy characterisation of when a closed set of conics is of Denniston type is given. Results on the geometric structure of the maximal arcs and their duals are proved, as well as on elements of their collineation stabilisers.

First report of three Kudoa species from Eastern Australia: Kudoa thyrsites from Mahi mahi (Coryphaena hippurus), Kudoa amamiensis and Kudoa minithyrsites n. sp. from sweeper (Pempheris ypsilychnus)

Fish species around the world are parasitized by myxozoans of the genus Kudoa, several of which infect and cause damage of commercial importance. In particular, Kudoa thyrsites and Kudoa amamiensis infect certain cultured fish species causing damage to muscle tissue, making the fish unmarketable. Kudoa thyrsites has a broad host and geographic range infecting over 35 different fish species worldwide, while K. amamiensis has only been reported from a few species in Japanese waters. Through morphological and molecular analyses we have confirmed the presence of both of these parasites in eastern Australian waters. In addition, a novel Kudoa species was identified, having stellate spores, with one polar capsule larger than the other three. The SSU rDNA sequence of this parasite was 1.5% different from K. thyrsites and is an outlier from K. thyrsites representatives in a phylogenetic analysis. Furthermore, the spores of this parasite are distinctly smaller than those of K. thyrsites, and thus it is described as Kudoa minithyrsites n. sp. Although the potential effects of K. minithyrsites n. sp. on its fish hosts are unknown, both K. thyrsites and K. amamiensis are associated with flesh quality problems in some cultured species and may be potential threats to an expanding aquaculture industry in Australia.

Microcanonical temperature for a classical field: Application to Bose-Einstein condensation

We show that the projected Gross-Pitaevskii equation (PGPE) can be mapped exactly onto Hamilton's equations of motion for classical position and momentum variables. Making use of this mapping, we adapt techniques developed in statistical mechanics to calculate the temperature and chemical potential of a classical Bose field in the microcanonical ensemble. We apply the method to simulations of the PGPE, which can be used to represent the highly occupied modes of Bose condensed gases at finite temperature. The method is rigorous, valid beyond the realms of perturbation theory, and agrees with an earlier method of temperature measurement for the same system. Using this method we show that the critical temperature for condensation in a homogeneous Bose gas on a lattice with a uv cutoff increases with the interaction strength. We discuss how to determine the temperature shift for the Bose gas in the continuum limit using this type of calculation, and obtain a result in agreement with more sophisticated Monte Carlo simulations. We also consider the behavior of the specific heat.