Gene mapping in marsupials: Detection of an ancient autosomal gene cluster

The genes HRAS, HBB, and CAT, which are located together on the short arm of human chromosome 11, appear to be part of a conserved synteny group found in many eutherian mammals. These genes were mapped to the chromosomes of two marsupial (metatherian) species by in situ hybridization. All three genes were located together on chromosome 3 in Macropus eugenii. Only HRAS and CAT were used to probe Dasykaluta rosamondae metaphases and these genes both mapped to chromosome 4. This suggests that the HRAS-HBB-CAT gene cluster has been conserved at least since the metatherians and eutherians diverged some 130 million years ago. These findings support the concept of a mammalian genome that has remained highly conserved throughout evolution.     

Search Algorithms as a Framework for the Optimization of Drug Combinations

Combination therapies are often needed for effective clinical outcomes in the management of complex diseases, but presently they are generally based on empirical clinical experience. Here we suggest a novel application of search algorithms—originally developed for digital communication—modified to optimize combinations of therapeutic interventions. In biological experiments measuring the restoration of the decline with age in heart function and exercise capacity in Drosophila melanogaster, we found that search algorithms correctly identified optimal combinations of four drugs using only one-third of the tests performed in a fully factorial search. In experiments identifying combinations of three doses of up to six drugs for selective killing of human cancer cells, search algorithms resulted in a highly significant enrichment of selective combinations compared with random searches. In simulations using a network model of cell death, we found that the search algorithms identified the optimal combinations of 6–9 interventions in 80–90% of tests, compared with 15–30% for an equivalent random search. These findings suggest that modified search algorithms from information theory have the potential to enhance the discovery of novel therapeutic drug combinations. This report also helps to frame a biomedical problem that will benefit from an interdisciplinary effort and suggests a general strategy for its solution.     

Mutation and Evolutionary Rates in Adélie Penguins from the Antarctic

Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I) of the mitochondrial genome using families of Adélie penguins (Pygoscelis adeliae) from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (μ) of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29–0.88 mutations/site/Myrs) after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k) of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17). Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent.     

Seed predation limits post-fire recruitment in the waratah (<Emphasis Type="Italic">Telopea speciosissima</Emphasis>)

Seed predation may reduce recruitment in populations that are limited by the availability of seeds rather than microsites. Fires increase the availability of both seeds and microsites, but in plants that lack a soil- or canopy-stored seed bank, post-fire recruitment is often delayed compared to the majority of species. Pyrogenic flowering species, such as Telopea speciosissima, release their non-dormant seeds more than 1 year after fire, by which time seed predation and the availability of microsites may differ from that experienced by plants recruiting soon after fire. I assessed the role of post-dispersal seed predation in limiting seedling establishment after fire in T. speciosissima, in southeastern Australia. Using a seed-planting experiment, I manipulated vertebrate access to seeds and the combined cover of litter and vegetation within experimental microsites in the 2 years of natural seed fall after a fire. Losses to vertebrate and invertebrate seed predators were rapid and substantial, with 50% of seeds consumed after 2 months in exposed locations and after 5 months when vertebrates were excluded. After 7 months, only 6% of seeds or seedlings survived, even where vertebrates were excluded. Removing litter and vegetation increased the likelihood of seed predation by vertebrates, but had little influence on losses due to invertebrates. Microsites with high-density vegetation and litter cover were more likely to have seed survival or germination than microsites with low-density cover. Recruitment in pyrogenic flowering species may depend upon the release of seeds into locations where dense cover may allow them to escape from vertebrate predators. Even here, conditions suitable for germination must occur soon after seed release for seeds to escape from invertebrate predators. Seed production will also affect recruitment after any one fire, while the ability of some juvenile and most adult plants to resprout after fire buffers populations against rapid declines when there is little successful recruitment.     

Spectral Estimation by Variable Span Log Periodogram Smoothing: An Application to Annual Lynx Numbers

Spectral estimation is commonly based on smoothing the periodogram or its logarithm. In such a smoothing exercise, it is not entirely sensible to use the same bandwidth for all frequencies, since the smoothness of the underlying spectrum may vary. This note describes the use of a variable span smoother in estimating the log spectrum. An application to annual lynx data is presented.     

Articulating School Countercultures

Starting from the observation that writings about student subcultures and antischool countercultures are much more common for wealthy English-speaking nations than elsewhere, this article develops the concept of "articulation" to help clarify the counterculture concept and differentiate fully developed countercultures from other forms of student resistance. Using examples from many nations, especially East Asia, I hope to contribute to an ethnology of schooling by exploring the social and cultural forces that promote and impede the articulation of school subcultures and countercultures.     

Electrochemical investigation of metal ion interactions of a ferrocene deoxyuridine conjugate

The metal ion interactions with ferrocene-modified deoxyuridine (FcdU) have been studied using cyclic voltammetry (CV) and differential pulse voltammetry (DPV) at a glassy carbon electrode in aqueous medium. Binding constants (K_n+) were determined from voltammetric data, i.e. shifts in potential and changes in limiting current with FcdU and after the addition of different metal ions. Electrospray ionization (ESI) mass spectra and matrix-assisted laser desorption/ionization-time flight mass spectrometry (MALDI-TOF MS) of FcdU recorded in presence of metal ions suggest that FcdU forms stable complexes with Cd²⁺.     

Reconfigurable Boolean Logic Using Magnetic Single-Electron Transistors

We propose a novel hybrid single-electron device for reprogrammable low-power logic operations, the magnetic single-electron transistor (MSET). The device consists of an aluminium single-electron transistor with a GaMnAs magnetic back-gate. Changing between different logic gate functions is realized by reorienting the magnetic moments of the magnetic layer, which induces a voltage shift on the Coulomb blockade oscillations of the MSET. We show that we can arbitrarily reprogram the function of the device from an n-type SET for in-plane magnetization of the GaMnAs layer to p-type SET for out-of-plane magnetization orientation. Moreover, we demonstrate a set of reprogrammable Boolean gates and its logical complement at the single device level. Finally, we propose two sets of reconfigurable binary gates using combinations of two MSETs in a pull-down network.