How do potentials derived from structural databases relate to “true” potentials?

Knowledge-based potentials are used widely in protein folding and inverse folding algorithms. Two kinds of derivation methods are used. (1) The interactions in a database of known protein structures are assumed to obey a Boltzmann distribution. (2) The stability of the native folds relative to a manifold of misfolded structures is optimized. Here, a set of previously derived contact and secondary structure propensity potentials, taken as the "true" potentials, are employed to construct an artificial protein structural database from protein fragments. Then, new sets of potentials are derived to see how they are related to the true potentials. Using the Boltzmann distribution method, when the stability of the structures in the database lies within a certain range, both contact potentials and secondary structure propensities can be derived separately with remarkable accuracy. In general, the optimization method was found to be less accurate due to errors in the "excess energy" contribution. When the excess energy terms are kept as a constraint, the true potentials are recovered exactly.     

Fixed and unstable I-related transposable elements in heterochromatin of Drosophila melanogaster

Transposable elements are disproportionately abundant in the heterochromatin of Drosophila melanogaster. Among the forces contributing to this bias in genomic distribution, fixation due to positive selection has been put forward. We have studied I-related elements which are located in pericentromeric heterochromatin and are believed to have a role in the control of active I elements. Flies straight from the wild have been studied where fixed elements are expected to emerge clearly over the highly polymorphic background in the genomic distribution of transposable elements. The results show that some restriction fragments due to I-related elements are conserved in size and are present in all individuals tested, consistent with a selective pressure for a role. Other fragments are polymorphic in presence/absence and intensity in individuals from the wild but appear homogeneous in laboratory stocks. Although the significance of this type of instability is unclear, the finding that these polymorphic bands are recurrent in populations from distant geographical locations is also suggestive of a selective pressure for a role.     

Characterization of scientific studies usually cited as evidence of adverse effects of GM food/feed

GM crops are the most studied crops in history. Approximately 5% of the safety studies on them show adverse effects that are a cause for concern and tend to be featured in media reports. Although these reports are based on just a handful of GM events, they are used to cast doubt on all GM crops. Furthermore, they tend to come from just a few laboratories and are published in less important journals. Importantly, a close examination of these reports invariably shows methodological flaws that invalidate any conclusions of adverse effects. Twenty years after commercial cultivation of GM crops began, a bona fide report of an adverse health effect due to a commercialized modification in a crop has yet to be reported.     

Conflict and cooperation among the Vikings: Contingent behavioral decisions

We analyze historical accounts of Viking populations in Scotland and Iceland to show that considerations of kinship play a role in individuals' decisions on whether to engage in and revenge murder, as well as in the formation of alliances. However, willingness to murder a relative or to demand vengeance for the murder of another individual depends on the costs and benefits that accrue from the action, as well as the degree of relatedness. When the potential gains from murder are high, individuals are more willing to murder relatives; when the costs of exacting vengeance for a murder are high, individuals are more likely to settle for blood-money compensation for the murder of a family member. Alliances are more likely to be formed with relatives than between unrelated families; moreover, alliances with related individuals are less likely to involve preconditions and are more likely to be stable in the long term.     

THE MAINTENANCE OF GYNODIOECY AND ANDRODIOECY IN A METAPOPULATION

Males and females are at a selective disadvantage relative to hermaphrodites (cosexuals) in species with a colonizing habit, as only cosexuals are able to establish new colonies on their own. The implications of this disadvantage are assessed by means of a computer model of metapopulation dynamics, in which individual colonies are established through different rates of immigration and suffer different rates of local extinction. Results are given for simulations of an island model, a stepping-stone model, and for a partial analysis of the island model with simplifying assumptions. It is shown that: (1) unisexual frequencies in a metapopulation can be reasonably approximated by a linear function of the logarithm of the ratio of the immigration rate to the colony extinction rate; (2) metapopulation dynamics favor the maintenance of females (gynodioecy) over males (androdioecy) with cosexuals when they would otherwise be equally likely in a panmictic situation; (3) the way in which extinction and immigration rates affect unisexual frequencies at metapopulation equilibrium interacts with whether sterility is determined by a dominant or a recessive allele; and (4) unisexual frequencies are affected in a qualitatively similar way by the dynamics of a metapopulation when cosexuals are self-incompatible to when they are self-compatible, although only in the former case are high frequencies of unisexuals maintained when extinction and colonization rates approach the threshold at which the metapopulation goes extinct. These results are discussed with reference to existing data from species with nuclear male or female sterility.     

Desmosome dynamics in migrating epithelial cells requires the actin cytoskeleton

Re-modeling of epithelial tissues requires that the cells in the tissue rearrange their adhesive contacts in order to allow cells to migrate relative to neighboring cells. Desmosomes are prominent adhesive structures found in a variety of epithelial tissues that are believed to inhibit cell migration and invasion. Mechanisms regulating desmosome assembly and stability in migrating cells are largely unknown. In this study we established a cell culture model to examine the fate of desmosomal components during scratch wound migration. Desmosomes are rapidly assembled between epithelial cells at the lateral edges of migrating cells and structures are transported in a retrograde fashion while the structures become larger and mature. Desmosome assembly and dynamics in this system are dependent on the actin cytoskeleton prior to being associated with the keratin intermediate filament cytoskeleton. These studies extend our understanding of desmosome assembly and provide a system to examine desmosome assembly and dynamics during epithelial cell migration.     

Coding of visual objects in the ventral stream

How are objects represented in the brain? Two facets of this question are currently under investigation. First, are objects represented by activity in a relatively small number of neurons that are each selective for the shape or identity of a specific object (a 'sparse code'), or are they represented by a pattern of activity across a large number of less selective neurons (a 'population code')? Second, how are the neurons that code for an object distributed across the cortex: are they clustered together in patches, or are they scattered widely across the cortex? The results from neurophysiology and functional magnetic resonance imaging studies are beginning to provide preliminary answers to both questions.     

On the propagation of a wave front in viscoelastic arteries

In formulating a mathematical model of the arterial system, the one-dimensional flow approximation yields realistic pressure and flow pulses in the proximal as well as in the distal regions of a simulated arterial conduit, provided that the viscoelastic damping induced by the vessel wall is properly taken into account. Models which are based on a purely elastic formulation of the arterial wall properties are known to produce shocklike transitions in the propagating pulses which are not observed in man under physiological conditions. The viscoelastic damping characteristics are such that they are expected to reduce the tendency of shock formation in the model. In order to analyze this phenomenon, the propagation of first and second-order pressure waves is calculated with the aid of a wave front expansion, and criteria for the formation of shocks are derived. The application of the results to the human arterial system show that shock waves are not to be expected under normal conditions, while in case of a pathologically increased pressure rise at the root of the aorta, shocklike transitions may develop in the periphery. In particular, it is shown that second-order waves never lead to shock formation in finite time for the class of initial conditions and mechanical wave guides which are of interest in the mammalian circulation.     

Zebra stripes and tiger stripes: the spatial frequency distribution of the pattern compared to that of the background is significant in display and crypsis

Some striped animals are camouflaged in their natural environment, whereas others are conspicuous. Mammals are known to have spatial frequency analysers in their visual mechanism, and it is suggested that the spatial characteristics of a striped pattern are different in camouflaged and conspicuous animals. Fourier analysis of the stripes of the zebra shows spatial frequencies in the pattern that are unlikely to be present so strongly in their natural background scene. A similar analysis of the camouflaging stripes of a tiger show that the distribution of spatial frequencies are similar to that in the background scene.     

A framework for estimating the fixation time of an advantageous allele in stepping-stone models

Determining how population subdivision increases the fixation time of an advantageous allele is an important problem in evolutionary genetics as this influences many processes. Here, I lay out a framework for calculating the fixation time of a positively selected allele in a subdivided population, as a function of the number of demes present, the migration rate between them and the manner in which they are connected. Using this framework, it becomes clear that a beneficial allele's fixation time is significantly reduced through migration continuously introducing copies of the allele into a newly colonized subpopulation, increasing its frequency within these demes. The effect that migration has on allele frequency needs to be explicitly taken into account to produce a realistic estimate of fixation time. This behaviour is most prominent when demes are arranged on a two-dimensional torus, in comparison with populations where demes are arranged in a circle. This is because each subpopulation is connected to several neighbours over a torus, so that there are multiple paths that an allele can take in order to fix. As a consequence, some demes experience a greater influx and efflux of migrants than others. Analytical results are found to be very accurate when compared to stochastic simulations, and are generally robust if there are a large number of demes, or if the allele is weakly selected for.     

Fine structure and functional role of the coverings of the eggs inMesostoma ehrenbergii (Focke) (Turbellaria,Neorhabdocoela)

Summary European populations of the turbellarianMesostoma ehrenbergii can produce two types of eggs according to a seasonal cycle. Subitaneous eggs (S eggs) are produced throughout the warm season and develop rapidly inside the parental uteri. They are meant to ensure a fast increase in the number of worms. Dormant eggs (D eggs) are produced during the warm season and are usually deposited in water at the death of the parent. They can hatch at the beginning of the next warm season and are, therefore, meant to ensure the survival of the population throughout the cold season, when adult worms are no longer present.S eggs are bounded by a thin, translucent covering which has a loose structure and is mainly proteinaceous in composition. These characteristics account for the functional role played by the S egg covering during embryonic development. The covering has, in fact, to be permeable to parental nutrients, and to keep pace, by stretching, with the enlargement of the embryo. By contrast, D eggs are bounded by a thick shell, presumably composed of a sclerotin, the precursors of which (polyphenols) are synthesized together with yolk in the vitelline cells. The shell has a smooth surface devoid of pores and has the function of isolating the developing D egg from the external environment.Supported by a grant from the Consiglio Nazionale della RicercheThe authors wish to thank Dr. P. Roach for his help in translating the paper     

Blebs lead the way: how to migrate without lamellipodia

Blebs are spherical membrane protrusions that are produced by contractions of the actomyosin cortex. Blebs are often considered to be a hallmark of apoptosis; however, blebs are also frequently observed during cytokinesis and during migration in three-dimensional cultures and in vivo. For tumour cells and a number of embryonic cells, blebbing migration seems to be a common alternative to the more extensively studied lamellipodium-based motility. We argue that blebs should be promoted to a more prominent place in the world of cellular protrusions.     

Aromatic side-chain interactions in proteins. II. Near- and far-sequence Phe-X pairs

We have collected all aromatic pairs (3152) involving an N-phenyl partner in a dataset of 593 proteins of the PDB: 728 of these pairs involve a partner residue less than 6 apart in the sequence. These near-sequence Phe-X pairs correspond to specific conformations that stabilize secondary structures, mainly alpha-helices when the residues are 1, 3, and 4 apart, and beta-strands when they are 2 apart in the sequence. These conformations are not spatially random and have been examined in detail. The remaining phenylalanine pairs (2424) are between partners more than 5 apart in the sequence. Of these far-sequence pairs, 34% of occurrences are in sheets. Next in frequencies are pairs that bridge a beta-strand to a helix (24%), followed by pairs that bridge a beta-strand to a random coiled structure (15%). Helix to helix pairs only constitute 12% of these far-sequence pairs. Analysis of the pairing frequency supports the hypothesis that aromatic interactions are late events of protein folding.     

Ultrastructural studies of epidermis, sense receptors and sperm of Craspedella sp. and Didymorchis sp. (Platyhelminthes, Rhabdocoela)

Craspedella has a non-ciliated epidermis with nuclei located in the epidermis and with short microvilli. There is a thin basal lamina and thick underlying fibrous matrix. Rhabdites are secreted through ducts lined by microtubules. Multiciliate sense receptors consist of bundles of dendrites in a depression of the epidermis. Each dendrite has a cilium with a cross-striated rootlet; there are no electron-dense collars. Spermatozoa have peripheral microtubules which in cross-section are arranged in a ring-like or spiral fashion, numerous electron-dense granules, mitochondria and a nucleus; axonemes of the 9 +'1'type are free for most of their length. Centrioles occur in some nerve fibres. In Didymorchis parts of the epidermis are ciliated and epidermal perikarya are 'insunk', connected to the surface part of the epidermis by a single cytoplasmic process. Epidermal cilia have cross-striated vertical and horizontal rootlets. In the ciliary tips a short electron-dense rod along the central pair of tubules extends to the tip, where it widens to become a terminal plate; peripheral doublets gradually disappear by losing their microtubules. Receptors observed are uniciliate. Spermatozoa are as in Craspedella . Ultrastructural evidence indicates that Craspedella and Didymorchis arc closely related and belong to the Rhabdocoela.     

A point process driven multiple change point model: A robust resistant approach

Helicases are a class of enzymes involved in Ribonucleic Acid (RNA) metabolism. In this work a statistical method is proposed to analyze the individual mechanistic cycle of these motor proteins which are crucial to the understanding of their cellular functions. The RNA unwinding by NS3 helicase is hypothesized to occur in a series of discrete steps and the steps themselves occurring in accordance to an underlying point process. A point process driven multiple change point model is proposed to model the RNA unwinding mechanism. The methods are portable to other areas of applications as well. Algorithms based on robust-resistant statistical procedures are proposed to detect the change points. Both sequential and a posteriori change point models are considered. The relevant parameters of interest are estimated using a maximum likelihood approach. Simulations are performed to assess the performance of the methodology.     

Nonlinear theory of ion-acoustic waves in an ideal plasma with degenerate electrons

A nonlinear theory is constructed that describes steady-state ion-acoustic waves in an ideal plasma in which the electron component is a degenerate Fermi gas and the ion component is a classical gas. The parameter ranges in which such a plasma can exist are determined, and dispersion relations for ion-acoustic waves are obtained that make it possible to find the linear ion-acoustic velocity. Analytic gas-dynamic models of ion sound are developed for a plasma with the ion component as a cold, an isothermal, or an adiabatic gas, and moreover, the solutions to the equations of all the models are brought to a quadrature form. Profiles of a subsonic periodic and a supersonic solitary wave are calculated, and the upper critical Mach numbers of a solitary wave are determined. For a plasma with cold ions, the critical Mach number is expressed by an explicit exact formula.     

Electron microscopical studies on the thyroid of a cyclostome,Lampetra japonica,during its upstream migration

Summary Electron microscopical studies were made of the thyroid gland of an adult lamprey, Lampetra japonica, in the upstream migration period.The thyroid consists of many usual follicles containing the colloid in their lumina, and a large parafollicle without colloid. The paper concerns only the usual follicle.The follicle cells found in the usual follicle wall are classified into three types; 1. a non-ciliated taller cell, 2. a ciliated taller one, and 3. a non-ciliated cuboidal one. From their cytoplasmic fine structure, it is considered that all these cells are essentially identical and differences among them are due to their functional state.All these type cells are characterized by irregularly developed interdigitations and aggregates of tonofilaments throughout the cytoplasm, especially in the perinuclear region. Although the rough-surfaced endoplasmic reticulum and the Golgi apparatus are fairly well developed in the first and second type cells, the cisternae are not so large-vacuolated but flattened, and the cytoplasm is more compact as compared with that of the higher vertebrate. In the third type cell, the cytomembranes are poorly developed.Large dense inclusion-bodies consisting of heterogeneously dense materials, of lamellar structures, and of less dense vacuoles, which are found often in taller follicle cells, are also characteristic for the lamprey thyroid. The body which might be intimately related to the Golgi apparatus is considered to be a kind of lysosomes and it perhaps corresponds to the yellow pigment observed by light microscopy.In the apical part of the cytoplasm in taller cells, there are three kinds of granules or vesicles; numerous small vesicles considered to be derived from the Golgi apparatus, a few small dense granules which seem to originate from the Golgi region, and a few large less-dense granules.In the third type cell, the cytomembranes are not so well developed as those of the first and second type cells. The large heterogeneously dense bodies and the cytoplasmic granules are very few in number.Around the follicle of the lamprey thyroid, there are a dense basement membrane and a relatively compact connective tissue with few blood capillaries. Characteristic fat cells are found in the connective tissue.     

Adaptive change in the resource-exploitation traits of a generalist consumer: the evolution and coexistence of generalists and specialists

Mathematical models of consumer-resource systems are used to explore the evolution of traits related to resource acquisition in a generalist consumer species that is capable of exploiting two resources. The analysis focuses on whether evolution of traits determining the capture rates of two resources by a consumer species produce one generalist, two specialists, or all three types, when all types are characterized by a common fitness function. In systems with a stable equilibrium, evolution produces one generalist or two specialists, depending on the second derivative of the trade-off relationship. When there are sustained population fluctuations, the nature of the trade-off between the consumer's capture rates of the two resources still plays a key role in determining the evolutionary outcome. If the trade-off is described by a choice variable between zero and one that is raised to a power n, polymorphic states are possible when n > 1, which implies a positive second derivative of the curve. These states are either dimorphism, with two relatively specialized consumer types, or trimorphism, with a single generalist type and two specialists. Both endogenously driven consumer-resource cycles, and fluctuations driven by an environmental variable affecting resource growth are considered. Trimorphic evolutionary outcomes are relatively common in the case of endogenous cycles. In contrast to a previous study, these trimorphisms can often evolve even when new lineages are constrained to have phenotypes very similar to existing lineages. Exogenous cycles driven by environmental variation in resource growth rates appear to be much less likely to produce a mixture of generalists and specialists than are endogenous consumer-resource cycles.     

Cytoplasmic structure in rapid-frozen axons

Turtle optic nerves were rapid-frozen from the living state, fractured, etched, and rotary shadowed. Stereo views of fractured axons show that axoplasm consists of three types of longitudinally oriented domains. One type consists of neurofilament bundles in which individual filaments are interconnected by a cross-bridging network. Contiguous to neurofilament domains are domains containing microtubules suspended in a loose, granular matrix. A third domain is confined to a zone, 80-100 nm wide, next to the axonal membrane and consists of a dense filamentous network connecting the longitudinal elements of the axonal cytoskeleton to particles on the inner surface of the axolemma. Three classes of membrane-limited organelles are distinguished: axoplasmic reticulum, mitochondria, and discrete vesicular organelles. The vesicular organelles must include lysosomes, multivesicular bodies, and vesicles which are retrogradely transported in axons, though some vesicular organelles may be components of the axoplasmic reticulum. Organelles in each class have a characteristic relationship to the axonal cytoskeleton. The axoplasmic reticulum enters all three domains of axoplasm, but mitochondria and vesicular organelles are excluded from the neurofilament bundles, a distribution confirmed in thin sections of cryoembedded axons. Vesicular organelles differ from mitochondria in at least three ways with respect to their relationships to adjacent axoplasm: (a) one, or sometimes both, of their ends are associated with a gap in the surrounding granular axoplasm; (b) an appendage is typically associated with one of their ends; and (c) they are not attached or closely apposed to microtubules. Mitochondria, on the other hand, are only rarely associated with gaps in the axoplasm, do not have an appendage, and are virtually always attached to one or more microtubules by an irregular array of side-arms. We propose that the longitudinally oriented microtubule domains are channels within which organelles are transported. We also propose that the granular material in these channels may constitute the myriad enzymes and other nonfibrous components that slowly move down the axon.