Phylogenetic distributions of British birds of conservation concern

Recent studies suggest that species' life histories and ecology can be used to forecast future extinction risk. Threatened species often share similar traits such that if a trait predisposing a species to decline or extinction is evolutionarily conserved, then close relatives of threatened species are themselves likely to be at risk. The phylogenetic distribution of current threat has been argued to provide insight into the species that could be threatened in the future when trait data are not available. Conservation criteria are typically based on multiple indices that capture different symptoms of threat including population trends and range contraction. However, there is no reason to assume consistent phylogenetic distributions of different symptoms. I construct a molecular phylogeny of 249 species of British birds (more than 93% of the breeding and wintering species) and use this to show that the species that are threatened due to population declines are phylogenetically more closely related than expected by chance alone. However, species that are listed for other reasons, including range contraction, are distributed randomly with respect to phylogeny. I suggest that while phylogeny can be informative with respect to identifying clades that are susceptible to some measures of extinction risk, such patterns are likely to be idiosyncratic with respect to symptom and taxa.     

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'.     

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.     

The demography of the coelacanth Latimeria chalumnae

Synopsis The very sparse data that are available on the abundance, population structure and biology of the coelacanth Latimeria chalumnae off Grand Comoro are summarised, and some simple numerical analyses are carried out to explore certain aspects of the population dynamics, particularly the age-profile of the population. The object has not been to provide estimates of key demographic parameters, such as mortality rates, but to propose various scenarios that are useful for comparison with real data as they become available. The analysis also makes it possible to reach some preliminary conclusions that are relevant to the management of the coelacanth population. For instance, it appears that the catch rate of coelacanths by artisanal fishermen may have a negligible effect on coelacanth survivorship, and it is more likely that population size and structure are determined by natural mortality rates and birth rates. It is suggested that predation is the main cause of natural mortality and that the main predators of coelacanths are likely to be large sharks. Interference with the traditional patterns of the Comoran artisanal fishery may threaten the coelacanth. Several important gaps in our knowledge of coelacanth demography are identified.     

Measurement of oxidatively generated base damage in cellular DNA

This survey focuses on the critical evaluation of the main methods that are currently available for monitoring single and complex oxidatively generated damage to cellular DNA. Among chromatographic methods, HPLC-ESI-MS/MS and to a lesser extent HPLC-ECD which is restricted to a few electroactive nucleobases and nucleosides are appropriate for measuring the formation of single and clustered DNA lesions. Such methods that require optimized protocols for DNA extraction and digestion are sensitive enough for measuring base lesions formed under conditions of severe oxidative stress including exposure to ionizing radiation, UVA light and high intensity UVC laser pulses. In contrast application of GC-MS and HPLC-MS methods that are subject to major drawbacks have been shown to lead to overestimated values of DNA damage. Enzymatic methods that are based on the use of DNA repair glycosylases in order to convert oxidized bases into strand breaks are suitable, even if they are far less specific than HPLC methods, to deal with low levels of single modifications. Several other methods including immunoassays and (32)P-postlabeling methods that are still used suffer from drawbacks and therefore are not recommended. Another difficult topic is the measurement of oxidatively generated clustered DNA lesions that is currently achieved using enzymatic approaches and that would necessitate further investigations.     

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.     

Identifying mRNAs bound by RNA-binding proteins using affinity purification and differential display

Many methods are available and widely used to determine specific proteins that bind to a particular RNA of interest. However, approaches to identify unknown substrate RNAs to which an RNA-binding protein binds and potentially regulates are not as common. In this article we describe a technique termed isolation of specific nucleic acids associated with proteins (SNAAP) that allows the identification of mRNAs associated with a protein. Methods are detailed for expressing and purifying fusion proteins that are used to isolate substrate mRNPs employing differential display technology. Lastly, experiments are described to confirm that the RNAs identified are indeed bonafide substrates for an RNA-binding protein. As the number of known RNA-binding proteins increases, of which many are involved in genetic disorders, it is essential that methodologies exist to identify RNA-protein interactions to better understand the manifestation of disease.     

Occlusal forces and mandibular bone strain: Is the primate jaw “overdesigned”?

Finite element modelling of the function of the periodontium and surrounding alveolar bone suggests these tissues are subjected to unusually large strains in comparison with the bone of the basal mandibular corpus. These studies, in addition to certain experimental investigations, have led to the suggestion that the strains experienced in the basal mandibular corpus are not functionally important. Under this view, size and shape of the basal corpus are not functionally linked to masticatory forces. Since previous comparative investigations have been premised on the assumption that masticatory strains in the basal corpus are functionally important, the assertion that masticatory stresses are concentrated primarily in the alveolar process undermines the credibility of this body of work. The hypothesis that the biomechanical effects of masticatory forces are localized in the alveolar process can be evaluated by reference to a number of bone strain investigations, as well as through consideration of current understanding of bone biology and behavior. Experimental studies indicate that the effects of occlusal forces during mastication are quite apparent in alveolar bone, although relatively large strains are also observed in regions well-removed from a loaded alveolus. It is also apparent that both alveolar and basal mandibular bone are subject to bending and twisting strains associated not only with occlusal forces, but also with muscular and condylar reaction forces. The result is that strain levels in alveolarvs.basal bone may be roughly similar, in contradiction to some published theoretical models. Based on empirical evidence and theoretical considerations, it is premature to conclude that mandibular corpus size and shape are not functionally linked to the biomechanics of chewing and biting.     

Abundance and genetic diversity of aerobic anoxygenic phototrophic bacteria of coastal regions of the pacific ocean

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophic microbes that are found in a broad range of aquatic environments. Although potentially significant to the microbial ecology and biogeochemistry of marine ecosystems, their abundance and genetic diversity and the environmental variables that regulate these properties are poorly understood. Using samples along nearshore/offshore transects from five disparate islands in the Pacific Ocean (Oahu, Molokai, Futuna, Aniwa, and Lord Howe) and off California, we show that AAP bacteria, as quantified by the pufM gene biomarker, are most abundant near shore and in areas with high chlorophyll or Synechococcus abundance. These AAP bacterial populations are genetically diverse, with most members belonging to the alpha- or gammaproteobacterial groups and with subclades that are associated with specific environmental variables. The genetic diversity of AAP bacteria is structured along the nearshore/offshore transects in relation to environmental variables, and uncultured pufM gene libraries suggest that nearshore communities are distinct from those offshore. AAP bacterial communities are also genetically distinct between islands, such that the stations that are most distantly separated are the most genetically distinct. Together, these results demonstrate that environmental variables regulate both the abundance and diversity of AAP bacteria but that endemism may also be a contributing factor in structuring these communities.     

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.     

Fast algorithm for generating CPK images on graphics workstations

An algorithm for generating CPK images of molecules is presented that uses bitmap operations to solve the hidden-surface problem. The algorithm makes certain assumptions: that the size and shading of each atom are determined only by its type and are unaffected by the atom's position, and that an intersection table comprised of entries for all pairs of atoms whose radii intersect is available. For speed, bit-maps of shaded and colored atom disks are predrawn. The atoms are projected from back to front. Atom intersections are explicitly calculated and used to generate mask bitmaps that are then used to truncate the predrawn disks, leaving the visible portions of the atom disks.     

Structure of Protein Interaction Networks and Their Implications on Drug Design

Protein-protein interaction networks (PINs) are rich sources of information that enable the network properties of biological systems to be understood. A study of the topological and statistical properties of budding yeast and human PINs revealed that they are scale-rich and configured as highly optimized tolerance (HOT) networks that are similar to the router-level topology of the Internet. This is different from claims that such networks are scale-free and configured through simple preferential-attachment processes. Further analysis revealed that there are extensive interconnections among middle-degree nodes that form the backbone of the networks. Degree distributions of essential genes, synthetic lethal genes, synthetic sick genes, and human drug-target genes indicate that there are advantageous drug targets among nodes with middle- to low-degree nodes. Such network properties provide the rationale for combinatorial drugs that target less prominent nodes to increase synergetic efficacy and create fewer side effects.     

Sex differences in the neural mechanisms mediating addiction: a new synthesis and hypothesis

In this review we propose that there are sex differences in how men and women enter onto the path that can lead to addiction. Males are more likely than females to engage in risky behaviors that include experimenting with drugs of abuse, and in susceptible individuals, they are drawn into the spiral that can eventually lead to addiction. Women and girls are more likely to begin taking drugs as self-medication to reduce stress or alleviate depression. For this reason women enter into the downward spiral further along the path to addiction, and so transition to addiction more rapidly. We propose that this sex difference is due, at least in part, to sex differences in the organization of the neural systems responsible for motivation and addiction. Additionally, we suggest that sex differences in these systems and their functioning are accentuated with addiction. In the current review we discuss historical, cultural, social and biological bases for sex differences in addiction with an emphasis on sex differences in the neurotransmitter systems that are implicated.     

The Hrs/STAM complex in the downregulation of receptor tyrosine kinases

Cell surface receptor proteins that have undergone endocytosis are transported to the endosome. From the endosome, ligand-activated receptor tyrosine kinases are further transported to the lysosome for degradation, a process called "receptor downregulation." By contrast, nutrient receptors, such as those for low-density lipoprotein and transferrin, are recycled back to the plasma membrane. Sorting of these two types of receptors occurs at the endosome, where ubiquitination of receptor proteins serves as the sorting signal. Namely, ubiquitinated receptors are incorporated into the lysosomal degradation pathway, whereas those that are not ubiquitinated are returned to the cell surface. Hrs and STAM are proteins that form a complex on the endosomal membrane. Recent studies have shown that the Hrs/STAM complex binds ubiquitin moieties and acts as sorting machinery that recognizes ubiquitinated receptors and transfers them to further sequential lysosomal sorting/trafficking processes.     

Are non-functional, unfolded proteins ('junk proteins') common in the genome?

It has recently been shown that many proteins are unfolded in their functional state. In addition, a large number of stretches of protein sequences are predicted to be unfolded. It has been argued that the high frequency of occurrence of these predicted unfolded sequences indicates that the majority of these sequences must also be functional. These sequences tend to be of low complexity. It is well established that certain types of low-complexity sequences are genetically unstable, and are prone to expand in the genome. It is possible, therefore, that in addition to these well-characterised functional unfolded proteins, there are a large number of unfolded proteins that are non-functional. Analogous to 'junk DNA' these protein sequences may arise due to physical characteristics of DNA. Their high frequency may reflect, therefore, the high probability of expansion in the genome. Such 'junk proteins' would not be advantageous, and may be mildly deleterious to the cell.     

Continuing professional development systems for medical physicists: A global survey and analysis

Continuing professional development (CPD) and continuing professional education (CPE) are seen as being necessary for medical physicists to ensure that they are up-to-date with current clinical practice. CPD is more than just continuing professional education, but can include research publication, working group contribution, thesis examination and many other activities. A systematic way of assessing and recording such activities that a medical physicist undertakes is used in a number of countries. This can be used for certification and licensing renewal purposes. Such systems are used in 27 countries, but they should be implemented in all countries where clinical medical physicists are employed.A survey of the CPD systems that are currently operated around the world is presented. In general they are quite similar although there are a few countries that have CPD systems that differ significantly from the others in many respects. Generally they ensure that medical physicists are kept up-to-date, although there are some that clearly will fail to achieve that.An analysis of what is required to construct a useful medical physics CPD system is made. Finally, the need for medical physicist professional organizations to cooperate and share in the production and distribution of CPD and CPE materials is emphasized.     

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.     

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.     

The ecosystem-service chain and the biological diversity crisis

The losses that are being incurred of the Earth''s biological diversity, at all levels, are now staggering. The trend lines for future loss are steeply upward as new adverse drivers of change come into play. The political processes for matching this crisis are now inadequate and the science needs to address this issue are huge and slow to fulfil, even though strong advances have been made. A more integrated approach to evaluating biodiversity in terms that are meaningful to the larger community is needed that can provide understandable metrics of the consequences to society of the losses that are occurring. Greater attention is also needed in forecasting likely diversity-loss scenarios in the near term and strategies for alleviating detrimental consequences. At the international level, the Convention on Biological Diversity must be revisited to make it more powerful to meet the needs that originally motivated its creation. Similarly, at local and regional levels, an ecosystem-service approach to conservation can bring new understanding to the value, and hence the need for protection, of the existing natural capital.     

The need for standardization in wildlife science: home range estimators as an example

Individual studies in wildlife science are indicative rather than conclusive. Although multiple studies can be meta-analyzed in such a way that scientific hypotheses can be tested, robust meta-analyses are often difficult or impossible if variables of interest are not measured in a uniform manner. We hypothesized that measurements, even of basic and unequivocal variables, are rarely standardized in wildlife sciences. We tested this assumption by reviewing randomly selected papers that describe the home range of mammals (n?=?25) and birds (n?=?25). In these papers, home ranges were calculated using 11 methods and 8 computer programs. The number of radiolocations used to calculate home ranges varied from 9 to >2,000. By estimating home ranges for two radiotelemetry data sets, we demonstrate that home ranges are not comparable if different methods are used and that estimates of home range are not standardized. We assume that measurements of other biological variables are even less consistent across studies. In order to advance wildlife sciences, we believe that standardization initiatives are required at an international level.