Clustered bottlenecks in mRNA translation and protein synthesis

We construct an algorithm that generates large, band-diagonal transition matrices for a totally asymmetric exclusion process (TASEP) with local hopping rate inhomogeneities. The matrices are diagonalized numerically to find steady-state currents of TASEPs with local variations in hopping rate. The results are then used to investigate clustering of slow codons along mRNA. Ribosome density profiles near neighboring clusters of slow codons interact, enhancing suppression of ribosome throughput when such bottlenecks are closely spaced. Increasing the slow codon cluster size, beyond $\approx 3-4$, does not significantly reduce ribosome current. Our results are verified by extensive Monte-Carlo simulations and provide a biologically-motivated explanation for the experimentally-observed clustering of low-usage codons

Extended haplodiploidy hypothesis

Evolution of altruistic behavior was a hurdle for the logic of Darwinian evolution. Soon after Hamilton formalized the concept of inclusive fitness, which explains how altruism can evolve, he suggested that the high sororal relatedness brought by haplodiploidy could be why Hymenopterans have a high prevalence in eusocial species, and why helpers in Hymenoptera are always female. Later it was noted that in order to capitalize on the high sororal relatedness, helpers would need to direct help toward sisters, and this would bias the population sex ratio. Under a 1:3 males:females sex ratio, the inclusive fitness valuation a female places on her sister, brother, and an own offspring are equalapparently removing the benefit of helping over independent reproduction. Based on this argumentation, haplodiploidy hypothesis has been considered a red herring. However, here we show that when population sex ratio, cost of altruism, and population growth rate are considered together, haplodiploidy does promote female helping even with female-biased sex ratio, due the lowered cost of altruism in such populations. Our analysis highlights the need to re-evaluate the role of haplodiploidy in the evolution of helping, and the importance of fully exploring the model assumptions when comparing interactions of population sex ratios and social behaviors.Peer reviewe

The statistical mechanics of a polygenic characterunder stabilizing selection, mutation and drift

By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation, and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the trait. These macroscopic variables are the expectations of: the trait mean and its square, the genetic variance, and of a measure of heterozygosity, and are derived from a generating function that is in turn derived by maximizing an entropy measure. These four macroscopics are enough to accurately describe the dynamics of the trait mean and of its genetic variance (and in principle of any other quantity). Unlike previous approaches that were based on an infinite series of moments or cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined approximation procedure. We apply the framework to abrupt and gradual changes in the optimum, as well as to changes in the strength of stabilizing selection. Our approximations are surprisingly accurate, even for systems with as few as 5 loci. We find that when the effects of drift are included, the expected genetic variance is hardly altered by directional selection, even though it fluctuates in any particular instance. We also find hysteresis, showing that even after averaging over the microscopic variables, the macroscopic trajectories retain a memory of the underlying genetic states.Comment: 35 pages, 8 figure

Negotiations of minority ethnic rugby league players in the Cathar country of France

This article is based on new empirical, qualitative research with minority ethnic rugby league players in the southwest of France. Drawing on similar research on rugby league in the north and the south of England, the article examines how rugby league, traditionally viewed as a white, working-class male game (Collins, 2006; Denham, 2004; Spracklen, 1995, 2001) has had to re-imagine its symbolic boundaries as they are constituted globally and locally to accommodate the needs of players from minority ethnic backgrounds. In particular, the article examines the sense in which experiences of minority ethnic rugby league players in France compare with those of their counterparts in England (Spracklen, 2001, 2007), how rugby league is used in France to construct identity, and in what sense the norms associated with the imaginary community of rugby league are replicated or challenged by the involvement of minority ethnic rugby league players in France. Questions about what it means to be (provincial, national) French (Kumar, 2006) are posed, questions that relate to the role of sport in the construction of Frenchness, and in particular the role of rugby league (and union). © Copyright ISSA and SAGE Publications

Automated Analysis of Cryptococcal Macrophage Parasitism Using GFP-Tagged Cryptococci

The human fungal pathogens Cryptococcus neoformans and C. gattii cause life-threatening infections of the central nervous system. One of the major characteristics of cryptococcal disease is the ability of the pathogen to parasitise upon phagocytic immune effector cells, a phenomenon that correlates strongly with virulence in rodent models of infection. Despite the importance of phagocyte/Cryptococcus interactions to disease progression, current methods for assaying virulence in the acrophage system are both time consuming and low throughput. Here, we introduce the first stable and fully characterised GFP–expressing derivatives of two widely used cryptococcal strains: C. neoformans serotype A type strain H99 and C. gattii serotype B type strain R265. Both strains show unaltered responses to environmental and host stress conditions and no deficiency in virulence in the macrophage model system. In addition, we report the development of a method to effectively and rapidly investigate macrophage parasitism by flow cytometry, a technique that preserves the accuracy of current approaches but offers a four-fold improvement in speed

Exploring the Subtle Effect of Aliphatic Ring Size on Minor Actinide-Extraction Properties and Metal Ion Speciation in Bis-1,2,4-Triazine Ligands

Calling all actinides! Bis-1,2,4-triazine ligands bearing five-membered rings were synthesized and evaluated as actinide-selective extractants. Tuning the size of the aliphatic ring leads to subtle changes in actinide-extraction properties. The origins of these changes were elucidated at the molecular level, paving the way for the rational design of improved actinide-selective extractants for reprocessing of spent nuclear fuel., The synthesis and evaluation of three novel bis-1,2,4-triazine ligands containing five-membered aliphatic rings are reported. Compared to the more hydrophobic ligands 1–3 containing six-membered aliphatic rings, the distribution ratios for relevant f-block metal ions were approximately one order of magnitude lower in each case. Ligand 10 showed an efficient, selective and rapid separation of AmIII and CmIII from nitric acid. The speciation of the ligands with trivalent f-block metal ions was probed using NMR titrations and competition experiments, time-resolved laser fluorescence spectroscopy and X-ray crystallography. While the tetradentate ligands 8 and 10 formed Ln$^{III}$ complexes of the same stoichiometry as their more hydrophobic analogues 2 and 3, significant differences in speciation were observed between the two classes of ligand, with a lower percentage of the extracted 1:2 complexes being formed for ligands 8 and 10. The structures of the solid state 1:1 and 1:2 complexes formed by 8 and 10 with Y$^{III}$, Lu$^{III}$ and Pr$^{III}$ are very similar to those formed by 2 and 3 with Ln$^{III}$. Ligand 10 forms Cm$^{III}$ and Eu$^{III}$ 1:2 complexes that are thermodynamically less stable than those formed by ligand 3, suggesting that less hydrophobic ligands form less stable An$^{III}$ complexes. Thus, it has been shown for the first time how tuning the cyclic aliphatic part of these ligands leads to subtle changes in their metal ion speciation, complex stability and metal extraction affinity

Production, characterization, and antigen specificity of recombinant 62-71-3, a candidate monoclonal antibody for rabies prophylaxis in humans

Rabies kills many people throughout the developing world every year. The murine monoclonal antibody (mAb) 62-71-3 was recently identified for its potential application in rabies postexposure prophylaxis (PEP). The purpose here was to establish a plant-based production system for a chimeric mouse-human version of mAb 62-71-3, to characterize the recombinant antibody and investigate at a molecular level its interaction with rabies virus glycoprotein. Chimeric 62-71-3 was successfully expressed in Nicotiana benthamiana. Glycosylation was analyzed by mass spectroscopy; functionality was confirmed by antigen ELISA, as well as rabies and pseudotype virus neutralization. Epitope characterization was performed using pseudotype virus expressing mutagenized rabies glycoproteins. Purified mAb demonstrated potent viral neutralization at 500 IU/mg. A critical role for antigenic site I of the glycoprotein, as well as for two specific amino acid residues (K226 and G229) within site I, was identified with regard to mAb 62-71-3 neutralization. Pseudotype viruses expressing glycoprotein from lyssaviruses known not to be neutralized by this antibody were the controls. The results provide the molecular rationale for developing 62-71-3 mAb for rabies PEP; they also establish the basis for developing an inexpensive plant-based antibody product to benefit low-income families in developing countries.—Both, L., van Dolleweerd, C., Wright, E., Banyard, A. C., Bulmer-Thomas, B., Selden, D., Altmann, F., Fooks, A. R., Ma, J. K.-C. Production, characterization, and antigen specificity of recombinant 62-71-3, a candidate monoclonal antibody for rabies prophylaxis in humans

Managing and monitoring equality and diversity in UK sport: An evaluation of the sporting equals Racial Equality Standard and its impact on organizational change

Despite greater attention to racial equality in sport in recent years, the progress of national sports organizations toward creating equality of outcomes has been limited in the United Kingdom. The collaboration of the national sports agencies, equity organizations and national sports organizations (including national governing bodies of sport) has focused on Equality Standards. The authors revisit an earlier impact study of the Racial Equality Standard in sport and supplement it with another round of interview material to assess changing strategies to manage diversity in British sport. In particular, it tracks the impact on organizational commitment to diversity through the period of the establishment of the Racial Equality Standard and its replacement by an Equality Standard that deals with other diversity issues alongside race and ethnicity. As a result, the authors question whether the new, generic Equality Standard is capable of addressing racial diversity and promoting equality of outcomes. © 2006 Sage Publications

Population genomics of domestic and wild yeasts

The natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy isolates of the domesticated baker's yeast, _Saccharomyces cerevisiae_, and its closest relative, the wild _S. paradoxus_, which has never been associated with human activity. These were collected from numerous geographic locations and sources (including wild, clinical, baking, wine, laboratory and food spoilage). These sequences provide an unprecedented view of the population structure, natural (and artificial) selection and genome evolution in these species. Variation in gene content, SNPs, indels, copy numbers and transposable elements provide insights into the evolution of different lineages. Phenotypic variation broadly correlates with global genome-wide phylogenetic relationships however there is no correlation with source. _S. paradoxus_ populations are well delineated along geographic boundaries while the variation among worldwide _S. cerevisiae_ isolates show less differentiation and is comparable to a single _S. paradoxus_ population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of _S. cerevisiae_ shows a few well defined geographically isolated lineages and many different mosaics of these lineages, supporting the notion that human influence provided the opportunity for outbreeding and production of new combinations of pre-existing variation