Evidence from the domestication of apple for the maintenance of autumn colours by coevolution

The adaptive value of autumn colours is still a puzzle for evolutionary biology. It has been suggested that autumn colours are a warning signal to insects that use the trees as a host. I show that aphids (Dysaphis plantaginea) avoid apple trees (Malus pumila) with red leaves in autumn and that their fitness in spring is lower on these trees, which suggests that red leaves are an honest signal of the quality of the tree as a host. Autumn colours are common in wild populations but not among cultivated apple varieties, which are no longer under natural selection against insects. I show that autumn colours remain only in the varieties that are very susceptible to the effects of a common insect-borne disease, fire blight, and therefore are more in need of avoiding insects. Moreover, varieties with red leaves have smaller fruits, which shows that they have been under less effective artificial selection. This suggests a possible trade off between fruit size, leaf colour and resistance to parasites. These results are consistent with the hypothesis that autumn colours are a warning signal to insects, but not with other hypotheses.     

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.     

The pro-life argument from substantial identity and the pro-choice argument from asymmetric value: a reply to Patrick Lee

Lee claims that foetuses and adult humans are phases of the same identical substance, and thus have the same moral status because: first, foetuses and adults are the same physical organism, and second, the development from foetus to adult is quantitative and thus not a change of substance. Versus the first argument, I contend that the fact that foetuses and adults are the same physical organism implies only that they are the same thing but not the same substance, much as living adults and their corpses are the same thing (same body) but not the same substance. Against Lee's second argument, I contend that Lee confuses the nature of a process with the nature of its result. A process of quantitative change can produce a change in substance. Lee also fails to show that foetuses are rational and thus have all the essential properties of adults, as required for them to be the same substance. Against the pro-choice argument from asymmetric value (that only the fact that a human has become conscious of its life and begun to count on its continuing can explain human life's asymmetric moral value, i.e. that it is vastly worse to kill a human than not to produce one), Lee claims that foetus's lives are asymmetrically valuable to them before consciousness. This leads to counterintuitive outcomes, and it confuses the goodness of life (a symmetric value that cannot account for why it is worse to kill a human than not produce one) with asymmetric value.     

Microarray analysis: basic strategies for successful experiments

Microarrays offer a powerful approach to the analysis of gene expression that can be used for a wide variety of experimental purposes. However, there are several types of microarray platforms that are available. In addition, microarray experiments are expensive and generate complicated data sets that can be difficult to interpret. Success with microarray approaches requires a sound experimental design and a coordinated and appropriate use of statistical tools. Here, the advantages and pitfalls of utilizing microarrays are discussed, as are practical strategies to help novice users succeed with this method that can empower them with the ability to assay changes in gene expression at the whole genome level.     

Determination of network of residues that regulate allostery in protein families using sequence analysis

Allosteric interactions between residues that are spatially apart and well separated in sequence are important in the function of multimeric proteins as well as single-domain proteins. This observation suggests that, among the residues that are involved in long-range communications, mutation at one site should affect interactions at a distant site. By adopting a sequence-based approach, we present an automated approach that uses a generalization of the familiar sequence entropy in conjunction with a coupled two-way clustering algorithm, to predict the network of interactions that trigger allosteric interactions in proteins. We use the method to identify the subset of dynamically important residues in three families, namely, the small PDZ family, G protein-coupled receptors (GPCR), and the Lectins, which are cell-adhesion receptors that mediate the tethering and rolling of leukocytes on inflamed endothelium. For the PDZ and GPCR families, our procedure predicts, in agreement with previous studies, a network containing a small number of residues that are involved in their function. Application to the Lectin family reveals a network of residues interspersed throughout the C-terminal end of the structure that are responsible for binding to ligands. Based on our results and previous studies, we propose that functional robustness requires that only a small subset of distantly connected residues be involved in transmitting allosteric signals in proteins.     

A search for conceptual congruence between individuals and species

A new argument that species are individuals has recently been presented based on the way species names are used and systemic logic. The alternate idea that species are a categorical item, i.e., collections of individuals, was rejected. We wanted to evaluate this approach by establishing concepts that apply to individuals in order to examine if they are also applicable to a species viewed as a categorical item. It is our thinking that if species are not such, then concepts applicable to individuals will not be applicable to species so viewed. Individuals and species are similar in the presence of conceptual boundaries, unidirectional change and the presence of past and future time. These are all central, and salient, biological phenomena. But, these are concepts that apply also to populations which, for the most part, are not the same as species. Thus, these considerations infer that species, when viewed as a collection of individuals, do not share relevant concepts with individuals. Our conclusion is that a species is a 'unity' rather than an 'individual'.     

Corynocarpus J. R. & G. Forst.– an isolated genus

The very varied relationships that have been proposed are reviewed. Floral morphology and floral vasculature are described and the interpretations of some floral structures, particularly staminodes, disk and gynoecium are discussed. It is concluded that the petaloid scales are equivalent to petals rather than staminodes, that the nectaries do not represent a disk and that the gynoecium is monocarpellary. Evidence from several other characters confirms that none of the relationships which have been suggested are valid. Corynocarpus thus appears to be a truly isolated genus.     

Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure?

We have constructed a model structure that we believe represents the strongest possible physically and chemically reasonable representation of a hypothesized catalytically active hammerhead ribozyme structure in which a single divalent metal ion bridges the A9 and scissile phosphate groups. It has been proposed that such a structure arises from a conformational change in which the so-called ground-state structure (as observed by X-ray crystallography) rearranges in such a way that the pro-R oxygen atoms of both the A9 and scissile phosphate groups are directly coordinated by a single divalent metal ion in the transition-state of the hammerhead ribozyme cleavage reaction. We show that even the small subset of possible model structures that are consistent with these requirements, and that are stereochemically and sterically reasonable, are contradicted by experimental evidence. We also demonstrate that even a minimal subset of assumptions, i.e. that stems I and II are helical and that the two phosphate groups are coordinated by a divalent metal ion in the standard octahedral geometry, are sufficient to lead to this contradiction. We therefore conclude that such a mechanism of hammerhead ribozyme catalysis is untenable, at least in its present formulation.     

Phylogeny and Biogeography of the Stapeliads

The stapeliads (Apocynaceae — Asclepiadoideae — Ceropegieae) form a group of highly succulent, practically leafless plants with a very diverse floral morphology. They are found in the drier parts of the Old World from southern Africa eastwards to Burma. 55 characters are selected on which a cladistic analysis is based and these are discussed in detail where necessary. From this a phylogeny is produced for the stapeliads. It is shown that they are monophyletic and that they are nested within a larger group among the tribe Ceropegieae of the subfamily Asclepiadoideae. Several of the important innovations that have led to the diversification of the stapeliads in semidesertic regions are discussed. The stapeliads appear to be mainly fly-pollinated. The methods of attraction of flies are mentioned and it is suggested that there are four basic floral types among the stapeliads.     

Nucleic acid aptamers for target validation and therapeutic applications.

In the simplest view, aptamers can be thought of as nucleic acid analogs to antibodies. They are able to bind specifically to proteins, and, in many cases, that binding leads to a modulation of protein activity. New aptamers are rapidly generated through the SELEX (Systematic Evolution of Ligands by Exponential enrichment) process and have a very high target affinity and specificity (picomoles to nanomoles). Furthermore, aptamers composed of modified nucleotides have a long in vivo half-life (hours to days), are nontoxic and nonimmunogenic, and are easily produced using standard nucleic acid synthesis methods. These properties make aptamers ideal for target validation and as a new class of therapeutics. As a target validation tool, aptamers provide important information that complements that provided by other methods. For example, siRNA is widely used to demonstrate that protein knock-out in a cellular assay can lead to a biological effect. Aptamers extend that information by showing that the dose-dependent modulation of protein activity can be used to derive a therapeutic benefit. That is, aptamers can be used to demonstrate that the protein is a good target for drug development. As a new class of therapeutics, aptamers bridge the gap between small molecules and biologics. Like biologics, biologically active aptamers are rapidly discovered, have no class-specific toxicity, and are adept at disrupting protein-protein interaction. Like small molecules, aptamers can be rationally engineered and optimized, are nonimmunogenic, and are produced by scalable chemical procedures at moderate cost. As such, aptamers are emerging as an important source of new therapeutic molecules.     

Bis-acyl-/aroyl-hydrazones as multidentate ligands

Bis-acyl-/aroyl-hydrazones can be divided into two basic structural categories: those that are derived from a dihydrazide and those that are derived from a dialdehyde (or diketone). They form various types of complexes that are herein reviewed.     

Modeling capsid self-assembly: design and analysis

A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication of a common underlying design, motivating the use of simplified, low-resolution models in exploring the assembly process. Several versions of a molecular dynamics approach are described. Polyhedral shells of different sizes are involved, the assembly pathways are either irreversible or reversible and an explicit solvent is optionally included. Model design, simulation methodology and analysis techniques are discussed. The analysis focuses on the growth pathways and the nature of the intermediate states, properties that are hard to access experimentally. Among the key observations are that efficient growth proceeds by means of a cascade of highly reversible stages, and that while there are a large variety of possible partial assemblies, only a relatively small number of strongly bonded configurations are actually encountered.     

Lithophyllum cuneatum sp. nov. (Corallinaceae, Rhodophyta), a new species of non-geniculate coralline alga semi-endophytic in Hydrolithon onkodes and Neogoniolithon sp. from Fiji, South Pacific

A new species of semi-endophytic coralline alga, Lithophyllum cuneatum (Corallinaceae: Lithophylloideae), is described from Fiji. The species is characterized by a wedge-like thallus that is partially buried in the thallus of the host coralline, Hydrolithon onkodes (Heydrich) Penrose et Woelkerling or occasionally Neogoniolithon sp., and that appears at the surface of the host as a small pustule that is usually paler in color than the host. The thallus consists of erect filaments that are derived from a single cell. The basal cell, when visible, is non-palisade, and areas of bistratose margin are absent. Cells of contiguous erect filaments are joined by secondary pit connections. Epithallial cells are present in 2–3 layers, and individual trichocytes are common. Gametangial plants are dioecious. Male conceptacles have simple spermatangial systems that are confined to the floors of their elliptical chambers. Carposporangial conceptacles contain 5–8 celled gonimoblast filaments that are borne at the margin of a more-or-less discoid fusion cell, and so occupy the periphery of the elliptical conceptacle chambers. Tetrasporangial conceptacles are uniporate, with roofs formed from peripheral filaments, and chambers lack a central columella of sterile filaments. Despite its semi-endophytic nature, haustorial cells are absent, and plastids and pigmentation are present.     

Blending of heritable recognition cues among ant nestmates creates distinct colony gestalt odours but prevents within‐colony nepotism

The evolution of sociality is facilitated by the recognition of close kin, but if kin recognition is too accurate, nepotistic behaviour within societies can dissolve social cohesion. In social insects, cuticular hydrocarbons act as nestmate recognition cues and are usually mixed among colony members to create a Gestalt odour. Although earlier studies have established that hydrocarbon profiles are influenced by heritable factors, transfer among nestmates and additional environmental factors, no studies have quantified these relative contributions for separate compounds. Here, we use the ant Formica rufibarbis in a cross‐fostering design to test the degree to which hydrocarbons are heritably synthesized by young workers and transferred by their foster workers. Bioassays show that nestmate recognition has a significant heritable component. Multivariate quantitative analyses based on 38 hydrocarbons reveal that a subset of branched alkanes are heritably synthesized, but that these are also extensively transferred among nestmates. In contrast, especially linear alkanes are less heritable and little transferred; these are therefore unlikely to act as cues that allow within‐colony nepotistic discrimination or as nestmate recognition cues. These results indicate that heritable compounds are suitable for establishing a genetic Gestalt for efficient nestmate recognition, but that recognition cues within colonies are insufficiently distinct to allow nepotistic kin discrimination.     

A two population model of prion transport through a tunnelling nanotube

This article develops a two prion population model that simulates prion trafficking between an infected dendritic cell and a neuron. The situation when the two cells are connected by a tunnelling nanotube (TNT) is simulated. Two mechanisms of prion transport are considered: lateral diffusion in the TNT membrane and active actin-dependent transport inside endocytic vesicles that are propelled by myosin Va molecular motors. Analytical solutions describing prion concentrations and fluxes are obtained. Numerical results are compared with those predicted by a single prion population model that relies on a single reaction–diffusion equation and accounts for the two modes of prion transport in an effective way.     

Soft anatomy and the affinities of conodonts

Recent claims that conodonts are members of the Craniata or Vertebrata are based in part upon soft tissue features that have been preserved in a small number of specimens. These features include what appear to be radials in the caudal fin and paired structures that have been identified as eye remnants. The evidence for radials is limited, but credible. However, the anatomy of extant cyclostomes suggests that the paired structures are more reasonably interpreted as otic capsules than the remnants of sclerotic eye capsules. Moreover, even if these structures are the remnants of eyes, conodonts might equally well be a sister group to the craniates as a member of that group. Aside from these paired structures, conodont fossils exhibit no features that are suggestive of a cartilaginous skeleton. Given that cyclostome fossils sometimes show evidence of the cartilages of the head, the apparent absence of a similar skeleton in conodont animals calls into question the claim that they are craniates. The simple single chevron shape of conodont myomeres also suggests that they lie outside of the Craniata. All living craniates have double-chevron myomeres as adults, whereas simple myomeres of the conodont type are found in the non-craniate cephalochordates. Thus the available soft tissue evidence suggests that conodonts are best regarded as the sister group of the craniates.     

Why Eberl is wrong. Reflections on the beginning of personhood

In a paper published in Bioethics, Jason Eberl has argued that early embryos are not persons and should not be granted the status possessed by them. Eberl bases this position upon the following claims: (1) The early embryo has a passive potentiality for development into a person. (2) The early embryo has not established both 'unique genetic identity' and 'ongoing ontological identity', which are necessary conditions for ensoulment. (3) The early embryo has a low probability of developing into a more developed embryo. This paper examines these claims. I argue against (1) that a plausible view is that the early embryo has an active potentiality to grow into a more developed embryo. Against (2), I argue that neither 'unique genetic identity' nor 'ongoing ontological identity' are necessary conditions for ensoulment, and that 'ongoing ontological identity' is established between early embryos and more developed embryos. Against (3), I argue that the fact that the early embryo has a low probability of developing into a more developed embryo, if true, does not warrant the conclusion that the early embryo is not a person. If Eberl is right that the human soul is that which organises the activities of a human being and that ensouled humans are persons, embryos are persons from conception.     

Prediction of amino acid sequence from structure

We have developed a method for the prediction of an amino acid sequence that is compatible with a three-dimensional backbone structure. Using only a backbone structure of a protein as input, the algorithm is capable of designing sequences that closely resemble natural members of the protein family to which the template structure belongs. In general, the predicted sequences are shown to have multiple sequence profile scores that are dramatically higher than those of random sequences, and sometimes better than some of the natural sequences that make up the superfamily. As anticipated, highly conserved but poorly predicted residues are often those that contribute to the functional rather than structural properties of the protein. Overall, our analysis suggests that statistical profile scores of designed sequences are a novel and valuable figure of merit for assessing and improving protein design algorithms.     

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.     

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.