The Word Problem for the Automorphism Groups of Right-Angled Artin Groups is in P

We provide an algorithm which takes any given automorphism f of any given right-angled Artin group G and determines whether or not f is the identity automorphism, thereby solving the word problem for the automorphism groups of right-angled Artin groups. We do this by solving the compressed word problem for right-angled Artin groups, a more general result. A key piece of this solution is the use of Plandowski\u27s algorithm. We also demonstrate that our algorithm runs in polynomial time in the size of the given automorphism, written as a word in Laurence\u27s generators of the automorphism group of the given right-angled Artin group

Gender-specific selection on codon usage in plant genomes

<p>Abstract</p> <p>Background</p> <p>Currently, there is little data available regarding the role of gender-specific gene expression on synonymous codon usage (translational selection) in most organisms, and particularly plants. Using gender-specific EST libraries (with > 4000 ESTs) from <it>Zea mays </it>and <it>Triticum aestivum</it>, we assessed whether gender-specific gene expression <it>per se </it>and gender-specific gene expression level are associated with selection on codon usage.</p> <p>Results</p> <p>We found clear evidence of a greater bias in codon usage for genes expressed in female than in male organs and gametes, based on the variation in GC content at third codon positions and the frequency of species-preferred codons. This finding holds true for both highly and for lowly expressed genes. In addition, we found that highly expressed genes have greater codon bias than lowly expressed genes for both female- and male-specific genes. Moreover, in both species, genes with female-specific expression show a greater usage of species-specific preferred codons for each of the 18 amino acids having synonymous codons. A supplemental analysis of <it>Brassica napus </it>suggests that bias in codon usage could also be higher in genes expressed in male gametophytic tissues than in heterogeneous (flower) tissues.</p> <p>Conclusion</p> <p>This study reports gender-specific bias in codon usage in plants. The findings reported here, based on the analysis of 1 497 876 codons, are not caused either by differences in the biological functions of the genes or by differences in protein lengths, nor are they likely attributable to mutational bias. The data are best explained by gender-specific translational selection. Plausible explanations for these findings and the relevance to these and other organisms are discussed.</p

Refuting the hypothesis that the acquisition of germ plasm accelerates animal evolution

Primordial germ cells (PGCs) give rise to the germ line in animals. PGCs are specified during embryogenesis either by an ancestral mechanism of cell-cell signalling (induction) or by a derived mechanism of maternally provided germ plasm (preformation). Recently, a hypothesis was set forth purporting that germ plasm liberates selective constraint and accelerates an organism's protein sequence evolution, especially for genes from early developmental stages, thereby leading to animal species radiations; empirical validation has been claimed in vertebrates. Here we present findings from global rates of protein evolution in vertebrates and invertebrates refuting this hypothesis. Contrary to assertions of the hypothesis, we find no effect of preformation on protein sequence evolution, the evolutionary rates of early-stage developmental genes, or on species diversification. We conclude that the hypothesis is mechanistically implausible, and our multi-faceted analysis shows no empirical support for any of its predictions.Organismic and Evolutionary Biolog

Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea

In protein-coding genes, synonymous codon usage and amino acid composition correlate to expression in some eukaryotes, and may result from translational selection. Here, we studied large-scale RNA-seq data from three divergent arthropod models, including cricket (Gryllus bimaculatus), milkweed bug (Oncopeltus fasciatus), and the amphipod crustacean Parhyale hawaiensis, and tested for optimization of codon and amino acid usage relative to expression level. We report strong signals of AT3 optimal codons (those favored in highly expressed genes) in G. bimaculatus and O. fasciatus, whereas weaker signs of GC3 optimal codons were found in P. hawaiensis, suggesting selection on codon usage in all three organisms. Further, in G. bimaculatus and O. fasciatus, high expression was associated with lowered frequency of amino acids with large size/complexity (S/C) scores in favor of those with intermediate S/C values; thus, selection may favor smaller amino acids while retaining those of moderate size for protein stability or conformation. In P. hawaiensis, highly transcribed genes had elevated frequency of amino acids with large and small S/C scores, suggesting a complex dynamic in this crustacean. In all species, the highly transcribed genes appeared to favor short proteins, high optimal codon usage, specific amino acids, and were preferentially involved in cell-cycling and protein synthesis. Together, based on examination of 1,680,067, 1,667,783, and 1,326,896 codon sites in G. bimaculatus, O. fasciatus, and P. hawaiensis, respectively, we conclude that translational selection shapes codon and amino acid usage in these three Pancrustacean arthropods

Radio Jet Feedback and Star Formation in Heavily Obscured Quasars at Redshifts ~0.3-3, I: ALMA Observations

We present ALMA 870 micron (345 GHz) data for 49 high redshift (0.47<z<2.85), luminous (11.7 < log L(bol) (Lsun) < 14.2) radio-powerful AGN, obtained to constrain cool dust emission from starbursts concurrent with highly obscured radiative-mode black hole (BH) accretion in massive galaxies which possess a small radio jet. The sample was selected from WISE with extremely steep (red) mid-infrared (MIR) colors and with compact radio emission from NVSS/FIRST. Twenty-six sources are detected at 870 microns, and we find that the sample has large mid- to far-infrared luminosity ratios consistent with a dominant and highly obscured quasar. The rest-frame 3 GHz radio powers are 24.7 < log P3.0 GHz (W/Hz) < 27.3, and all sources are radio-intermediate or radio-loud. BH mass estimates are 7.7 < log M(BH) (Msun) < 10.2. The rest frame 1-5 um SEDs are very similar to the "Hot DOGs" (Hot Dust Obscured Galaxies), and steeper (redder) than almost any other known extragalactic sources. ISM masses estimated for the ALMA detected sources are 9.9 < log M(ISM) (Msun) < 11.75 assuming a dust temperature of 30K. The cool dust emission is consistent with star formation rates (SFRs) reaching several thousand Msun/yr, depending on the assumed dust temperature, however we cannot rule out the alternative that the AGN powers all the emission in some cases. Our best constrained source has radiative transfer solutions with ~ equal contributions from an obscured AGN and a young (10-15 Myr) compact starburst.Comment: 29 pages, 8 figures. To appear in Astrophysical Journal. Update on Sept 14 to correct the ALMA proposal id. to ADS/JAO.ALMA#2011.0.00397.S and to add a missing acknowledgemen

Masculine femininities/feminine masculinities: power, identities and gender

This paper is basically about terminology. In it I discuss the terms 'masculinity' and 'femininity' and how they relate to being male and being female. My theme arises from an increasing difficulty that I am finding in understanding how individual identities relate to dominant constructions of masculinity and femininity. Christine Skelton and Becky Francis argue that we should not be afraid to name certain behaviours as masculine even when they are performed by girls. After a discussion of the problems of defining both 'masculinity' and 'femininity', and a consideration of the power relations between these terms, I go on to consider the concept of 'female masculinity' (Halberstam). I argue that this formulation is problematic, due to its dependence on a main term whose definition is unclear. Finally, I argue that we need to distinguish 'masculinity' and 'femininity' from 'masculinities' and 'femininities'

The problem of gender categorisation: addressing dilemmas past and present in gender and education research

Developments in the field of gender theory as applied to education since the 1970s are briefly reviewed in order to highlight key challenges and debates around gender categorisation and identification in gender and education. We argue that conundrums of categorisation have haunted, and continue to haunt, the field of gender theory, and empirical applications (such as the case of education) in particular. We explain how we have attempted to address some of the conundrums arising in our own theoretical work, and analyse remaining challenges that we feel the field of education needs to address in order to advance theoretically. Identifying two key tensions underpinning this empirical dilemma of gender categorisation – the tension between agency and determinism in gender identification, and that between gender deconstruction and gender analysis – we seek to weave a path through some of these complex debates, and to indicate ways in which they may be addressed in future work. We argue that in order to avoid essentialism and reification of gender distinction, we need to apply a ‘three-fold’ analysis that incorporates three different elements in our categorisation of gender: spectator perspective; respondent perspective and social context

Recent Acceleration of Plastid Sequence and Structural Evolution Coincides with Extreme Mitochondrial Divergence in the Angiosperm Genus Silene

The angiosperm genus Silene exhibits some of the most extreme and rapid divergence ever identified in mitochondrial genome architecture and nucleotide substitution rates. These patterns have been considered mitochondrial specific based on the absence of correlated changes in the small number of available nuclear and plastid gene sequences. To better assess the relationship between mitochondrial and plastid evolution, we sequenced the plastid genomes from four Silene species with fully sequenced mitochondrial genomes. We found that two species with fast-evolving mitochondrial genomes, S. noctiflora and S. conica, also exhibit accelerated rates of sequence and structural evolution in their plastid genomes. The nature of these changes, however, is markedly different from those in the mitochondrial genome. For example, in contrast to the mitochondrial pattern, which appears to be genome wide and mutationally driven, the plastid substitution rate accelerations are restricted to a subset of genes and preferentially affect nonsynonymous sites, indicating that altered selection pressures are acting on specific plastid-encoded functions in these species. Indeed, some plastid genes in S. noctiflora and S. conica show strong evidence of positive selection. In contrast, two species with more slowly evolving mitochondrial genomes, S. latifolia and S. vulgaris, have correspondingly low rates of nucleotide substitution in plastid genes as well as a plastid genome structure that has remained essentially unchanged since the origin of angiosperms. These results raise the possibility that common evolutionary forces could be shaping the extreme but distinct patterns of divergence in both organelle genomes within this genus

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine