Sex-specific SCAR markers in the dioecious plant Rumex nivalis (Polygonaceae) and implications for the evolution of sex chromosomes

We developed SCAR primers based on isolated and sequenced male-specific fragments as identified in an AFLP analysis of the dioecious plant Rumex nivalis. PCR amplification using these primers on females and males resulted in fragments exclusively present in males. Co-amplification of the nuclear rDNA internal transcribed spacer 2 together with the male-specific fragment was applied as an internal control for successful PCR reactions to avoid false-negative sex scoring. With a length of about 164bp, the AFLP fragment was of a similar size as the tandemly arranged, repetitive sequences of 180bp located on the Y chromosomes of Rumex acetosa. The genetic distances between the Y-chromosomal sequences of R. nivalis and R. acetosa, both members of the section Acetosa, were substantial. We found intra-individual divergence among cloned sequences of the male-specific fragment in R. nivalis. The patterns of interspecific and intra-individual sequence variation found are in accordance with proposed modes of the evolution of sex chromosomes. Y chromosomes possibly arose only once in the genus Rumex and consist mainly of heterochromatic DNA. Due to the almost complete absence of selection on them, Y chromosomes are likely to accumulate large numbers of mutation

NWA 6356: unequilibrated polymict ureilite

Polymict ureilite NWA 6356 has not suffered an intensive metamorphism and keeps the evidence of multistage carbon injections, reducing sulphuric metasomatism, and consists of feldspathic clasts and best preserved CM-like chondrite fragments

Multiphoton Transitions in a Spin System Driven by Strong Bichromatic Field

EPR transient nutation spectroscopy is used to measure the effective field (Rabi frequency) for multiphoton transitions in a two-level spin system bichromatically driven by a transverse microwave (MW) field and a longitudinal radio-frequency (RF) field. The behavior of the effective field amplitude is examined in the case of a relatively strong MW field, when the derivation of the effective Hamiltonian cannot be reduced to first-order perturbation theory in w_{1} / w_{rf} (w_{1} is the microwave Rabi frequency, w_{rf} is the RF frequency). Experimental results are consistently interpreted by taking into account the contributions of second and third order in w_{1} / w_{rf} evaluated by Krylov-Bogolyubov-Mitropolsky averaging. In the case of inhomogeneously broadened EPR line, the third-order correction modifies the nutation frequency, while the second-order correction gives rise to a change in the nutation amplitude due to a Bloch-Siegert shift.Comment: 7 pages, 6 figure

Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae)

Recent evidence suggests that survival of arctic-alpine organisms in peripheral or interior glacial refugia are not mutually exclusive and may both be involved in shaping an organism’s Pleistocene history, yet potentially at different time levels. Here, we test this hypothesis in a high-mountain plant (diploid lineage of Senecio carniolicus, Asteraceae) from the Eastern European Alps, in which patterns of morphological variation and current habitat requirements suggest survival in both types of refugia. To this end, we used AFLPs, nuclear and plastid DNA sequences and analysed them, among others, within a graph theoretic framework and using novel Bayesian methods of phylogeographic inference. On the basis of patterns of genetic diversity, occurrence of rare markers, distribution of distinct genetic lineages and patterns of range connectivity both interior refugia in the formerly strongly glaciated central Alps and peripheral refugia along the southern margin of the Alps were identified. The presence of refugia congruently inferred by markers resolving at different time levels suggests that these refugia acted as such throughout several glacial cycles. The high degree of range persistence together with gradual range expansion, which contrasts with the extent of range shifts implied for other Alpine species, is likely responsible for incipient lineage differentiation evident from the genetic data. Replacing a simplistic peripheral vs. interior refugia dualism by more complex models involving both types of refugia and considering different time levels will help identifying common phylogeographic patterns with respect to, for instance, location of refugia and colonization routes and elucidating their underlying genetic and/or ecological causes

Q methodology and rural research

Traditionally, rural scholarship has been limited in its methodological approach. This has begun to change in recent years as rural researchers have embraced a range of different methodological tools. The aim of this article is to contribute to greater methodological pluralism in rural sociology by introducing readers to a method of research that is rarely engaged in the field, that is, Q methodology. The article describes the defining features of the approach as well as providing examples of its application to argue that it is a method that offers particular opportunities and synergies for rural social science research

Does Landscape Fragmentation Influence Sex Ratio of Dioecious Plants? A Case Study of Pistacia chinensis in the Thousand-Island Lake Region of China

The Thousand-Island Lake region in Zhejiang Province, China is a highly fragmented landscape with a clear point-in-time of fragmentation as a result of flooding to form the reservoir. Islands in the artificial lake were surveyed to examine how population sex ratio of a dioecious plant specie Pistacia chinensis B. was affected by landscape fragmentation. A natural population on the mainland near the lake was also surveyed for comparison. Population size, sex ratio and diameter at breast height (DBH) of individuals were measured over 2 years. More than 1,500 individuals, distributed in 31 populations, were studied. Soil nitrogen in the different populations was measured to identify the relationship between sex ratio and micro-environmental conditions. In accordance with the results of many other reports on biased sex ratio in relation to environmental gradient, we found that poor soil nitrogen areas fostered male-biased populations. In addition, the degree of sex ratio bias increased with decreasing population size and population connectivity. The biased sex ratios were only found in younger individuals (less than 50 years old) in small populations, while a stable 1∶1 sex ratio was found in the large population on the mainland. We concluded that the effects of landscape fragmentation on the dioecious population sex ratio were mainly achieved in relation to changing soil nitrogen conditions in patches and pollen limitation within and among populations. Large populations could maintain a more suitable environment in terms of nutrient conditions and pollen flow, subsequently maintaining a stable sex ratio in dioecious plant populations. Both micro-environmental factors and spatial structure should be considered in fragmented landscape for the conservation of dioecious plant species

Molecular basis of caspase-1 polymerization and its inhibition by a new capping mechanism

Inflammasomes are cytosolic caspase-1-activation complexes that sense intrinsic and extrinsic danger signals, and trigger inflammatory responses and pyroptotic cell death. Homotypic interactions among Pyrin domains and caspase recruitment domains (CARDs) in inflammasome-complex components mediate oligomerization into filamentous assemblies. Several cytosolic proteins consisting of only interaction domains exert inhibitory effects on inflammasome assembly. In this study, we determined the structure of the human caspase-1 CARD domain (caspase-1[superscript CARD]) filament by cryo-electron microscopy and investigated the biophysical properties of two caspase-1-like CARD-only proteins: human inhibitor of CARD (INCA or CARD17) and ICEBERG (CARD18). Our results reveal that INCA caps caspase-1 filaments, thereby exerting potent inhibition with low-nanomolar K[subscript i] on caspase-1[superscript CARD] polymerization in vitro and inflammasome activation in cells. Whereas caspase-1[superscript CARD] uses six complementary surfaces of three types for filament assembly, INCA is defective in two of the six interfaces and thus terminates the caspase-1 filament

Missense Mutations in the MEFV Gene Are Associated with Fibromyalgia Syndrome and Correlate with Elevated IL-1β Plasma Levels

BACKGROUND:Fibromyalgia syndrome (FMS), a common, chronic, widespread musculoskeletal pain disorder found in 2% of the general population and with a preponderance of 85% in females, has both genetic and environmental contributions. Patients and their parents have high plasma levels of the chemokines MCP-1 and eotaxin, providing evidence for both a genetic and an immunological/inflammatory origin for the syndrome (Zhang et al., 2008, Exp. Biol. Med. 233: 1171-1180). METHODS AND FINDINGS:In a search for a candidate gene affecting inflammatory pathways, among five screened in our patient samples (100 probands with FMS and their parents), we found 10 rare and one common alleles for MEFV, a gene in which various compound heterozygous mutations lead to Familial Mediterranean Fever (FMF). A total of 2.63 megabases of genomic sequence of the MEFV gene were scanned by direct sequencing. The collection of rare missense mutations (all heterozygotes and tested in the aggregate) had a significant elevated frequency of transmission to affecteds (p = 0.0085, one-sided, exact binomial test). Our data provide evidence that rare missense variants of the MEFV gene are, collectively, associated with risk of FMS and are present in a subset of 15% of FMS patients. This subset had, on average, high levels of plasma IL-1beta (p = 0.019) compared to FMS patients without rare variants, unaffected family members with or without rare variants, and unrelated controls of unknown genotype. IL-1beta is a cytokine associated with the function of the MEFV gene and thought to be responsible for its symptoms of fever and muscle aches. CONCLUSIONS:Since misregulation of IL-1beta expression has been predicted for patients with mutations in the MEFV gene, we conclude that patients heterozygous for rare missense variants of this gene may be predisposed to FMS, possibly triggered by environmental factors

Diel Variations in Survey Catch Rates and Survey Catchability of Spiny Dogfish and their Pelagic Prey in the Northeast US Continental Shelf Large Marine Ecosystem

This study examines the potential uncertainty in survey biomass estimates of Spiny Dogfish Squalus acanthias in the Northeast U.S. Continental Shelf Large Marine Ecosystem (NES LME). Diel catch-per-unit-effort (CPUE) estimates are examined from the Northeast Fisheries Science Center bottom trawl surveys conducted during autumn (1963-2009) and spring (1968-2009). Influential environmental variables on survey catchability are identified for Spiny Dogfish life history stages and five pelagic prey species: Butterfish Peprilus triacanthus, Atlantic Herring Clupea harengus, shortfin squid Illex spp., longfin squid Doryteuthis spp., and Atlantic Mackerel Scomber scombrus. Daytime survey catchability was significantly higher than nighttime catchability for most species during autumn and for mature male Spiny Dogfish, shortfin squid, and longfin squid during spring in the NES LME. For most stages and species examined, breakpoint analyses identified significant increases in CPUE in the morning, peak CPUE during the day, and significant declines in CPUE in the late afternoon. Seasonal probabilities of daytime catch were largely driven by solar zenith angle for most species, with stronger trends identified during autumn. Unadjusted CPUE estimates appear to overestimate absolute abundance, with adjustments resulting in reductions in absolute abundance ranging from 41% for Spiny Dogfish to 91% for shortfin and longfin squids. These findings have important implications for Spiny Dogfish regarding estimates of population consumption of key pelagic prey species and their ecological footprint within the NES LME