A new level of conotoxin diversity, a non-native disulfide bond connectivity in alpha-conotoxin AuIB reduces structural definition but increases biological activity

alpha-Conotoxin AuIB and a disulfide bond variant of AuIB have been synthesized to determine the role of disulfide bond connectivity on structure and activity. Both of these peptides contain the 15 amino acid sequence GCCSYPPCFATNPDC, with the globular (native) isomer having the disulfide connectivity Cys(2-8 and 3-15) and the ribbon isomer having the disulfide connectivity Cys(2-15 and 3-8). The solution structures of the peptides were determined by NAIR spectroscopy, and their ability to block the nicotinic acetylcholine receptors on dissociated neurons of the rat parasympathetic ganglia was examined. The ribbon disulfide isomer, although having a less well defined structure, is surprisingly found to have approximately 10 times greater potency than the native peptide. To our knowledge this is the first demonstration of a non-native disulfide bond isomer of a conotoxin exhibiting greater biological activity than the native isomer.

The structural and functional diversity of naturally occurring antimicrobial peptides

Antimicrobial peptides occur in a diverse range of organisms from microorganisms to insects, plants and animals. Although they all have the common function of inhibiting or killing invading microorganisms they achieve this function using an extremely diverse range of structural motifs. Their sizes range from approximately 10-90 amino acids. Most carry an overall positive charge, reflecting a preferred mode of electrostatic interaction with negatively charged microbial membranes. This article describes the structural diversity of a representative set of antimicrobial peptides divided into five structural classes: those with agr-helical structure, those with bgr-sheet structure, those with mixed helical / bgr- sheet structure, those with irregular structure, and those incorporating a macrocyclic structure. There is a significant diversity in both the size and charge of molecules within each of these classes and between the classes. The common feature of their three-dimensional structures is, however, that they have a degree of amphipathic character in which there is separate localisation of hydrophobic regions and positively charged regions. An emerging trend amongst antimicrobial proteins is the discovery of more macrocyclic analogues. Cyclisation appears to impart an additional degree of stability on these molecules and minimizes proteolytic cleavage. In conclusion, there appear to be a number of promising opportunities for the development of novel clinically useful antimicrobial peptides based on knowledge of the structures of naturally occurring antimicrobial molecules.

Synthesis and structural analysis of the N-terminal domain of the thyroid hormone-binding protein transthyretin

Transthyretin (TTR) is a 55 kDa protein responsible for the transport of thyroid hormones and retinol in human serum. Misfolded forms of the protein are implicated in the amyloid diseases familial amyloidotic polyneuropathy and senile systemic amyloidosis. Its folding properties and stabilization by ligands are of current interest due to their importance in understanding and combating these diseases. To assist in such studies we developed a method for the solid phase synthesis of the monomeric unit of a TTR analogue and its folding to form a functional 55 kDa tetramer. The monomeric unit of the protein was chemically synthesized in three parts, comprising amino acid residues 151, 5499 and 102127, and ligated using chemoselective thioether ligation chemistry. The synthetic protein was folded and assembled to a tetrameric structure in the presence of the TTRs native ligand, thyroxine, as shown by gel filtration chromatography, native gel electrophoresis, TTR antibody recognition and thyroid hormone binding. In the current study the solution structure of the first of these fragment peptides, TTR(151) is examined to determine its intrinsic propensity to form beta-sheet structure, potentially involved in amyloid fibril formation by TTR. Despite the presence of extensive beta-structure in the native form of the protein, the Nterminal fragment adopts an essentially random coil conformation in solution.

Fitting genetic models to twin data with binary and ordered categorical responses: A comparison of structural equation modelling and Bayesian hierarchical models

We compare Bayesian methodology utilizing free-ware BUGS (Bayesian Inference Using Gibbs Sampling) with the traditional structural equation modelling approach based on another free-ware package, Mx. Dichotomous and ordinal (three category) twin data were simulated according to different additive genetic and common environment models for phenotypic variation. Practical issues are discussed in using Gibbs sampling as implemented by BUGS to fit subject-specific Bayesian generalized linear models, where the components of variation may be estimated directly. The simulation study (based on 2000 twin pairs) indicated that there is a consistent advantage in using the Bayesian method to detect a correct model under certain specifications of additive genetics and common environmental effects. For binary data, both methods had difficulty in detecting the correct model when the additive genetic effect was low (between 10 and 20%) or of moderate range (between 20 and 40%). Furthermore, neither method could adequately detect a correct model that included a modest common environmental effect (20%) even when the additive genetic effect was large (50%). Power was significantly improved with ordinal data for most scenarios, except for the case of low heritability under a true ACE model. We illustrate and compare both methods using data from 1239 twin pairs over the age of 50 years, who were registered with the Australian National Health and Medical Research Council Twin Registry (ATR) and presented symptoms associated with osteoarthritis occurring in joints of the hand.

A structural basis for the selection of dominant alpha beta T cell receptors in antiviral immunity

We have examined the basis for immunodominant or public TCR usage in an antiviral CTL response. Residues encoded by each of the highly selected genetic elements of an immunodominant clonotype recognizing Epstein-Barr virus were critical to the antigen specificity of the receptor. Upon recognizing antigen the immunodominant TCR undergoes extensive conformational changes in the complementarity determining regions (CDRs), including the disruption of the canonical structures of the germline-encoded CDR1alpha and CDR2alpha loops to produce an enhanced fit with the HLA-peptide complex. TCR ligation induces conformational changes in the TCRalpha constant domain thought to form part of the docking site for CD3epsilon. These findings indicate that TCR immunodominance is associated with structural properties conferring receptor specificity and suggest a novel structural link between TCR ligation and intracellular signaling.

Exact results for a tunnel-coupled pair of trapped Bose-Einstein condensates

A model describing coherent quantum tunnelling between two trapped Bose-Einstein condensates is discussed. It is not well known that the model admits an exact solution, obtained some time ago, with the energy spectrum derived through the algebraic Bethe ansatz. An asymptotic analysis of the Bethe ansatz equations leads us to explicit expressions for the energies of the ground and the first excited states in the limit of weak tunnelling and all energies for strong tunnelling. The results are used to extract the asymptotic limits of the quantum fluctuations of the boson number difference between the two Bose-Einstein condensates and to characterize the degree of coherence in the system.

Dynamics of Gray Matter Loss in Alzheimer's Disease

We detected and mapped a dynamically spreading wave of gray matter loss in the brains of patients with Alzheimer's disease (AD). The loss pattern was visualized in four dimensions as it spread over time from temporal and limbic cortices into frontal and occipital brain regions, sparing sensorimotor cortices. The shifting deficits were asymmetric (left hemisphere >right hemisphere) and correlated with progressively declining cognitive status ( p 15% loss). The maps distinguished different phases of AD and differentiated AD from normal aging. Local gray matter loss rates (5.3 +/- 2.3% per year in AD v 0.9 +/- 0.9% per year in controls) were faster in the left hemisphere ( p < 0.029) than the right. Transient barriers to disease progression appeared at limbic/frontal boundaries. This degenerative sequence, observed in vivo as it developed, provides the first quantitative, dynamic visualization of cortical atrophic rates in normal elderly populations and in those with dementia.

The trans-membrane protein p25 forms highly specialized domains that regulate membrane composition and dynamics

Trans-membrane proteins of the p24 family are abundant, oligomeric proteins predominantly found in cis-Golgi membranes. They are not easily studied in vivo and their functions are controversial. We found that p25 can be targeted to the plasma membrane after inactivation of its canonical KKXX motif (KK to SS, p25SS), and that p25SS causes the co-transport of other p24 proteins beyond the Golgi complex, indicating that wild-type p25 plays a crucial role in retaining p24 proteins in cis-Golgi membranes. We then made use of these observations to study the intrinsic properties of these proteins, when present in a different membrane context. At the cell surface, the p25SS mutant segregates away from both the transferrin receptor and markers of lipid rafts, which are enriched in cholesterol and glycosphingolipids. This suggests that p25SS localizes to, or contributes to form, specialized membrane domains, presumably corresponding to oligomers of p25SS and other p24 proteins. Once at the cell surface, p25SS is endocytosed, together with other p24 proteins, and eventually accumulates in late endosomes, where it remains confined to well-defined membrane regions visible by electron microscopy. We find that this p25SS accumulation causes a concomitant accumulation of cholesterol in late endosomes, and an inhibition of their motility - two processes that are functionally linked. Yet, the p25SS-rich regions themselves seem to-exclude not only Lamp1 but also accumulated cholesterol. One may envision that p25SS accumulation, by excluding cholesterol from oligomers, eventually overloads neighboring late endosomal membranes with cholesterol beyond their capacity (see Discussion). In any case, our data show that p25 and presumably other p24 proteins are endowed with the intrinsic capacity to form highly specialized domains that control membrane composition and dynamics. We propose that p25 and other p24 proteins control the fidelity of membrane transport by maintaining cholesterol-poor membranes in the Golgi complex.

Learning the dynamics of embedded clauses

Recent work by Siegelmann has shown that the computational power of recurrent neural networks matches that of Turing Machines. One important implication is that complex language classes (infinite languages with embedded clauses) can be represented in neural networks. Proofs are based on a fractal encoding of states to simulate the memory and operations of stacks. In the present work, it is shown that similar stack-like dynamics can be learned in recurrent neural networks from simple sequence prediction tasks. Two main types of network solutions are found and described qualitatively as dynamical systems: damped oscillation and entangled spiraling around fixed points. The potential and limitations of each solution type are established in terms of generalization on two different context-free languages. Both solution types constitute novel stack implementations - generally in line with Siegelmann's theoretical work - which supply insights into how embedded structures of languages can be handled in analog hardware.

Physicochemical and structural characterization of mesoporous aluminosilicates synthesized from leached saponite with additional aluminum incorporation

A thorough investigation was performed on the physical (mechanical, thermal, and hydrothermal stability) and chemical (ion exchange capacity and silanol number) characteristics of aluminosilicate FSMs, synthesized via a new successful short-time synthesis route using leached saponite and a low concentration of CTAB. Moreover, the influence of an additional Al incorporation, utilizing different aluminum sources, on the structure of the FSM derived from saponite is studied. A mesoporous aluminosilicate with a low Si/Al ratio of 12.8 is synthesized, and still has a very large surface area of 1130 m(2)/g and pore volume of 0.92 cm(3)/g. The aluminum-containing samples all have a high cation exchange capacity of around 1 mmol/9 while they still have a silanol number of about 0.9 OH/nm(2); both characteristics being interesting for high-yield postsynthesis modification reactions. Finally, a study is performed on the transformation of the aluminosilicates into their Bronsted acid form via the exchange with ammonium ions and a consecutive heat treatment.

Influence of hysteresis on tidal capillary fringe dynamics in a well-sorted sand

Nielsen and Perrochet [Adv. Water Resour. 23 (2000) 503] presented experimental data for cyclic water movement in the vadose zone above an oscillating watertable. The response of the watertable to cyclic forcing was characterised by the ratios of the forcing head to watertable amplitudes and their associated phase lag. They found that their non-hysteretic Richards' equation model failed to represent the observed behaviour of these parameters. This paper explores the effect on the simulated capillary fringe dynamics (in terms of these parameters) of including varying degrees of hysteresis in the moisture retention curve used in a numerical model of their experiment. It is clear that hysteresis can indeed account for observed discrepancies between simulation and experiment and that the effect of hysteresis varies with the frequency of oscillation. The use of a single-valued mean retention curve, as advocated by some authors, fails to provide a match between the simulated and observed behaviour of the Nielsen and Perrochet parameters, but is shown to be adequate for predicting time-averaged soil moisture profiles. (C) 2003 Elsevier Ltd. All rights reserved.

Impacts of structural characteristics on activated sludge floc stability

Activated sludge samples from seven full-scale plants were investigated in order to determine the relationship between floc structure and floc stability. Floc stability was determined by shear sensitivity and floc strength. Floc structure was considered in terms of two size scales, the micro- and macrostructure. The microstructure refers to the organization of the floc components, such as the individual microorganisms. The macrostructure refers to the overall floc. The floc macrostructure was characterized by filament index, sludge volume index, size, and fractal dimension. It had a significant impact on floc stability. Large and open floes with low fractal dimensions containing large number of filaments were more shear sensitive and had lower floc strength compared to small and dense floes. Fluorescent in situ hybridization analysis indicated that the organization of the bacterial cells might also have an effect on the floc stability. (C) 2003 Elsevier Ltd. All rights reserved.

Insights into the structural basis for zinc inhibition of the glycine receptor

Histidines 107 and 109 in the glycine receptor ( GlyR) alpha(1) subunit have previously been identified as determinants of the inhibitory zinc-binding site. Based on modeling of the GlyR alpha(1) subunit extracellular domain by homology to the acetylcholine-binding protein crystal structure, we hypothesized that inhibitory zinc is bound within the vestibule lumen at subunit interfaces, where it is ligated by His(107) from one subunit and His(109) from an adjacent subunit. This was tested by co-expressing alpha(1) subunits containing the H107A mutation with alpha(1) subunits containing the H109A mutation. Although sensitivity to zinc inhibition is markedly reduced when either mutation is individually incorporated into all five subunits, the GlyRs formed by the co-expression of H107A mutant subunits with H109A mutant subunits exhibited an inhibitory zinc sensitivity similar to that of the wild type alpha(1) homomeric GlyR. This constitutes strong evidence that inhibitory zinc is coordinated at the interface between adjacent alpha(1) subunits. No evidence was found for beta subunit involvement in the coordination of inhibitory zinc, indicating that a maximum of two zinc-binding sites per alpha(1)beta receptor is sufficient for maximal zinc inhibition. Our data also show that two zinc-binding sites are sufficient for significant inhibition of alpha(1) homomers. The binding of zinc at the interface between adjacent alpha(1) subunits could restrict intersubunit movements, providing a feasible mechanism for the inhibition of channel activation by zinc.

Genotype and environment effects on dynamics of harvest index during grain filling in sorghum

An approach based on a linear rate of increase in harvest index (141) with time after anthesis has been used as a simple means-to predict grain growth and yield in many crop simulation models. When applied to diverse situations, however, this approach has been found to introduce significant error in grain yield predictions. Accordingly, this study was undertaken to examine the stability of the HI approach for yield prediction in sorghum [Sorghum bicolor (L.) Moench]. Four field experiments were conducted under nonlimiting water. and N conditions. The experiments were sown at times that ensured a broad range in temperature and radiation conditions. Treatments consisted of two population densities and three genotypes varying in maturity. Frequent sequential harvests were used to monitor crop growth, yield, and the dynamics of 111. Experiments varied greatly in yield and final HI. There was also a tendency for lower HI with later maturity. Harvest index dynamics also varied among experiments and, to a lesser extent, among treatments within experiments. The variation was associated mostly with the linear rate of increase in HI and timing of cessation of that increase. The average rate of HI increase was 0.0198 d(-1), but this was reduced considerably (0.0147) in one experiment that matured in cool conditions. The variations found in IN dynamics could be largely explained by differences in assimilation during grain filling and remobilization of preanthesis assimilate. We concluded that this level of variation in HI dynamics limited the general applicability of the HI approach in yield prediction and suggested a potential alternative for testing.

SPAnDX: a process-based population dynamics model to explore management and climate change impacts on an invasive alien plant, Acacia nilotica

This paper describes a process-based metapopulation dynamics and phenology model of prickly acacia, Acacia nilotica, an invasive alien species in Australia. The model, SPAnDX, describes the interactions between riparian and upland sub-populations of A. nilotica within livestock paddocks, including the effects of extrinsic factors such as temperature, soil moisture availability and atmospheric concentrations of carbon dioxide. The model includes the effects of management events such as changing the livestock species or stocking rate, applying fire, and herbicide application. The predicted population behaviour of A. nilotica was sensitive to climate. Using 35 years daily weather datasets for five representative sites spanning the range of conditions that A. nilotica is found in Australia, the model predicted biomass levels that closely accord with expected values at each site. SPAnDX can be used as a decision-support tool in integrated weed management, and to explore the sensitivity of cultural management practices to climate change throughout the range of A. nilotica. The cohort-based DYMEX modelling package used to build and run SPAnDX provided several advantages over more traditional population modelling approaches (e.g. an appropriate specific formalism (discrete time, cohort-based, process-oriented), user-friendly graphical environment, extensible library of reusable components, and useful and flexible input/output support framework). (C) 2003 Published by Elsevier Science B.V.