Self-organized intracellular twisters

Life in complex systems, such as cities and organisms, comes to a standstill when global coordination of mass, energy, and information flows is disrupted. Global coordination is no less important in single cells, especially in large oocytes and newly formed embryos, which commonly use fast fluid flows for dynamic reorganization of their cytoplasm. Here, we combine theory, computing, and imaging to investigate such flows in the Drosophila oocyte, where streaming has been proposed to spontaneously arise from hydrodynamic interactions among cortically anchored microtubules loaded with cargo-carrying molecular motors. We use a fast, accurate, and scalable numerical approach to investigate fluid-structure interactions of 1000s of flexible fibers and demonstrate the robust emergence and evolution of cell-spanning vortices, or twisters. Dominated by a rigid body rotation and secondary toroidal components, these flows are likely involved in rapid mixing and transport of ooplasmic components.

Self-organized intracellular twisters

Life in complex systems, such as cities and organisms, comes to a standstill when global coordination of mass, energy, and information flows is disrupted. Global coordination is no less important in single cells, especially in large oocytes and newly formed embryos, which commonly use fast fluid flows for dynamic reorganization of their cytoplasm. Here, we combine theory, computing, and imaging to investigate such flows in the Drosophila oocyte, where streaming has been proposed to spontaneously arise from hydrodynamic interactions among cortically anchored microtubules loaded with cargo-carrying molecular motors. We use a fast, accurate, and scalable numerical approach to investigate fluid-structure interactions of 1000s of flexible fibers and demonstrate the robust emergence and evolution of cell-spanning vortices, or twisters. Dominated by a rigid body rotation and secondary toroidal components, these flows are likely involved in rapid mixing and transport of ooplasmic components.

The many behaviors of deformable active droplets

Active fluids consume fuel at the microscopic scale, converting this energy into forces that can drive macroscopic motions over scales far larger than their microscopic constituents. In some cases, the mechanisms that give rise to this phenomenon have been well characterized, and can explain experimentally observed behaviors in both bulk fluids and those confined in simple stationary geometries. More recently, active fluids have been encapsulated in viscous drops or elastic shells so as to interact with an outer environment or a deformable boundary. Such systems are not as well understood. In this work, we examine the behavior of droplets of an active nematic fluid. We study their linear stability about the isotropic equilibrium over a wide range of parameters, identifying regions in which different modes of instability dominate. Simulations of their full dynamics are used to identify their nonlinear behavior within each region. When a single mode dominates, the droplets behave simply: as rotors, swimmers, or extensors. When parameters are tuned so that multiple modes have nearly the same growth rate, a pantheon of modes appears, including zigzaggers, washing machines, wanderers, and pulsators.

Swirling Instability of the Microtubule Cytoskeleton

In the cellular phenomena of cytoplasmic streaming, molecular motors carrying cargo along a network of microtubules entrain the surrounding fluid. The piconewton forces produced by individual motors are sufficient to deform long microtubules, as are the collective fluid flows generated by many moving motors. Studies of streaming during oocyte development in the fruit fly Drosophila melanogaster have shown a transition from a spatially disordered cytoskeleton, supporting flows with only short-ranged correlations, to an ordered state with a cell-spanning vortical flow. To test the hypothesis that this transition is driven by fluid-structure interactions, we study a discrete-filament model and a coarse-grained continuum theory for motors moving on a deformable cytoskeleton, both of which are shown to exhibit a swirling instability to spontaneous large-scale rotational motion, as observed.

Stoichiometric interactions explain spindle dynamics and scaling across 100 million years of nematode evolution

The spindle shows remarkable diversity, and changes in an integrated fashion, as cells vary over evolution. Here, we provide a mechanistic explanation for variations in the first mitotic spindle in nematodes. We used a combination of quantitative genetics and biophysics to rule out broad classes of models of the regulation of spindle length and dynamics, and to establish the importance of a balance of cortical pulling forces acting in different directions. These experiments led us to construct a model of cortical pulling forces in which the stoichiometric interactions of microtubules and force generators (each force generator can bind only one microtubule), is key to explaining the dynamics of spindle positioning and elongation, and spindle final length and scaling with cell size. This model accounts for variations in all the spindle traits we studied here, both within species and across nematode species spanning over 100 million years of evolution.

Rotating Membrane Inclusions Crystallize Through Hydrodynamic and Steric Interactions

We show that rotating membrane inclusions can crystallize due to combined hydrodynamic and steric interactions. Alone, steric repulsion of unconfined particles, even with thermal fluctuations, does not lead to crystallization, nor do rotational hydrodynamic interactions which allow only a marginally stable lattice. Hydrodynamic interactions enable particles to explore states inaccessible to a nonrotational system, yet, unlike Brownian motion, Hamiltonian conservation confines the ensemble which, when combined with steric interactions, anneals into a stable crystal state.

Chloroplast DNA evolution and systematics of Phanerophlebia (Dryopteridaceae) and related fern genera

Restriction site variation in chloroplast DNA was examined in the neotropical fern genus Phanerophlebia and in selected species of the related Asiatic genus Cyrtomium and the cosmopolitan progenitor of these two, Polystichum. A total of 103 restriction site mutations was identified; these were used to construct phylogenetic networks and trees based on Wagner and Dollo parsimony and Fitch-Margoliash distance algorithms. The analyses provided evidence that Phanerophlebia did not arise from Cyrtomium. Both genera are convergent descendants from different progenitor groups in Polystichum, and Asiatic Cyrtomium is more closely related to temperate New World Polystichum than it is to neotropical Phanerophlebia. Reticulate venation, previously considered an important taxonomic character for infrageneric classification in Phanerophlebia, most likely evolved independently twice within the genus. Diploid maternal progenitors are suggested for two of four tetraploid species analyzed, and species-level distinctions for two closely related taxa of Phanerophlebia are questioned.

Tracking progress towards universal childhood immunisation and the impact of global initiatives: a systematic analysis of three-dose diphtheria, tetanus, and pertussis immunisation coverage

BACKGROUND

Substantial resources have been invested in increasing childhood immunisation coverage through global initiatives such as the Universal Childhood Immunisation (UCI) campaign and the Global Alliance on Vaccines and Immunisations (GAVI). There are longstanding concerns that target-oriented and performance-oriented initiatives such as UCI and GAVI's immunisation services support (ISS) might encourage over-reporting. We estimated the coverage of three doses of diphtheria, tetanus, and pertussis vaccine (DTP3) based on surveys using all available data.

METHODS

We estimated DTP3 coverage by analysing unit record data from surveys and supplemented this with reported coverage from other surveys and administrative data. We used bidirectional distance-dependent regression to estimate trends in survey-based coverage in 193 countries during 1986-2006. We used standard time-series cross-sectional analysis to investigate any association in the difference between countries' official reports and survey-based coverage as the dependent variable and the presence of GAVI ISS as the independent variable, controlling for country and time effects.

FINDINGS

Crude coverage of DTP3 based on surveys increased from 59% (95% uncertainty interval 51-65) in 1986 to 65% (60-68) in 1990, 70% (65-74) in 2000, and 74% (70-77) in 2006. There were substantial differences between officially reported and survey-based coverage during UCI. GAVI ISS significantly increased the difference between officially reported coverage and survey coverage. Up to 2006, in 51 countries receiving GAVI ISS payments, 7.4 million (5.7 million to 9.2 million) additional children were immunised with DTP3 based on surveys compared with officially reported estimates of 13.9 million. On the basis of the number of additional children immunised from surveys at a rate of US$20 each, GAVI ISS payments are estimated at $150 million (115 million to 184 million) compared with actual disbursements of $290 million.

INTERPRETATION

Survey-based DTP3 immunisation coverage has improved more gradually and not to the level suggested by countries' official reports or WHO and UNICEF estimates. There is an urgent need for independent and contestable monitoring of health indicators in an era of global initiatives that are target-oriented and disburse funds based on performance.

A boy who stops taking stimulants for "ADHD": commentaries on a Pediatrics case study

This article presents eight commentaries on a case study published in the journal Pediatrics in 2001. The case study, introduced in Pediatrics to highlight the issue of adolescents' compliance with drug treatment in a "high-prevalence neurobehavioral condition," briefly describes an adolescent boy who announces that he no longer needs the methylphenidate he was prescribed for ADHD and had been taking for the last five years. We invited experienced professionals from the disciplines of psychiatry, psychology, counseling, education, and occupational therapy to comment on the case and make recommendations to the adolescent boy in the case study, his family, and professionals. Their commentaries highlight issues rarely discussed in the mainstream literature, including: the extent to which ADHD is erroneously portrayed and vigorously managed as a disease; the lack of validity of the ADHD construct in adolescence; the widespread use of stimulants as performance-enhancing drugs; the need to respect an adolescent's gut instinct and developing decisions; the importance of family dynamics in ADHD-like situations; the need to ease stimulant withdrawal effects; and the human rights of children prescribed psychotropic drugs.

Structural rearrangements of the chloroplast genome provide an important phylogenetic link in ferns

The chloroplast genome of most land plants is highly conserved. In contrast, physical and gene mapping studies have revealed a highly rearranged chloroplast genome in species representing four families of ferns. In all four, there has been a rare duplication of the psbA gene and the order of the psbA, 16S, and 23S rRNA genes has been inverted. Our analysis shows that the described rearrangement results from a minimum of two inversions within the inverted repeat. This chloroplast DNA structure provides unambiguous evidence that phylogenetically links families of ferns once thought to belong to different major evolutionary lineages.

A fern spore storage protein is genetically similar to the 1.7 S seed storage protein of Brassica napus

The ostrich fern, Matteuccia struthiopteris L., contains two globulin spore storage proteins of 2.2 S and 11.3 S, with physical characteristics similar to those of seed storage proteins of Brassica napus (rapeseed) and Raphanus sativus (radish). By the use of a cloned cDNA that encodes the 1.7 S B. napus storage protein (napin), gene sequences that hybridized with napin were detected in fern nuclear DNA, and a 900-nucleotide homologous mRNA was detected in developing spores. In vitro translation of this fern mRNA produced a 22-kD polypeptide comparable in size to the 21-kD precursor polypeptide identified in Brassica. No hybridizations were observed between the Brassica 12 S clone and either fern DNA or developing spore mRNA.

The development of acetylcholinesterase activity in the embryonic nervous system of the frog, Xenopus laevis

Histochemical detection of acetylcholinesterase (AChE) activity in Xenopus embryos was found first in primary motoneurons, Rohon-Beard neurons and somitic myotubes at early tail bud stages. At late tail bud stages all primary neurons, including primary interneurons, cranial ganglion cells and ventral brainstem cells expressed this enzyme. The onset of detectable AChE activity in some primary neurons occurred near the time of initial axon outgrowth, whereas in others it occurred at much later stages. At early independent-feeding and continuous-swimming stages nearly all seemingly postmitotic neurons began to express AChE activity, and by the beginning of limb bud stages, when many secondary neuronal populations were going through their final rounds of mitosis, nearly all CNS cells outside the ventricular zone were intensely stained. Thus, the onset of detectable AChE activity in secondary neurons occurred near the time of their final mitoses. In trunk somites the enzyme activity initially was located diffusely throughout the myotube, and with progressing development it became localized to the myocommata. From the onset of AChE activity both head somites and head muscles had discrete patches of reaction product all over their surfaces. The onset of detectable AChE activity occurred in muscles near the time that they were contacted by motor axons. These data demonstrate that the primary neurons are the first to express AChE activity, and that as the secondary neurons begin to proliferate, AChE is expressed by nearly all embryonic neuronal populations.

Promotion of Stomatal Opening by Indoleacetic Acid and Ethrel in Epidermal Strips of Vicia faba L

Indole-3-acetic acid (IAA), at concentrations of 0.01 to 1.0 millimolar, and ethephon (0.3% v/v Ethrel) promote stomatal opening when applied to epidermal peels of Vicia faba L. in light or dark. The effect of ethylene is seen by 30 minutes and maximal opening (over two times that of untreated controls) occurs after only 60 to 90 minutes in the light. Stomatal opening by IAA and Ethrel in both light and dark is prevented by 0.14 millimolar AgCl. It is suggested that the effect of added IAA, but not that of light, is linked to ethylene production. The possible role of ethylene in stomatal opening during fungal infection is discussed. The stomates of Vicia faba provide a new system to study the effects of ethylene on certain membrane-regulated processes.

Nucleoprotein subunit structure in an unusual prokaryotic organism: Thermoplasma acidophilum

The freeliving thermophilic mycoplasma, Thermoplasma acidophilum, has a small acid-soluble protein tightly bound to its DNA. This protein is similar to eukaryotic histones in both size and amino acid composition. Here we report that the protein condenses DNA into globular particles that are about half the size of eukaryotic nucleosomes. Our conclusions are based primarily upon the following observations: (1) Nuclease digestion produced DNA fragments of 40 base-pairs. (2) The ratio of protein to DNA was such that 4--5 molecules of protein were associated with each 40 base-pair segment of DNA. (3) Protein crosslinking reagents produced tetramers of the histone-like protein. (4) Electron microscopy revealed globular particles 5--6 nm in diameter. (5) Each globular particle reduced the apparent contour length of the DNA by 40 base-pairs. Thus, each nucleoprotein particle is apparently composed of 40 base-pairs of DNA coiled around four molecules of proteins.

Studies on DNA sequences in the Osmundaceae

Phylogenetic relationships of Osmunda cinnamomea, O. claytoniana, and O. regalis were explored by means of DNA sequence comparisons. Hydroxyapatite thermal elution profiles of self-reassociated repetitive DNA fragments were very similar, indicating the absence of gross differences in the amount of recent amplification or addition of repetitive DNA in any of these three genomes. Interspecific DNA sequence comparisons showed, in contrast to our earlier interpretation, that repeated DNA sequences of O. claytoniana are nearly equally diverged from those of O. cinnamomea and O. regalis. Differences between repetitive sequences of the three species can be interpreted as reflecting amplification events which occurred subsequent to speciation. The data obtained suggest that the three Osmunda species most likely arose more or less simultaneously from a common ancestor. These findings were verified in experiments with tracer DNA preparations enriched for single copy sequences. On the basis of the hydridization data presented here and of the fossil record, the rate of single copy sequence divergence in the ferns is comparable to that in the primates, although slower than that observed in other animal taxa. From this first evaluation of rates of DNA evolution in plants it would seem that the rates for plants and animals are roughly comparable. The evidence suggests that species divergence is accompanied by further reiteration of preexisting repeat sequences. The rate of addition of repetitive sequences probably is slower in ferns than in angiosperms. This difference might be attributable to the much larger effective generation time in ferns.

Physiologically important stabilization of DNA by a prokaryotic histone-like protein

The thermophilic mycoplasma Thermoplasma acidophilum has tightly bound to its DNA a protein that closely resembles the histones of eukaryotes. DNA associated with this protein is more stable than free DNA against thermal denaturation by about 40 degrees C, as shown in both native nucleoprotein and in hybrid nucleoprotein reconstituted in vitro with calf DNA. Since only about 20 percent of the DNA in this organism is associated with the histone-like protein, we suggest that its physiological function is to prevent complete separation of the DNA strands during brief exposures of the organism to denaturing conditions, and thus to facilitate rapid renaturation when normal environmental conditions return.

Phylogenetic affinities between eukaryotic cells and a thermophilic mycoplasma

Thermoplasma acidophilum, a thermophilic mycoplasma, has several unusual features suggesting a possible relationship to eukaryotic cells. One feature is a histone-like protein that is associated with the DNA, condensing it into subunits similar to those in eukaryotic chromatin. A second feature is an association of cytoplasmic proteins that resembles eukaryotic actin and myosin. These two components are widely distributed in different groups of eukaryotic cells, but are typically lacking in prokaryotic cells. Furthermore, T. acidophilum lacks cytochromes and respires by enzymes that apparently are not coupled to oxidative phosphorylation. This primitive type of respiration resembles that of microbodies, another feature which is represented in the cytoplasm of all groups of eukaryotic cells. Furthermore, since T. acidophilum lacks a cell wall and appears to have a primitive correlate of endocytosis, it would appear to be mechanically capable of acquiring a symbiotic mitochondrion. Thus, our observations are consistent with the symbiotic hypothesis for the origin of eukaryotic cells. We suggest that an organism similar to T. acidophilum was the host cell for the original symbiosis, becoming the nucleus and cytoplasm of modern eukaryotic cells.

DNA Hybridization and Evolutionary Relationships in Three Osmunda Species

Molecular hybridization techniques have been used to estimate the degree of DNA base sequence homology between some members of the fern genus Osmunda. Under conditions permitting extensive reassociation, measurements of the extent of inter-specific reaction and the thermal stability of the hybrid molecules indicated that O. claytoniana L. (interrupted fern) shares more DNA homology with O. cinnamomea L. (cinnamon fern) than it does with O. regalis L. (royal fern). These findings are in conflict with predictions from a recent analysis of living and fossil specimens by numerical techniques. However, they are consistent with the earlier, more traditional, taxonomic assignments.

Gibberellin-induced Fertility in the Fern Ceratopteris thalictroides (L.) Brongn

Treatment of the homosporous fern Ceratopteris thalictroides L. sporophyte with gibberellic acid results in fertile fronds appearing 3 to 5 weeks after treatment. The hetero-blastic leaf sequence is markedly reduced, and the entire life cycle can be completed in 3 months on defined medium. Treatment with gibberellic acid also stimulates the accumulation of starch in mature leaves.