Solution conformations of unmodified and A(37)N(6)-dimethylallyl modified anticodon stem-loops of Escherichia coli tRNA(Phe)

The modification of RNA nucleotide bases, a fundamental process in all cells, alters the chemical and physical properties of RNA molecules and broadly impacts the physiological properties of cells. tRNA molecules are by far the most diverse-modified RNA species within cells, containing as a group >80% of the known 96 chemically unique nucleic acid modifications. The greatest varieties of modifications are located on residue 37 and play a role in ensuring fidelity and efficiency of protein synthesis. The enzyme dimethylallyl (Delta(2)-isopentenyl) diphosphate:tRNA transferase catalyzes the addition of a dimethylallyl group to the exocyclic amine nitrogen (N6) of A(37) in several tRNA species. Using a 17 residue oligoribonucleotide corresponding to the anticodon arm of Escherichia coli tRNA(Phe), we have investigated the structural and dynamic changes introduced by the dimethylallyl group. The unmodified RNA molecule adopts stem-loop conformation composed of seven base-pairs and a compact three nucleotide loop. This conformation is distinctly different from the U-turn motif that characterizes the anticodon arm in the X-ray crystal structure of the fully modified yeast tRNA(Phe). The adoption of the tri-nucleotide loop by the purine-rich unmodified tRNA(Phe) anticodon arm suggests that other anticodon sequences, especially those containing pyrimidine bases, also may favor a tri-loop conformation. Introduction of the dimethylallyl modification increases the mobility of nucleotides of the loop region but does not dramatically alter the RNA conformation. The dimethylallyl modification may enhance ribosome binding through multiple mechanisms including destabilization of the closed anticodon loop and stabilization of the codon-anticodon helix.     

Non-linear dynamics models characterizing long-term virological data from AIDS clinical trials

Human immunodeficiency virus (HIV) dynamics represent a complicated variant of the text-book case of non-linear dynamics: predator-prey interaction. The interaction can be described as naturally reproducing T-cells (prey) hunted and killed by virus (predator). Virus reproduce and increase in number as a consequence of successful predation; this is countered by the production of T-cells and the reaction of the immune system. Multi-drug anti-HIV therapy attempts to alter the natural dynamics of the predator-prey interaction by decreasing the reproductive capability of the virus and hence predation. These dynamics are further complicated by varying compliance to treatment and insurgence of resistance to treatment. When following the temporal progression of viral load in plasma during therapy one observes a short-term (1-12 weeks) decrease in viral load. In the long-term (more than 12 weeks from the beginning of therapy) the reduction in viral load is either sustained, or it is followed by a rebound, oscillations and a new (generally lower than at the beginning of therapy) viral load level. Biomathematicians have investigated these dynamics by means of simulations. However the estimation of the parameters associated with the dynamics from real data has been mostly limited to the case of simplified, in particular linearized, models. Linearized model can only describe the short-term changes of viral load during therapy and can only predict (apparent) suppression. In this paper we put forward relatively simple models to characterize long-term virus dynamics which can incorporate different factors associated with resurgence: (Fl) the intrinsic non-linear HIV-1 dynamics, (F2) drug exposure and in particular compliance to treatment, and (F3) insurgence of resistant HIV-1 strains. The main goal is to obtain models which are mathematically identifiable given only measurements of viral load, while retaining the most crucial features of HIV dynamics. For the purpose of illustration we demonstrate an application of the models using real AIDS clinical trial data involving patients treated with a combination of anti-retroviral agents using a model which incorporates compliance data.     

Eukaryotic cell locomotion depends on the propagation of self-organized reaction-diffusion waves and oscillations of actin filament assembly

Actin filament (F-actin) assembly kinetics determines the locomotion and shape of crawling eukaryotic cells, but the nature of these kinetics and their determining reactions are unclear. Live BHK21 fibroblasts, mouse melanoma cells, and Dictyostelium amoebae, locomoting on glass and expressing Green Fluorescent Protein-actin fusion proteins, were examined by confocal microscopy. The cells demonstrated three-dimensional bands of F-actin, which propagated throughout the cytoplasm at rates usually ranging between 2 and 5 microm/min in each cell type and produced lamellipodia or pseudopodia at the cell boundary. F-actin's dynamic behavior and supramolecular spatial patterns resembled in detail self-organized chemical waves in dissipative, physico-chemical systems. On this basis, the present observations provide the first evidence of self-organized, and probably autocatalytic, chemical reaction-diffusion waves of reversible actin filament assembly in vertebrate cells and a comprehensive record of wave and locomotory dynamics in vegetative-stage Dictyostelium cells. The intensity and frequency of F-actin wavefronts determine locomotory cell projections and the rotating oscillatory waves, which structure the cell surface. F-actin assembly waves thus provide a fundamental, deterministic, and nonlinear mechanism of cell locomotion and shape, which complements mechanisms based exclusively on stochastic molecular reaction kinetics.     

Studies on functional response and prey selection using zooplankton in the anostracan Chirocephalus diaphanus Prevost, 1803

Freshwater cladocerans and rotifers were used as prey to study functional response and prey selection by adult females of Chirocephalus diaphanus under laboratory conditions. For functional response studies, we offered three rotifer species (Brachionus calyciflorus, B. patulus and Euchlanis dilatata) and three cladoceran species (Alona rectangula, Ceriodaphnia dubia and Moina macrocopa) at various densities ranging from 0.5 to 16 ind. ml^–1. We found increased zooplankton consumption with increasing prey density but beyond 4 ind ml^–1 cladocerans and 8 ind. ml^–1 rotifers, the number of animals eaten plateaued. In general, C. diaphanus consumed fewer large prey (cladocerans) and many more smaller zooplankton (rotifers). For prey selection experiments, we used B. calyciflrous, B. patulus, C. dubia and M. macrocopa, offered at the ratio of two rotifers: one cladoceran and at three prey densities (total zooplankton numbers: 3, 6 and 12 ind. ml^–1). Prey selectivity patterns followed the functional response trends. In general, regardless of prey types, with an increase in the available zooplankton, there was an increase in the number of prey consumed. At any given prey density, C. diaphanus consumed higher numbers of rotifers than cladocerans. Among the prey offered, B. patulus and M. macrocopa were positively selected. Results are discussed in light of possible control of zooplankton by anostracans in temporary ponds.     

NMR solution structure and dynamics of motilin in isotropic phospholipid bicellar solution

The structure and dynamics of the gastrointestinal peptide hormone motilin, consisting of 22 amino acid residues, have been studied in the presence of isotropic q=0.5 phospholipid bicelles. The NMR solution structure of the peptide in acidic bicelle solution was determined from 203 NOE-derived distance constraints and six backbone torsion angle constraints. Dynamic properties for the ¹³C-¹H vector in Leu10 were determined for motilin specifically labeled with ¹³C at this position by analysis of multiple-field relaxation data. The structure reveals an ordered -helical conformation between Glu9 and Lys20. The N-terminus is also well structured with a turn resembling that of a classical -turn. The ¹³C dynamics clearly show that motilin tumbles slowly in solution, with a correlation time characteristic of a large object. It was also found that motilin has a large degree of local flexibility as compared with what has previously been reported in SDS micelles. The results show that motilin interacts with the bicelle, displaying motional properties of a peptide bound to a membrane. In comparison, motilin in neutral bicelles seems less structured and more flexible. This study shows that the small isotropic bicelles are well suited for use as membrane-mimetic for structural as well as dynamical investigations of membrane-bound peptides by high-resolution NMR.     

Metazoan motor models: kinesin superfamily in C. elegans

In eukaryotic cells members of the kinesin family mediate intracellular transport by carrying cellular cargo on microtubule tracks. The nematode Caenorhabditis elegans genome encodes 21 members of the kinesin family, which show significant homology to their mammalian orthologs. Based on motor domain sequence homology and placement of the motor domain in the protein, the C. elegans kinesins have been placed in eight distinct groups; members of which participate in embryonic development, protein transport, synaptic membrane vesicles movement and in the axonal growth. Among 21 kinesins, at least 11 play a central role in spindle movement and chromosomal segregation. Understanding the function of C. elegans kinesins and related proteins may help navigate through the intricacies of intracellular traffic in a simple animal.     

Phytoseiid predators suppress populations of Bemisia tabaci on cucumber plants with alternative food

Phytoseiids are known to attack whiteflies, but it is an open question whether they can be used for biological control of these pest insects. Preselection experiments in the laboratory showed that two out of five phytoseiid species tested, Euseius scutalis and Typhlodromips swirskii, stood out in terms of their ability to develop and reproduce on a diet of Bemisia tabaci immatures. In this paper, we show that both predators are able to suppress whitefly populations on isolated cucumber plants in a greenhouse. Predatory mites were released 2 weeks in advance of the release of B. tabaci. To enable their survival and promote their population growth, they were provided weekly with alternative food, that is, Typha sp. pollen. A few weeks after whitefly introduction, the numbers of adult whiteflies on plants with predators were consistently lower than on plants without predators, where B. tabaci populations grew exponentially. After 9 weeks, this amounted to a 16- to 21-fold difference in adult whitefly population size. This shows that the two phytoseiid species are promising biocontrol agents of B. tabaci on greenhouse cucumber. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation

Photoactive yellow protein (PYP) is a prototype of the PAS domain superfamily of signaling proteins. The signaling process is coupled to a three-state photocycle. After the photoinduced trans-cis isomerization of the chromophore, 4-hydroxycinnamic acid (pCA), an early intermediate (pR) is formed, which proceeds to a second intermediate state (pB) on a sub-millisecond time scale. The signaling process is thought to be connected to the conformational changes upon the formation of pB and its recovery to the ground state (pG), but the exact signaling mechanism is not known. Experimental studies of PYP by solution NMR and X-ray crystallography suggest a very flexible protein backbone in the ground as well as in the signaling state. The relaxation from the pR to the pB state is accompanied by the protonation of the chromophore's phenoxyl group. This was found to be of crucial importance for the relaxation process. With the goal of gaining a better understanding of these experimental observations on an atomistic level, we performed five MD simulations on the three different states of PYP: a 1 ns simulation of PYP in its ground state [pG(MD)], a 1 ns simulation of the pR state [pR(MD)], a 2 ns simulation of the pR state with the chromophore protonated (pRprot), a 2 ns simulation of the pR state with Glu46 exchanged by Gln (pRGln) and a 2 ns simulation of PYP in its signaling state [pB(MD)]. Comparison of the pG simulation results with X-ray and NMR data, and with the results obtained for the pB simulation, confirmed the experimental observations of a rather flexible protein backbone and conformational changes during the recovery of the pG from the pB state. The conformational changes in the region around the chromophore pocket in the pR state were found to be crucially dependent on the strength of the Glu46-pCA hydrogen bond, which restricts the mobility of the chromophore in its unprotonated form considerably. Both the mutation of Glu46 with Gln and the protonation of the chromophore weaken this hydrogen bond, leading to an increased mobility of pCA and large structural changes in its surroundings. These changes, however, differ considerably during the pRGln and pRprot simulations, providing an atomistic explanation for the enhancement of the rate constant in the Gln46 mutant. Electronic supplementary material to this article is available at and is accessible for athorized users. Electronic Publication     

Transmission dynamics of lymphatic filariasis: density-dependence in the uptake of Wuchereria bancrofti microfilariae by vector mosquitoes

Gaining a better understanding of parasite infection dynamics in the vector mosquito (Diptera: Culicidae) population is central to improving knowledge regarding the transmission, persistence and hence control of lymphatic filariasis. Here, we use data on mosquito feeding experiments collated from the published literature to examine the available evidence regarding the functional form of the first component of this parasite-vector relationship for Wuchereria bancrofti (Filarioidea: Onchocercidae) causing Bancroftian filariasis, i.e. the rate of microfilariae (mf) uptake from the blood of infected humans by the feeding mosquito vector. Using a simple logarithmic regression model for describing the observed relationships between the mean numbers of mf ingested per mosquito and parasite load in humans in each study, and a linear mixed-effects meta-analytical framework for synthesizing the observed regressions across studies, we show here for the first time clear evidence for the existence of density-dependence in this process for all the three major filariasis transmitting mosquito vectors. An important finding of this study is that this regulation of mf uptake also varies significantly between the vector genera, being weakest in Culex, comparatively stronger in Aedes and most severe and occurring at significantly lower human mf loads in Anopheles mosquitoes. The analysis of the corresponding mf uptake prevalence data has further highlighted how density-dependence in mf uptake may influence the observed distributions of mf in vector populations. These results show that whereas strong regulation of mf uptake, especially when it leads to saturation in uptake at low human parasite intensities, can lead to static distributions of mf per mosquito with host parasite intensity, a weaker regulation of mf ingestion can give rise to changes in both mean mf loads and in the frequency distribution of parasites/mosquito with increasing human parasite intensity. These findings highlight the importance of considering local vector infection dynamics when attempting to predict the impacts of community-based filariasis control. They also emphasize the value of developing and applying robust meta-analytic methods for estimating functional relationships regarding parasitic infection from population ecological data.     

How do Rho family GTPases direct axon growth and guidance? A proposal relating signaling pathways to growth cone mechanics

For a neuron to play its assigned role in a neural circuit, it has to extend elaborate projections, dendrites and axons, to make precise connections with specific target cells. The past decade has seen the identification of a vast diversity of molecules that assist in the guidance of axons toward their intended targets: guidance cues, growth cone receptors, signaling proteins (Tessier-Lavigne and Goodman, 1996; Song and Poo, 2001). But just how do all of these proteins work together to cause the axon to grow, stop, or turn in a specific direction? In this review, we examine this process from several different perspectives - cytoskeletal dynamics; biochemistry of intracellular signaling proteins; molecular analysis of axon guidance receptors - to try to collapse some of the apparent complexity of axon guidance into a more coherent picture. In particular, we will see how relatively simple and consistent manipulations of the kinetic constants of Rho family GTPases could account for many aspects of the cycle of actin dynamics that underlies axon growth and guidance. This review will intentionally be highly selective in its treatment of this subject in order to synthesize a simplified view that may be of value in directing further thinking and experiments.