Isolation of microsatellite loci in the Capricorn silvereye, Zosterops lateralis chlorocephalus (Aves : Zosteropidae)

The Capricorn silvereye (Zosterops lateralis chlorocephalus ) is ideally suited to investigating the genetic basis of body size evolution. We have isolated and characterized a set of microsatellite markers for this species. Seven out of 11 loci were polymorphic. The number of alleles detected ranged from two to five and observed heterozygosities between 0.12 and 0.67. One locus, ZL49, was found to be sex-linked. This moderate level of diversity is consistent with that expected in an isolated, island population

PADAMOT : project overview report

Background and relevance to radioactive waste management International consensus confirms that placing radioactive wastes and spent nuclear fuel deep underground in a geological repository is the generally preferred option for their long-term management and disposal. This strategy provides a number of advantages compared to leaving it on or near the Earth’s surface. These advantages come about because, for a well chosen site, the geosphere can provide: • a physical barrier that can negate or buffer against the effects of surface dominated natural disruptive processes such as deep weathering, glaciation, river and marine erosion or flooding, asteroid/comet impact and earthquake shaking etc. • long and slow groundwater return pathways from the facility to the biosphere along which retardation, dilution and dispersion processes may operate to reduce radionuclide concentration in the groundwater. • a stable, and benign geochemical environment to maximise the longevity of the engineered barriers such as the waste containers and backfill in the facility. • a natural radiation shield around the wastes. • a mechanically stable environment in which the facility can be constructed and will afterwards be protected. • an environment which reduces the likelihood of the repository being disturbed by inadvertent human intrusion such as land use changes, construction projects, drilling, quarrying and mining etc. • protection against the effects of deliberate human activities such as vandalism, terrorism and war etc. However, safety considerations for storing and disposing of long-lived radioactive wastes must take into account various scenarios that might affect the ability of the geosphere to provide the functionality listed above. Therefore, in order to provide confidence in the ability of a repository to perform within the deep geological setting at a particular site, a demonstration of geosphere “stability” needs to be made. Stability is defined here to be the capacity of a geological and hydrogeological system to minimise the impact of external influences on the repository environment, or at least to account for them in a manner that would allow their impacts to be evaluated and accounted for in any safety assessments. A repository should be sited where the deep geosphere is a stable host in which the engineered containment can continue to perform according to design and in which the surrounding hydrogeological, geomechanical and geochemical environment will continue to operate as a natural barrier to radionuclide movement towards the biosphere. However, over the long periods of time during which long-lived radioactive wastes will pose a hazard, environmental change at the surface has the potential to disrupt the stability of the geosphere and therefore the causes of environmental change and their potential consequences need to be evaluated. As noted above, environmental change can include processes such as deep weathering, glaciation, river and marine erosion. It can also lead to changes in groundwater boundary conditions through alternating recharge/discharge relationships. One of the key drivers for environmental change is climate variability. The question then arises, how can geosphere stability be assessed with respect to changes in climate? Key issues raised in connection with this are: • What evidence is there that 'going underground' eliminates the extreme conditions that storage on the surface would be subjected to in the long term? • How can the additional stability and safety of the deep geosphere be demonstrated with evidence from the natural system? As a corollary to this, the capacity of repository sites deep underground in stable rock masses to mitigate potential impacts of future climate change on groundwater conditions therefore needs to be tested and demonstrated. To date, generic scenarios for groundwater evolution relating to climate change are currently weakly constrained by data and process understanding. Hence, the possibility of site-specific changes of groundwater conditions in the future can only be assessed and demonstrated by studying groundwater evolution in the past. Stability of groundwater conditions in the past is an indication of future stability, though both the climatic and geological contexts must be taken into account in making such an assertion

Density of mechanisms within the flexibility window of zeolites

By treating idealized zeolite frameworks as periodic mechanical trusses, we show that the number of flexible folding mechanisms in zeolite frameworks is strongly peaked at the minimum density end of their flexibility window. 25 of the 197 known zeolite frameworks exhibit an extensive flexibility, where the number of unique mechanisms increases linearly with the volume when long wavelength mechanisms are included. Extensively flexible frameworks therefore have a maximum in configurational entropy, as large crystals, at their lowest density. Most real zeolites do not exhibit extensive flexibility, suggesting that surface and edge mechanisms are important, likely during the nucleation and growth stage. The prevalence of flexibility in real zeolites suggests that, in addition to low framework energy, it is an important criterion when searching large databases of hypothetical zeolites for potentially useful realizable structures.Comment: 11 pages, 3 figure

Male Accessory Gland Protein Reduces Egg Laying in a Simultaneous Hermaphrodite

Seminal fluid is an important part of the ejaculate of internally fertilizing animals. This fluid contains substances that nourish and activate sperm for successful fertilization. Additionally, it contains components that influence female physiology to further enhance fertilization success of the sperm donor, possibly beyond the recipient's optimum. Although evidence for such substances abounds, few studies have unraveled their identities, and focus has been exclusively on separate-sex species. We present the first detailed study into the seminal fluid composition of a hermaphrodite (Lymnaea stagnalis). Eight novel peptides and proteins were identified from the seminal-fluid-producing prostate gland and tested for effects on oviposition, hatching and consumption. The gene for the protein found to suppress egg mass production, Ovipostatin, was sequenced, thereby providing the first fully-characterized seminal fluid substance in a simultaneous hermaphrodite. Thus, seminal fluid peptides and proteins have evolved and can play a crucial role in sexual selection even when the sexes are combined

Probiotics, prebiotics, and the host microbiome: the science of translation

Recent advances in our understanding of the community structure and function of the human microbiome have implications for the potential role of probiotics and prebiotics in promoting human health. A group of experts recently met to review the latest advances in microbiota/microbiome research and discuss the implications for development of probiotics and prebiotics, primarily as they relate to effects mediated via the intestine. The goals of the meeting were to share recent advances in research on the microbiota, microbiome, probiotics, and prebiotics, and to discuss these findings in the contexts of regulatory barriers, evolving healthcare environments, and potential effects on a variety of health topics, including the development of obesity and diabetes; the long-term consequences of exposure to antibiotics early in life to the gastrointestinal (GI) microbiota; lactose intolerance; and the relationship between the GI microbiota and the central nervous system, with implications for depression, cognition, satiety, and mental health for people living in developed and developing countries. This report provides an overview of these discussions

Phenomenology of the Lense-Thirring effect in the Solar System

Recent years have seen increasing efforts to directly measure some aspects of the general relativistic gravitomagnetic interaction in several astronomical scenarios in the solar system. After briefly overviewing the concept of gravitomagnetism from a theoretical point of view, we review the performed or proposed attempts to detect the Lense-Thirring effect affecting the orbital motions of natural and artificial bodies in the gravitational fields of the Sun, Earth, Mars and Jupiter. In particular, we will focus on the evaluation of the impact of several sources of systematic uncertainties of dynamical origin to realistically elucidate the present and future perspectives in directly measuring such an elusive relativistic effect.Comment: LaTex, 51 pages, 14 figures, 22 tables. Invited review, to appear in Astrophysics and Space Science (ApSS). Some uncited references in the text now correctly quoted. One reference added. A footnote adde

Quantification of codon selection for comparative bacterial genomics

<p>Abstract</p> <p>Background</p> <p>Statistics measuring codon selection seek to compare genes by their sensitivity to selection for translational efficiency, but existing statistics lack a model for testing the significance of differences between genes. Here, we introduce a new statistic for measuring codon selection, the Adaptive Codon Enrichment (ACE).</p> <p>Results</p> <p>This statistic represents codon usage bias in terms of a probabilistic distribution, quantifying the extent that preferred codons are over-represented in the gene of interest relative to the mean and variance that would result from stochastic sampling of codons. Expected codon frequencies are derived from the observed codon usage frequencies of a broad set of genes, such that they are likely to reflect nonselective, genome wide influences on codon usage (<it>e.g</it>. mutational biases). The relative adaptiveness of synonymous codons is deduced from the frequency of codon usage in a pre-selected set of genes relative to the expected frequency. The ACE can predict both transcript abundance during rapid growth and the rate of synonymous substitutions, with accuracy comparable to or greater than existing metrics. We further examine how the composition of reference gene sets affects the accuracy of the statistic, and suggest methods for selecting appropriate reference sets for any genome, including bacteriophages. Finally, we demonstrate that the ACE may naturally be extended to quantify the genome-wide influence of codon selection in a manner that is sensitive to a large fraction of codons in the genome. This reveals substantial variation among genomes, correlated with the tRNA gene number, even among groups of bacteria where previously proposed whole-genome measures show little variation.</p> <p>Conclusions</p> <p>The statistical framework of the ACE allows rigorous comparison of the level of codon selection acting on genes, both within a genome and between genomes.</p

Sponge non-metastatic Group I Nme gene/protein - structure and function is conserved from sponges to humans

<p>Abstract</p> <p>Background</p> <p>Nucleoside diphosphate kinases NDPK are evolutionarily conserved enzymes present in Bacteria, Archaea and Eukarya, with human Nme1 the most studied representative of the family and the first identified metastasis suppressor. Sponges (Porifera) are simple metazoans without tissues, closest to the common ancestor of all animals. They changed little during evolution and probably provide the best insight into the metazoan ancestor's genomic features. Recent studies show that sponges have a wide repertoire of genes many of which are involved in diseases in more complex metazoans. The original function of those genes and the way it has evolved in the animal lineage is largely unknown. Here we report new results on the metastasis suppressor gene/protein homolog from the marine sponge <it>Suberites domuncula</it>, NmeGp1Sd. The purpose of this study was to investigate the properties of the sponge Group I Nme gene and protein, and compare it to its human homolog in order to elucidate the evolution of the structure and function of Nme.</p> <p>Results</p> <p>We found that sponge genes coding for Group I Nme protein are intron-rich. Furthermore, we discovered that the sponge NmeGp1Sd protein has a similar level of kinase activity as its human homolog Nme1, does not cleave negatively supercoiled DNA and shows nonspecific DNA-binding activity. The sponge NmeGp1Sd forms a hexamer, like human Nme1, and all other eukaryotic Nme proteins. NmeGp1Sd interacts with human Nme1 in human cells and exhibits the same subcellular localization. Stable clones expressing sponge NmeGp1Sd inhibited the migratory potential of CAL 27 cells, as already reported for human Nme1, which suggests that Nme's function in migratory processes was engaged long before the composition of true tissues.</p> <p>Conclusions</p> <p>This study suggests that the ancestor of all animals possessed a NmeGp1 protein with properties and functions similar to evolutionarily recent versions of the protein, even before the appearance of true tissues and the origin of tumors and metastasis.</p

Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects

Comparative genomics has become a real tantalizing challenge in the postgenomic era. This fact has been mostly magnified by the plethora of new genomes becoming available in a daily bases. The overwhelming list of new genomes to compare has pushed the field of bioinformatics and computational biology forward toward the design and development of methods capable of identifying patterns in a sea of swamping data noise. Despite many advances made in such endeavor, the ever-lasting annoying exceptions to the general patterns remain to pose difficulties in generalizing methods for comparative genomics. In this review, we discuss the different tools devised to undertake the challenge of comparative genomics and some of the exceptions that compromise the generality of such methods. We focus on endosymbiotic bacteria of insects because of their genomic dynamics peculiarities when compared to free-living organisms