An Efficient and Reliable DNA-based Sex Identification Method for Archaeological Pacific Salmonid (Oncorhynchus spp.) Remains

Pacific salmonid (Oncorhynchus spp.) remains are routinely recovered from archaeological sites in northwestern North America but typically lack sexually dimorphic features, precluding the sex identification of these remains through morphological approaches. Consequently, little is known about the deep history of the sex-selective salmonid fishing strategies practiced by some of the region\u27s Indigenous peoples. Here, we present a DNA-based method for the sex identification of archaeological Pacific salmonid remains that integrates two PCR assays that each co-amplify fragments of the sexually dimorphic on the Y chromosome (sdY) gene and an internal positive control (Clock1a or D-loop). The first assay coamplifies a 95 bp fragment of sdY and a 108 bp fragment of the autosomal Clock1a gene, whereas the second assay co-amplifies the same sdY fragment and a 249 bp fragment of the mitochondrial D-loop region. This method\u27s reliability, sensitivity, and efficiency, were evaluated by applying it to 72 modern Pacific salmonids from five species and 75 archaeological remains from six Pacific salmonids. The sex identities assigned to each of the modern samples were concordant with their known phenotypic sex, highlighting the method\u27s reliability. Applications of the method to dilutions of modern DNA samples indicate it can correctly identify the sex of samples with as little as ~39 pg of total genomic DNA. The successful sex identification of 70 of the 75 (93%) archaeological samples further demonstrates the method\u27s sensitivity. The method\u27s reliance on two co-amplifications that preferentially amplify sdY helps validate the sex identities assigned to samples and reduce erroneous identifications caused by allelic dropout and contamination. Furthermore, by sequencing the D-loop fragment used as a positive control, species-level and sex identifications can be simultaneously assigned to samples. Overall, our results indicate the DNA-based method reported in this study is a sensitive and reliable sex identification method for ancient salmonid remains

Nuclear Astrophysics in Rare Isotope Facilities

Nuclear reactions in stars are difficult to measure directly in the laboratory at the small astrophysical energies. In recent years indirect methods with rare isotopes have been developed and applied to extract low-energy astrophysical cross sections.Comment: Invited talk (parallel section) at the Int. Conf. Nucleus-Nucleus Collisions (NN2009), Beijing, China, August 16-21, 2009. To appear in Nucl. Phys.

Gender, war and militarism: making and questioning the links

The gender dynamics of militarism have traditionally been seen as straightforward, given the cultural mythologies of warfare and the disciplining of ‘masculinity’ that occurs in the training and use of men's capacity for violence in the armed services. However, women's relation to both war and peace has been varied and complex. It is women who have often been most prominent in working for peace, although there are no necessary links between women and opposition to militarism. In addition, more women than ever are serving in many of today's armies, with feminists rather uncertain on how to relate to this phenomenon. In this article, I explore some of the complexities of applying gender analyses to militarism and peace work in sites of conflict today, looking most closely at the Israeli feminist group, New Profile, and their insistence upon the costs of the militarized nature of Israeli society. They expose the very permeable boundaries between the military and civil society, as violence seeps into the fears and practices of everyday life in Israel. I place their work in the context of broader feminist analysis offered by researchers such as Cynthia Enloe and Cynthia Cockburn, who have for decades been writing about the ‘masculinist’ postures and practices of warfare, as well as the situation of women caught up in them. Finally, I suggest that rethinking the gendered nature of warfare must also encompass the costs of war to men, whose fundamental vulnerability to psychological abuse and physical injury is often downplayed, whether in mainstream accounts of warfare or in more specific gender analysis. Feminists need to pay careful attention to masculinity and its fragmentations in addressing the topic of gender, war and militarism

Defining biodiverse reforestation: Why it matters for climate change mitigation and biodiversity

Reforestation to capture and store atmospheric carbon is increasingly championed as a climate change mitigation policy response. Reforestation plantings have the potential to provide conservation co-benefits when diverse mixtures of native species are planted, and there are growing attempts to monetise biodiversity benefits from carbon reforestation projects, particularly within emerging carbon markets. But what is meant by ‘biodiverse’ across different stakeholders and groups implementing and overseeing these projects and how do these perceptions compare with long-standing scientific definitions? Here, we discuss approaches to, and definitions of, biodiversity in the context of reforestation for carbon sequestration. Our aim is to review how the concept of biodiversity is defined and applied among stakeholders (e.g., governments, carbon certifiers and farmers) and rights holders (i.e., First Nations people) engaging in reforestation, and to identify best-practice methods for restoring biodiversity in these projects. We find that some stakeholders have a vague understanding of diversity across varying levels of biological organisation (genes to ecosystems). While most understand that biodiversity underpins ecosystem functions and services, many stakeholders may not appreciate the difficulties of restoring biodiversity akin to reference ecosystems. Consequently, biodiversity goals are rarely explicit, and project goals may never be achieved because the levels of restored biodiversity are inadequate to support functional ecosystems and desired ecosystem services. We suggest there is significant value in integrating biodiversity objectives into reforestation projects and setting specific restoration goals with transparent reporting outcomes will pave the way for ensuring reforestation projects have meaningful outcomes for biodiversity, and legitimate incentive payments for biodiversity and natural capital accounting

Is bicarbonate in Photosystem II the equivalent of the glutamate ligand to the iron atom in bacterial reaction centers?

Photosystem II of oxygen-evolving organisms exhibits a bicarbonate-reversible formate effect on electron transfer between the primary and secondary acceptor quinones, QA and QB. This effect is absent in the otherwise similar electron acceptor complex of purple bacteria, e.g. Rhodobacter sphaeroides. This distinction has led to the suggestion that the iron atom of the acceptor quinone complex in PS II might lack the fifth and sixth ligands provided in the bacterial reaction center (RC) by a glutamate residue at position 234 of the M-subunit in Rb. sphaeroides,RCs (M232 in Rps. viridis). By site-directed mutagenesis we have altered GluM234 in RCs from Rb. sphaeroides, replacing it with valine, glutamine and glycine to form mutants M234EV, M234EQ and M234EG, respectively. These mutants grew competently under phototrophic conditions and were tested for the formate-bicarbonate effect. In chromatophores there were no detectable differences between wild type (Wt) and mutant M234EV with respect to cytochrome b-561 reduction following a flash, and no effect of bicarbonate depletion (by incubation with formate). In isolated RCs, several electron transfer activities were essentially unchanged in Wt and M234EV, M234EQ and M234EG mutants, and no formate-bicarbonate effect was observed on: (a) the fast or slow phases of recovery of the oxidized primary donor (P+) in the absence of exogenous donor, i.e., the recombination of P+QA− or P+QB−, respectively; (b) the kinetics of electron transfer from QA− to QB; or (c) the flash dependent oscillations of semiquinone formation in the presence of donor to P+ (QB turnover). The absence of a formate-bicarbonate effect in these mutants suggests that GluM234 is not responsible for the absence of the formate-bicarbonate effect in Wt bacterial RCs, or at least that other factors must be taken into account. The mutant RCs were also examined for the fast primary electron transfer along the active (A-)branch of the pigment chain, leading to reduction of QA. The kinetics were resolved to reveal the reduction of the monomer bacteriochlorophyll (τ = 3.5 ps), followed by reduction of the bacteriopheophytin (τ = 0.9 ps). Both steps were essentially unaltered from the wild type. However, the rate of reduction of QA was slowed by a factor of 2 (τ = 410 ± 30 and 47 ± 30 ps for M234EQ and M234EV, respectively, compared to 220 ps in the wild type). EPR studies of the isolated RCs showed a characteristic g = 1.82 signal for the QA semiquinone coupled to the iron atom, which was indistinguishable from the wild type. It is concluded that GluM234 is not essential to the normal functioning of the acceptor quinone complex in bacterial RCs and that the role of bicarbonate in PS II is distinct from the role of this residue in bacterial RCs

Analysis of a spatial Lotka-Volterra model with a finite range predator-prey interaction

We perform an analysis of a recent spatial version of the classical Lotka-Volterra model, where a finite scale controls individuals' interaction. We study the behavior of the predator-prey dynamics in physical spaces higher than one, showing how spatial patterns can emerge for some values of the interaction range and of the diffusion parameter.Comment: 7 pages, 7 figure

Perspicuity and Granularity in Refinement

This paper reconsiders refinements which introduce actions on the concrete level which were not present at the abstract level. It draws a distinction between concrete actions which are "perspicuous" at the abstract level, and changes of granularity of actions between different levels of abstraction. The main contribution of this paper is in exploring the relation between these different methods of "action refinement", and the basic refinement relation that is used. In particular, it shows how the "refining skip" method is incompatible with failures-based refinement relations, and consequently some decisions in designing Event-B refinement are entangled.Comment: In Proceedings Refine 2011, arXiv:1106.348

Modern topics in theoretical nuclear physics

Over the past five years there have been profound advances in nuclear physics based on effective field theory and the renormalization group. In this brief, we summarize these advances and discuss how they impact our understanding of nuclear systems and experiments that seek to unravel their unknowns. We discuss future opportunities and focus on modern topics in low-energy nuclear physics, with special attention to the strong connections to many-body atomic and condensed matter physics, as well as to astrophysics. This makes it an exciting era for nuclear physics.Comment: 8 pages, 1 figure, prepared for the Nuclear Physics Town Hall Meeting at TRIUMF, Sept. 9-10, 2005, comments welcome, references adde

Leptonic and Semileptonic Decays of Charm and Bottom Hadrons

We review the experimental measurements and theoretical descriptions of leptonic and semileptonic decays of particles containing a single heavy quark, either charm or bottom. Measurements of bottom semileptonic decays are used to determine the magnitudes of two fundamental parameters of the standard model, the Cabibbo-Kobayashi-Maskawa matrix elements $V_{cb}$ and $V_{ub}$. These parameters are connected with the physics of quark flavor and mass, and they have important implications for the breakdown of CP symmetry. To extract precise values of $|V_{cb}|$ and $|V_{ub}|$ from measurements, however, requires a good understanding of the decay dynamics. Measurements of both charm and bottom decay distributions provide information on the interactions governing these processes. The underlying weak transition in each case is relatively simple, but the strong interactions that bind the quarks into hadrons introduce complications. We also discuss new theoretical approaches, especially heavy-quark effective theory and lattice QCD, which are providing insights and predictions now being tested by experiment. An international effort at many laboratories will rapidly advance knowledge of this physics during the next decade.Comment: This review article will be published in Reviews of Modern Physics in the fall, 1995. This file contains only the abstract and the table of contents. The full 168-page document including 47 figures is available at http://charm.physics.ucsb.edu/papers/slrevtex.p