bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved Neutron-Capture Element Abundances in Planetary Nebulae
Authors: Sterling N. C. , Dinerstein H. L. , Hwang S. , Redfield S. , Aguilar A. , Witthoeft M. C. , Esteves D. , Kilcoyne A. L. D. , Bautista M. , Phaneuf R. , Bilodeau R. C. , Ballance C. P. , McLaughlin B. , Norrington P. H.
Published: September 2009

Spectroscopy of planetary nebulae (PNe) provides the means to investigate s-process enrichments of neutron(n)-capture elements that cannot be detected in Asymptotic Giant Branch (AGB) stars. However, accurate abundance determinations of these elements present a challenge. Corrections for unobserved ions can be large and uncertain, since in many PNe only one ion of a given n-capture element has been detected. Furthermore, the atomic data governing the ionization balance of these species are not well-determined, inhibiting the derivation of accurate ionization corrections. We present initial results of a program that addresses these challenges. Deep high-resolution optical spectroscopy of ∼20 PNe has been performed to detect emission lines from trans-iron species including Se, Br, Kr, Rb and Xe. The optical spectral region provides access to multiple ions of these elements, which reduces the magnitude and importance of uncertainties in the ionization corrections. In addition, experimental and theoretical efforts are providing determinations of the photoionization cross sections and recombination rate coefficients of Se, Kr and Xe ions. These new atomic data will make it possible to derive robust ionization corrections for these elements. Together, our observational and atomic data results will enable n-capture element abundances to be determined with unprecedented accuracy in ionized nebulae.
Carbon-Enhanced, Metal-Poor Stars and Modeling of the Asymptotic Giant Branch
Authors: Lucatello Sara , Masseron Thomas , Johnson Jennifer A.
Published: September 2009

The very high fraction of C-enriched stars among the low end of the Galactic-halo metallicity distribution, along with the wide variety in content of their neutron-capture elements, make the understanding of their formation scenario(s) of extreme interest. The combination of accurate determinations of their chemical composition with long-term radial-velocity monitoring is crucial to address this issue. We discuss the first results of long-term radial-velocity monitoring for C-enhanced, metal-poor stars and explore the connection with chemical peculiarities; the data suggest that belonging to a close binary affects nucleosynthesis on the Asymptotic Giant Branch. We also present abundances for the poorly studied element fluorine in a sample of 10 C-enhanced stars with metallicities ranging from [Fe/H] = –1.3 to –2.9 and compare our measurements to the predictions of state-of-the-art nucleosynthesis models. We show how the observed abundances of fluorine in CEMP stars are considerable lower than expected on the basis of the current state-of-the-art theoretical calculations, hinting at our poor understanding of the nucleosynthetic processes that produce this element.
On the Mass and Metallicity Distributions of the Parent AGB Stars of O-Rich Presolar Stardust Grains
Authors: Nittler Larry R.
Published: September 2009

Presolar grains in meteorites formed in a sample of Asymptotic Giant Branch (AGB) stars that ended their lives within ≈1 Gyr of the origin of the Solar System 4.6 Gyr ago. The O-isotopic compositions of presolar O-rich stardust reflect the masses and metallicities of their parent stars. We present simple Monte Carlo simulations of the parent AGB stars of presolar grains. Comparison of model predictions with the grain data allow some broad conclusions to be drawn: (1) Presolar O-rich grains formed in AGB stars of mass ∼1.15–2.2 M⊙. The upper-mass cutoff reflects dredge-up of C in more massive AGB stars, leading to C-rich dust rather than O-rich, but the lack of grains from intermediate-mass AGB stars (>4 M⊙) is a major puzzle; (2) The grain O-isotopic data are reproduced well if the Galaxy in presolar times was assumed to have a moderate age-metallicity relationship, but with significant metallicity scatter for stars born at the same time; (3) The Sun appears to have a moderately low metallicity for its age and/or unusual 17O/16O and 18O/16O ratios for its metallicity; and (4) The Solar 17O/18O ratio, while unusual relative to present-day molecular clouds and protostars, was not atypical for the presolar disk and does not require self-pollution of the protosolar molecular cloud by supernova ejecta.
Metallurgy Beyond Iron
Authors: Gallino Isabella , Busch Ralf
Published: September 2009

Metallurgy is one of the oldest sciences. Its history can be traced back to 6000 BCE with the discovery of Gold, and each new discovery — Copper, Silver, Lead, Tin, Iron and Mercury — marked the beginning of a new era of civilization. Currently there are 86 known metals, but until the end of the 17th century, only 12 of these were known. Steel (Fe–C alloy) was discovered in the 11th century BCE; however, it took until 1709 CE before we mastered the smelting of pig-iron by using coke instead of charcoal and started the industrial revolution. The metallurgy of nowadays is mainly about discovering better materials with superior properties to fulfil the increasing demand of the global market. Promising are the Glassy Metals or Bulk Metallic Glasses (BMGs) — discovered at first in the late 50s at the California Institute of Technology — which are several times stronger than the best industrial steels and 10-times springier. The unusual structure that lacks crystalline grains makes BMGs so promising. They have a liquid-like structure that means they melt at lower temperatures, can be moulded nearly as easily as plastics, and can be shaped into features just 10 nm across. The best BMG formers are based on Zr, Pd, Pt, Ca, Au and, recently discovered, also Fe. They have typically three to five components with large atomic size mismatch and a composition close to a deep eutectic. Packing in such liquids is very dense, with a low content of free volume, resulting in viscosities that are several orders of magnitude higher than in pure metal melts.
Measuring Cosmic Elements with Gamma-Ray Telescopes
Authors: Diehl Roland
Published: September 2009

Gamma-ray telescopes are capable of measuring radioactive trace isotopes from cosmic nucleosynthesis events. Such measurements address new isotope production rather directly for a few key isotopes such as 44Ti, 26Al, 60Fe, and 56Ni, as well as positrons from the β+-decay variety. Experiments of the past decades have now established an astronomy with γ-ray lines, which is an important part of the study of nucleosynthesis environments in cosmic sources. For massive stars and supernovae, important constraints have been set: Co isotope decays in SN1987A directly demonstrated the synthesis of new isotopes in core-collapse supernovae, 44Ti from the 340-year-old Cas A supernova supports the concept of α-rich freeze-out, but results in interesting puzzles pursued by theoretical studies and future experiments. 26Al and 60Fe has been measured from superimposed nucleosynthesis within our Galaxy, and sets constraints on massive-star interior structure through its intensity ratio of ∼15%. The 26Al γ-ray line is now seen to trace current star formation and even the kinematics of interstellar medium throughout the Galaxy. Positron annihilation emission from nucleosynthesis throughout the plane of our Galaxy appears to be mainly from 26Al and other supernova radioactivity, but the striking brightness of the Galaxy's bulge region in positron annihilation γ-rays presents a puzzle involving several astrophysics issues beyond nuclear astrophysics. This paper focuses mainly on a discussion of 26Al and 60Fe from massive-star nucleosynthesis.
montage: AGB Nucleosynthesis with Full s-Process Calculations
Authors: Church R. P. , Cristallo S. , Lattanzio J. C. , Stancliffe R. J. , Straniero O. , Cannon R. C.
Published: September 2009

We present montage, a post-processing nucleosynthesis code that combines a traditional network for isotopes lighter than calcium with a rapid algorithm for calculating the s-process nucleosynthesis of the heavier isotopes. The separation of those parts of the network where only neutron-capture and beta-decay reactions are significant provides a substantial advantage in computational efficiency. We present the yields for a complete set of s-process isotopes for a 3-M⊙, Z = 0.02 stellar model, as a demonstration of the utility of the approach. Future work will include a large grid of models suitable for use in calculations of Galactic chemical evolution.
Inhibition of Hsp90 via 17-DMAG induces apoptosis in a p53-dependent manner to prevent medulloblastoma
Authors: Ayrault Olivier , Godeny Michael D. , Dillon Christopher , Zindy Frederique , Fitzgerald Patrick , Roussel Martine F. , Beere Helen M.
Published: September 2009

Elevated expression of HSP90 is observed in many tumor types and is associated with a limited clinical response. Targeting HSP90 using inhibitors such as 17-DMAG (17-desmethoxy-17-N,N-dimethylaminoethylaminogeldanamycin) has shown limited therapeutic success. HSP90 regulates the function of several proteins implicated in tumorigenesis although the precise mechanism through which 17-DMAG regulates tumor cell survival remains unclear. We observed a requirement for p53 in mediating 17-DMAG-induced cell death. The sensitivity of primary mouse embryonic fibroblasts and tumor cells to 17-DMAG-induced apoptosis depended on the p53 status. Wild-type MEFs underwent 17-DMAG-induced caspase-dependent cell death, whilst those lacking p53 failed to do so. Interestingly p53-dependent cell death occurred independently ofAtmorArf. Primary tumor cells derived from two models of murine medulloblastoma (Ptch1+/−;Ink4c−/−andp53FL/FL;Nestin-Cre+;Ink4c−/−) that retain and lack p53 function, respectively, displayed a dependence on functional p53 to engage 17-DMAG-induced apoptosis. Strikingly, 17-DMAG treatment in an allograft model ofPtch1+/−;Ink4c−/−but notp53FL/FL;Nestin-Cre+;Ink4c−/−tumor cells prevented tumor growth in vivo. Our data suggest that p53 status is a likely predictor of the sensitivity of tumors to 17-DMAG.
Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas
Authors: Phillips Matthew J. , Bennett Thomas H. , Lee Michael S. Y.
Published: September 2009

The semiaquatic platypus and terrestrial echidnas (spiny anteaters) are the only living egg-laying mammals (monotremes). The fossil record has provided few clues as to their origins and the evolution of their ecological specializations; however, recent reassignment of the Early CretaceousTeinolophosandSteropodonto the platypus lineage implies that platypuses and echidnas diverged >112.5 million years ago, reinforcing the notion of monotremes as living fossils. This placement is based primarily on characters related to a single feature, the enlarged mandibular canal, which supplies blood vessels and dense electrosensory receptors to the platypus bill. Our reevaluation of the morphological data instead groups platypus and echidnas to the exclusion ofTeinolophosandSteropodonand suggests that an enlarged mandibular canal is ancestral for monotremes (partly reversed in echidnas, in association with general mandibular reduction). A multigene evaluation of the echidna–platypus divergence using both a relaxed molecular clock and direct fossil calibrations reveals a recent split of 19–48 million years ago. Platypus-like monotremes (Monotrematum) predate this divergence, indicating that echidnas had aquatically foraging ancestors that reinvaded terrestrial ecosystems. This ecological shift and the associated radiation of echidnas represent a recent expansion of niche space despite potential competition from marsupials. Monotremes might have survived the invasion of marsupials into Australasia by exploiting ecological niches in which marsupials are restricted by their reproductive mode. Morphology, ecology, and molecular biology together indicate thatTeinolophosandSteropodonare basal monotremes rather than platypus relatives, and that living monotremes are a relatively recent radiation.
Targeting lymphotoxin-mediated negative selection to prevent prostate cancer in mice with genetic predisposition
Authors: Zhou Penghui , Fang Xianfeng , McNally Beth A. , Yu Ping , Zhu Mingzhao , Fu Yang-Xin , Wang Lizhong , Liu Yang , Zheng Pan
Published: September 2009

The identification of individuals genetically susceptible to cancer calls for preventive measures to minimize the cancer risk in these high-risk populations. Immune prevention is made necessary by the anticipated health threat, but lack of enough high-affinity T cells against tumor-associated antigens and the unpredictability of tumor antigens make antigen-based immune prevention untenable for cancer. To address this issue, we explored a non-antigen-based cancer immune prevention strategy using the transgenic adenocarcinoma of mouse prostate model that spontaneously develops prostate cancer with 100% penetrance. We show that targeted mutation of the lymphotoxin α (
LT
α) gene efficiently rescued tumor-reactive T cells, drastically reduced cancer incidence, and almost completely ablated metastasis. Remarkably, short-term treatments with the fusion protein consisting of constant region of IgG and extracellular domain of lymphotoxin β receptor (LTβRIg) interrupted clonal deletion, reduced the size of the primary cancer, and completely prevented metastasis later in life. Our data demonstrated the value of non-antigen-based immune prevention for those with a genetic predisposition to cancer.
Direct measurements of kinesin torsional properties reveal flexible domains and occasional stalk reversals during stepping
Authors: Gutiérrez-Medina Braulio , Fehr Adrian N. , Block Steven M.
Published: September 2009

Kinesin is a homodimeric motor with two catalytic heads joined to a stalk via short neck linkers (NLs). We measured the torsional properties of single recombinant molecules by tracking the thermal angular motions of fluorescently labeled beads bound to the C terminus of the stalk. When kinesin heads were immobilized on microtubules (MTs) under varied nucleotide conditions, we observed bounded or unbounded angular diffusion, depending on whether one or both heads were attached to the MT. Free rotation implies that NLs act as swivels. From data on constrained diffusion, we conclude that the coiled-coil stalk domains are ≈30-fold stiffer than its flexible “hinge” regions. Surprisingly, while tracking processive kinesin motion at low ATP concentrations, we observed occasional abrupt reversals in the directional orientations of the stalk. Our results impose constraints on kinesin walking models and suggest a role for rotational freedom in cargo transport.
A coiled-coil motif that sequesters ions to the hydrophobic core
Authors: Hartmann Marcus D. , Ridderbusch Oswin , Zeth Kornelius , Albrecht Reinhard , Testa Oli , Woolfson Derek N. , Sauer Guido , Dunin-Horkawicz Stanislaw , Lupas Andrei N. , Alvarez Birte Hernandez
Published: September 2009

Most core residues of coiled coils are hydrophobic. Occasional polar residues are thought to lower stability, but impart structural specificity. The coiled coils of trimeric autotransporter adhesins (TAAs) are conspicuous for their large number of polar residues in position
d
of the core, which often leads to their prediction as natively unstructured regions. The most frequent residue, asparagine (N@
d
), can occur in runs of up to 19 consecutive heptads, frequently in the motif [I/V]xxNTxx. In the
Salmonella
TAA, SadA, the core asparagines form rings of interacting residues with the following threonines, grouped around a central anion. This conformation is observed generally in N@
d
layers from trimeric coiled coils of known structure. Attempts to impose a different register on the motif show that the asparagines orient themselves specifically into the core, even against conflicting information from flanking domains. When engineered into the GCN4 leucine zipper, N@
d
layers progressively destabilized the structure, but zippers with 3 N@
d
layers still folded at high concentration. We propose that N@
d
layers maintain the coiled coils of TAAs in a soluble, export-competent state during autotransport through the outer membrane. More generally, we think that polar motifs that are both periodic and conserved may often reflect special folding requirements, rather than an unstructured state of the mature proteins.
The Weil-Steinberg character of finite classical groups
Authors: Hiss G. , Zalesski A.
Published: September 2009

Let GGbe one of the groupsGL⁡(n,q)\operatorname {GL}(n,q)orU(n,q)U(n,q), and let HHdenote the subgroupGL⁡(n−1,q)\operatorname {GL}({n-1},q)orU(n−1,q)U(n-1,q), respectively. We show that the restriction of the Steinberg character of GGto HHequals the product of the Weil character and the Steinberg character of HH.
Gα12 Inhibits α2β1 Integrin–mediated Madin-Darby Canine Kidney Cell Attachment and Migration on Collagen-I and Blocks Tubulogenesis
Authors: Kong Tianqing , Xu Daosong , Yu Wanfeng , Takakura Ayumi , Boucher Ilene , Tran Mei , Kreidberg Jordan A. , Shah Jagesh , Zhou Jing , Denker Bradley M.
Published: September 2009

Regulation of epithelial cell attachment and migration are essential for normal development and maintenance of numerous tissues. G proteins and integrins are critical signaling proteins regulating these processes, yet in polarized cells little is known about the interaction of these pathways. Herein, we demonstrate that Gα12 inhibits interaction of MDCK cells with collagen-I, the major ligand for α2β1 integrin. Activating Gα12 (QL point mutation or stimulating endogenous Gα12 with thrombin) inhibited focal adhesions and lamellipodia formation and led to impaired cell migration. Consistent with Gα12-regulated attachment to collagen-I, Gα12-silenced MDCK cells revealed a more adherent phenotype. Inhibiting Rho kinase completely restored normal attachment in Gα12-activated cells, and there was partial recovery with inhibition of Src and protein phosphatase pathways. Gα12 activation led to decreased phosphorylation of focal adhesion kinase and paxillin with displacement of α2 integrin from the focal adhesion protein complex. Using the MDCK cell 3D-tubulogenesis assay, activated Gα12 inhibited tubulogenesis and led to the formation of cyst-like structures. Furthermore, Gα12-silenced MDCK cells were resistant to thrombin-stimulated cyst development. Taken together, these studies provide direct evidence for Gα12–integrin regulation of epithelial cell spreading and migration necessary for normal tubulogenesis.
Dkk-1 Inhibits Intestinal Epithelial Cell Migration by Attenuating Directional Polarization of Leading Edge Cells
Authors: Koch Stefan , Capaldo Christopher T. , Samarin Stanislav , Nava Porfirio , Neumaier Irmgard , Skerra Arne , Sacks David B. , Parkos Charles A. , Nusrat Asma
Published: September 2009

Wnt signaling pathways regulate proliferation, motility, and survival in a variety of human cell types. Dickkopf-1 (Dkk-1) is a secreted Wnt antagonist that has been proposed to regulate tissue homeostasis in the intestine. In this report, we show that Dkk-1 is secreted by intestinal epithelial cells after wounding and that it inhibits cell migration by attenuating the directional orientation of migrating epithelial cells. Dkk-1 exposure induced mislocalized activation of Cdc42 in migrating cells, which coincided with a displacement of the polarity protein Par6 from the leading edge. Consequently, the relocation of the microtubule organizing center and the Golgi apparatus in the direction of migration was significantly and persistently inhibited in the presence of Dkk-1. Small interfering RNA-induced down-regulation of Dkk-1 confirmed that extracellular exposure to Dkk-1 was required for this effect. Together, these data demonstrate a novel role of Dkk-1 in the regulation of directional polarization of migrating intestinal epithelial cells, which contributes to the effect of Dkk-1 on wound closure in vivo.
Early-Arriving Syp1p and Ede1p Function in Endocytic Site Placement and Formation in Budding Yeast
Authors: Stimpson Helen E. M. , Toret Christopher P. , Cheng Aaron T. , Pauly Barbara S. , Drubin David G.
Published: September 2009

Recent studies have revealed the detailed timing of protein recruitment to endocytic sites in budding yeast. However, little is understood about the early stages of their formation. Here we identify the septin-associated protein Syp1p as a component of the machinery that drives clathrin-mediated endocytosis in budding yeast. Syp1p arrives at endocytic sites early in their formation and shares unique dynamics with the EH-domain protein Ede1p. We find that Syp1p is related in amino acid sequence to several mammalian proteins one of which, SGIP1-α, is an endocytic component that binds the Ede1p homolog Eps15. Like Syp1p, SGIP1-α arrives early at sites of clathrin-mediated endocytosis, suggesting that Syp1p/Ede1p and SGIP1-α/Eps15 may have a conserved function. In yeast, both Syp1p and Ede1p play important roles in the rate of endocytic site turnover. Additionally, Ede1p is important for endocytic site formation, whereas Syp1p acts as a polarized factor that recruits both Ede1p and endocytic sites to the necks of emerging buds. Thus Ede1p and Syp1p are conserved, early-arriving endocytic proteins with roles in the formation and placement of endocytic sites, respectively.
Spatiotemporal Regulation of Chloride Intracellular Channel Protein CLIC4 by RhoA
Authors: Ponsioen Bas , van Zeijl Leonie , Langeslag Michiel , Berryman Mark , Littler Dene , Jalink Kees , Moolenaar Wouter H.
Published: September 2009

Chloride intracellular channel (CLIC) 4 is a soluble protein structurally related to omega-type glutathione-S-transferases (GSTs) and implicated in various biological processes, ranging from chloride channel formation to vascular tubulogenesis. However, its function(s) and regulation remain unclear. Here, we show that cytosolic CLIC4 undergoes rapid but transient translocation to discrete domains at the plasma membrane upon stimulation of G13-coupled, RhoA-activating receptors, such as those for lysophosphatidic acid, thrombin, and sphingosine-1-phosphate. CLIC4 recruitment is strictly dependent on Gα13-mediated RhoA activation and F-actin integrity, but not on Rho kinase activity; it is constitutively induced upon enforced RhoA-GTP accumulation. Membrane-targeted CLIC4 does not seem to enter the plasma membrane or modulate transmembrane chloride currents. Mutational analysis reveals that CLIC4 translocation depends on at least six conserved residues, including reactive Cys35, whose equivalents are critical for the enzymatic function of GSTs. We conclude that CLIC4 is regulated by RhoA to be targeted to the plasma membrane, where it may function not as an inducible chloride channel but rather by displaying Cys-dependent transferase activity toward a yet unknown substrate.
Membrane Insertion of the Pleckstrin Homology Domain Variable Loop 1 Is Critical for Dynamin-catalyzed Vesicle Scission
Authors: Ramachandran Rajesh , Pucadyil Thomas J. , Liu Ya-Wen , Acharya Sharmistha , Leonard Marilyn , Lukiyanchuk Vasyl , Schmid Sandra L.
Published: September 2009

The GTPase dynamin catalyzes the scission of deeply invaginated clathrin-coated pits at the plasma membrane, but the mechanisms governing dynamin-mediated membrane fission remain poorly understood. Through mutagenesis, we have altered the hydrophobic nature of the membrane-inserting variable loop 1 (VL1) of the pleckstrin homology (PH) domain of dynamin-1 and demonstrate that its stable insertion into the lipid bilayer is critical for high membrane curvature generation and subsequent membrane fission. Dynamin PH domain mutants defective in curvature generation regain function when assayed on precurved membrane templates in vitro, but they remain defective in the scission of clathrin-coated pits in vivo. These results demonstrate that, in concert with dynamin self-assembly, PH domain membrane insertion is essential for fission and vesicle release in vitro and for clathrin-mediated endocytosis in vivo.
SimCT: a generic tool to visualize ontology-based relationships for biological objects
Authors: Herrmann Carl , Bérard Sèverine , Tichit Laurent
Published: September 2009

Summary: We present a web-based service, SimCT, which allows to graphically display the relationships between biological objects (e.g. genes or proteins) based on their annotations to a biomedical ontology. The result is presented as a tree of these objects, which can be viewed and explored through a specific java applet designed to highlight relevant features. Unlike the numerous tools that search for overrepresented terms, SimCT draws a simplified representation of biological terms present in the set of objects, and can be applied to any ontology for which annotation data is available. Being web-based, it does not require prior installation, and provides an intuitive, easy-to-use service.

Availability:  http://tagc.univ-mrs.fr/SimCT

Contact:  carl.herrmann@univmed.fr

Supplementary information:  Supplementary data are available at Bioinformatics online
In response to ‘Can sugars be produced from fatty acids? A test case for pathway analysis tools’
Authors: Faust Karoline , Croes Didier , van Helden Jacques
Published: September 2009

Motivation: In their article entitled ‘Can sugars be produced from fatty acids? A test case for pathway analysis tools’ de Figueiredo and co-authors assess the performance of three pathway prediction tools (METATOOL, PathFinding and Pathway Hunter Tool) using the synthesis of glucose-6-phosphate (G6P) from acetyl-CoA in humans as a test case. We think that this article is biased for three reasons: (i) the metabolic networks used as input for the respective tools were of very different sizes; (ii) the ‘assessment’ is restricted to two study cases; (iii) developers are inherently more skilled to use their own tools than those developed by other people. We extended the analyses led by de Figueiredo and clearly show that the apparent superior performance of their tool (METATOOL) is partly due to the differences in input network sizes. We also see a conceptual problem in the comparison of tools that serve different purposes. In our opinion, metabolic path finding and elementary mode analysis are answering different biological questions, and should be considered as complementary rather than competitive approaches.

Contact:  kfaust@ulb.ac.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
Capture efficiency and size selectivity of hydraulic clam dredges used in fishing for ocean quahogs (Arctica islandica): simultaneous estimation in the SELECT model
Authors: Thorarinsdóttir Gudrun G. , Jacobson Larry , Ragnarsson Stefan Áki , Garcia Elena Guijarro , Gunnarsson Karl
Published: September 2009

Thorarinsdóttir, G. G., Jacobson, L., Ragnarsson, S. Á., Garcia, E. G., and Gunnarsson, K. 2010. Capture efficiency and size selectivity of hydraulic clam dredges used in fishing for ocean quahogs (Arctica islandica): simultaneous estimation in the SELECT model. – ICES Journal of Marine Science, 67: 345–354. Estimates of capture efficiency and size selectivity for commercial dredges are important in estimating stock biomass and setting catch limits for the ocean quahog off Iceland and the United States. Ocean quahogs are long-lived, slow-growing, and sensitive to overharvest resulting from poor estimates of capture efficiency and stock biomass. Capture efficiency and size selectivity were estimated simultaneously in mixed-effect SELECT models using diver and commercial dredge experiment data from the shallow-water habitats off Iceland. Estimated capture efficiency for the commercial dredge E = 92% (CV = 8%) was high for large [107.5 mm shell length (SL)] ocean quahogs. Size selectivity followed an ascending logistic curve, with L50 = 70.5 mm SL (CV 4%), a selectivity range of 17.6 mm SL, and substantial variability among experimental dredge tows. Estimated capture efficiency was higher than that for ocean quahogs in US waters, possibly because of the deep habitats off the United States or uncertainty about dredge position during US depletion experiments. Scaling maximum selectivity from the SELECT model to one reduces correlations between size-selectivity and capture-efficiency parameters and may enhance the utility of selectivity estimates in stock assessment modelling. Our experimental and modelling approach may be useful for studies with other non-mobile benthic species.
Are female monarch butterflies declining in eastern North America? Evidence of a 30-year change in sex ratios at Mexican overwintering sites
Authors: Davis Andrew K. , Rendón-Salinas Eduardo
Published: September 2009

Every autumn the entire eastern North American population of monarch butterflies (
Danaus plexippus
) undergoes a spectacular migration to overwintering sites in the mountains of central Mexico, where they form massive clusters and can number in the millions. Since their discovery, these sites have been extensively studied, and in many of these studies, monarchs were captured and sexes recorded. In a recent effort to compile the sex ratio data from these published records, a surprising trend was found, which appears to show a gradual decline in proportion of females over time. Sex ratio data from 14 collections of monarchs, all spanning 30 years and totaling 69 113 individuals, showed a significant negative correlation between proportion of females and year (
r
= −0.69,
p
= 0.007). Between 1976 and 1985, 53 per cent of overwintering monarchs were female, whereas in the last decade, 43 per cent were female. The relationship was significant with and without weighting the analyses by sampling effort. Moreover, analysis of a recent three-year dataset of sex ratios revealed no variation among nine separate colonies, so differences in sampling location did not influence the trend. Additional evidence from autumn migration collections appears to confirm that proportions of females are declining, and also suggests the sex ratio is shifting on breeding grounds. While breeding monarchs face a number of threats, one possibility is an increase in prevalence of the protozoan parasite,
Ophryocystis elektroscirrha
, which recent evidence shows affects females more so than males. Further study will be needed to determine the exact cause of this trend, but for now it should be monitored closely.
Exposure to seismic survey alters blue whale acoustic communication
Authors: Di Iorio Lucia , Clark Christopher W.
Published: September 2009

The ability to perceive biologically important sounds is critical to marine mammals, and acoustic disturbance through human-generated noise can interfere with their natural functions. Sounds from seismic surveys are intense and have peak frequency bands overlapping those used by baleen whales, but evidence of interference with baleen whale acoustic communication is sparse. Here we investigated whether blue whales (
Balaenoptera musculus
) changed their vocal behaviour during a seismic survey that deployed a low-medium power technology (sparker). We found that blue whales called consistently more on seismic exploration days than on non-exploration days as well as during periods within a seismic survey day when the sparker was operating. This increase was observed for the discrete, audible calls that are emitted during social encounters and feeding. This response presumably represents a compensatory behaviour to the elevated ambient noise from seismic survey operations.
Morphological communication: exploiting coupled dynamics in a complex mechanical structure to achieve locomotion
Authors: Rieffel John A. , Valero-Cuevas Francisco J. , Lipson Hod
Published: September 2009

Traditional engineering approaches strive to avoid, or actively suppress, nonlinear dynamic coupling among components. Biological systems, in contrast, are often rife with these dynamics. Could there be, in some cases, a benefit to high degrees of dynamical coupling? Here we present a distributed robotic control scheme inspired by the biological phenomenon of tensegrity-based mechanotransduction. This emergence of morphology-as-information-conduit or ‘morphological communication’, enabled by time-sensitive spiking neural networks, presents a new paradigm for the decentralized control of large, coupled, modular systems. These results significantly bolster, both in magnitude and in form, the idea of morphological computation in robotic control. Furthermore, they lend further credence to ideas of embodied anatomical computation in biological systems, on scales ranging from cellular structures up to the tendinous networks of the human hand.
Enhancement of natural background gamma-radiation dose around uranium microparticles in the human body
Authors: Pattison John E. , Hugtenburg Richard P. , Green Stuart
Published: September 2009

Ongoing controversy surrounds the adverse health effects of the use of depleted uranium (DU) munitions. The biological effects of gamma-radiation arise from the direct or indirect interaction between secondary electrons and the DNA of living cells. The probability of the absorption of X-rays and gamma-rays with energies below about 200 keV by particles of high atomic number is proportional to the third to fourth power of the atomic number. In such a case, the more heavily ionizing low-energy recoil electrons are preferentially produced; these cause dose enhancement in the immediate vicinity of the particles. It has been claimed that upon exposure to naturally occurring background gamma-radiation, particles of DU in the human body would produce dose enhancement by a factor of 500–1000, thereby contributing a significant radiation dose in addition to the dose received from the inherent radioactivity of the DU. In this study, we used the Monte Carlo code EGSnrc to accurately estimate the likely maximum dose enhancement arising from the presence of micrometre-sized uranium particles in the body. We found that although the dose enhancement is significant, of the order of 1–10, it is considerably smaller than that suggested previously.
Environment, but not migration rate, influences extinction risk in experimental metapopulations
Authors: Griffen Blaine D. , Drake John M.
Published: September 2009

Ecological theory suggests that several demographic factors influence metapopulation extinction risk, including synchrony in population size between subpopulations, metapopulation size and the magnitude of fluctuations in population size. Theoretically, each of these is influenced by the rate of migration between subpopulations. Here we report on an experiment where we manipulated migration rate within metapopulations of the freshwater zooplanktonDaphnia magnato examine how migration influenced each of these demographic variables, and subsequent effects on metapopulation extinction. In addition, our experimental procedures introduced unplanned but controlled differences between metapopulations in light intensity, enabling us to examine the relative influences of environmental and demographic factors. We found that increasing migration rate increased subpopulation synchrony. We failed to detect effects of migration on population size and fluctuations in population size at the metapopulation or subpopulation level, however. In contrast, light intensity did not influence synchrony, but was positively correlated with population size and negatively correlated with population fluctuation. Finally, synchrony did not influence time to extinction, while population size and the magnitude of fluctuations did. We conclude that environmental factors had a greater influence on extinction risk than demographic factors, and that metapopulation size and fluctuation were more important to extinction risk than metapopulation synchrony.
Life history influences rates of climatic niche evolution in flowering plants
Authors: Smith Stephen A. , Beaulieu Jeremy M.
Published: September 2009

Across angiosperms, variable rates of molecular substitution are linked with life-history attributes associated with woody and herbaceous growth forms. As the number of generations per unit time is correlated with molecular substitution rates, it is expected that rates of phenotypic evolution would also be influenced by differences in generation times. Here, we make the first broad-scale comparison of growth-form-dependent rates of niche evolution. We examined the climatic niches of species on large time-calibrated phylogenies of five angiosperm clades and found that woody lineages have accumulated fewer changes per million years in climatic niche space than related herbaceous lineages. Also, climate space explored by woody lineages is consistently smaller than sister lineages composed mainly of herbaceous taxa. This pattern is probably linked to differences in the rate of climatic niche evolution. These results have implications for niche conservatism; in particular, the role of niche conservatism in the distribution of plant biodiversity. The consistent differences in the rate of climatic niche evolution also emphasize the need to incorporate models of phenotypic evolution that allow for rate heterogeneity when examining large datasets.
Noise improves collective decision-making by ants in dynamic environments
Authors: Dussutour A. , Beekman M. , Nicolis S. C. , Meyer B.
Published: September 2009

Recruitment via pheromone trails by ants is arguably one of the best-studied examples of self-organization in animal societies. Yet it is still unclear if and how trail recruitment allows a colony to adapt to changes in its foraging environment. We study foraging decisions by colonies of the antPheidole megacephalaunder dynamic conditions. Our experiments show thatP. megacephala, unlike many other mass recruiting species, can make a collective decision for the better of two food sources even when the environment changes dynamically. We developed a stochastic differential equation model that explains our data qualitatively and quantitatively. Analysing this model reveals that both deterministic and stochastic effects (noise) work together to allow colonies to efficiently track changes in the environment. Our study thus suggests that a certain level of noise is not a disturbance in self-organized decision-making but rather serves an important functional role.
LIN, a Novel Type of U-Box/WD40 Protein, Controls Early Infection by Rhizobia in Legumes
Authors: Kiss Ernö , Oláh Boglárka , Kaló Péter , Morales Monica , Heckmann Anne B. , Borbola Andrea , Lózsa Anita , Kontár Katalin , Middleton Patrick , Downie J. Allan , Oldroyd Giles E.D. , Endre Gabriella
Published: September 2009

The formation of a nitrogen-fixing nodule requires the coordinated development of rhizobial colonization and nodule organogenesis. Based on its mutant phenotype, lumpy infections (lin), LIN functions at an early stage of the rhizobial symbiotic process, required for both infection thread growth in root hair cells and the further development of nodule primordia. We show that spontaneous nodulation activated by the calcium- and calmodulin-dependent protein kinase is independent of LIN; thus, LIN is not necessary for nodule organogenesis. From this, we infer that LIN predominantly functions during rhizobial colonization and that the abortion of this process in lin mutants leads to a suppression of nodule development. Here, we identify the LIN gene in Medicago truncatula and Lotus japonicus, showing that it codes for a predicted E3 ubiquitin ligase containing a highly conserved U-box and WD40 repeat domains. Ubiquitin-mediated protein degradation is a universal mechanism to regulate many biological processes by eliminating rate-limiting enzymes and key components such as transcription factors. We propose that LIN is a regulator of the component(s) of the nodulation factor signal transduction pathway and that its function is required for correct temporal and spatial activity of the target protein(s).
Altered Architecture and Enhanced Drought Tolerance in Rice via the Down-Regulation of Indole-3-Acetic Acid by TLD1/OsGH3.13 Activation
Authors: Zhang Sheng-Wei , Li Chen-Hui , Cao Jia , Zhang Yong-Cun , Zhang Su-Qiao , Xia Yu-Feng , Sun Da-Ye , Sun Ying
Published: September 2009

Plant architecture is determined by genetic and developmental programs as well as by environmental factors. Sessile plants have evolved a subtle adaptive mechanism that allows them to alter their growth and development during periods of stress. Phytohormones play a central role in this process; however, the molecules responsible for integrating growth- and stress-related signals are unknown. Here, we report a gain-of-function rice (Oryza sativa) mutant, tld1-D, characterized by (and named for) an increased number of tillers, enlarged leaf angles, and dwarfism. TLD1 is a rice GH3.13 gene that encodes indole-3-acetic acid (IAA)-amido synthetase, which is suppressed in aboveground tissues under normal conditions but which is dramatically induced by drought stress. The activation of TLD1 reduced the IAA maxima at the lamina joint, shoot base, and nodes, resulting in subsequent alterations in plant architecture and tissue patterning but enhancing drought tolerance. Accordingly, the decreased level of free IAA in tld1-D due to the conjugation of IAA with amino acids greatly facilitated the accumulation of late-embryogenesis abundant mRNA compared with the wild type. The direct regulation of such drought-inducible genes by changes in the concentration of IAA provides a model for changes in plant architecture via the process of drought adaptation, which occurs frequently in nature.
Mesalazine inhibits the β‐catenin signalling pathway acting through the upregulation of μ‐protocadherin gene in colo‐rectal cancer cells
Authors: PARENTI S. , FERRARINI F. , ZINI R. , MONTANARI M. , LOSI L. , CANOVI B. , FERRARI S. , GRANDE A.
Published: September 2009

Background  Several reports indicate that mesalazine (5‐aminosalicylic acid, 5‐ASA) is a promising candidate for the chemoprevention of colo‐rectal cancer because of its ability to reach the purpose avoiding the unwanted side effects usually associated with prolonged administration of nonsteroidal anti‐inflammatory drugs. This activity of 5‐ASA is probably the consequence of a number of effects determined on colo‐rectal cancer cells, consisting of reduced proliferation, increased apoptosis and activation of cell cycle checkpoints and DNA repair processes. A recent observation has suggested that inhibition of β‐catenin signalling could induce these cellular effects.

Aim  To characterize better the capacity of 5‐ASA to inhibit the β‐catenin signalling pathway.

Methods  Genes belonging to the β‐catenin signalling pathway were analysed in colo‐rectal cancer cell lines treated with 5‐ASA using a combination of laboratory assays that are able to detect their phenotypic expression and functional activity.

Results  The results obtained indicated that 5‐ASA induces the expression of a protein called μ‐protocadherin that belongs to the cadherin superfamily and is able to sequester β‐catenin on the plasmatic membrane of treated cells hampering its function.

Conclusion  These findings suggest that μ‐protocadherin might be employed as a biological marker to monitor the chemopreventive efficacy of 5‐ASA.
A comparison of the acid‐inhibitory effects of esomeprazole and pantoprazole in relation to pharmacokinetics and CYP2C19 polymorphism
Authors: HUNFELD N. G. , TOUW D. J. , MATHOT R. A. , MULDER P. G. H. , VAN SCHAIK R. H. , KUIPERS E. J. , KOOIMAN J. C. , GEUS W. P.
Published: September 2009

Background Esomeprazole and pantoprazole are metabolized in the liver and the polymorphic CYP2C19 enzyme is involved in that process. This genetic polymorphism determines fast (70% of Caucasians), intermediate (25–30% of Caucasians) and slow (2–5% of Caucasians) metabolism of PPIs.

Aim To compare the acid‐inhibitory effects of esomeprazole 40 mg and pantoprazole 40 mg at 4, 24 and 120 h after oral administration in relation to CYP2C19 genotype and pharmacokinetics.

Methods CYP2C19*2, *3, *4, *5 and *17 genotypes were determined in healthyHelicobacter pylori‐negative Caucasian subjects. 7 wt/wt, 7 wt/*2, 2 wt/*17, 2 *2/*17 and 1 *2/*2 were included in a randomized investigator‐blinded cross‐over study with esomeprazole 40 mg and pantoprazole 40 mg. Intragastric 24‐h pH‐monitoring was performed on days 0, 1 and 5 of oral dosing.

Results A total of 19 subjects (mean age 24 years, 7 male) completed the study. At day 1 and 5, acid‐inhibition with esomeprazole was significantly greater and faster than with pantoprazole. Differences in acid‐inhibition and pharmacokinetics between wt/wt and wt/*2 genotype were significant for pantoprazole at day 1 and 5.

Conclusions Esomeprazole provides acid‐inhibition faster than and superior to pantoprazole after single and repeated administration. The acid‐inhibitory effect and the kinetics of pantoprazole are influenced by CYP2C19 genotype.
An investigation of medication adherence to 5‐aminosalicylic acid therapy in patients with ulcerative colitis, using self‐report and urinary drug excretion measurements
Authors: MOSHKOVSKA T. , STONE M. A. , CLATWORTHY J. , SMITH R. M. , BANKART J. , BAKER R. , WANG J. , HORNE R. , MAYBERRY J. F.
Published: September 2009

Background Non‐adherence to 5‐aminosalicylic acid (5‐ASA) medication can limit the established benefits of this therapy in ulcerative colitis (UC).

Aim To determine rates and predictors of non‐adherence to 5‐ASA therapy in UC patients.

Methods Medication adherence was assessed using self‐report data and urinary drug excretion measurements. Participants completed a study‐specific questionnaire and two validated questionnaires: Beliefs about Medicine Questionnaire (BMQ)‐Specific and Satisfaction with Information about Medicines Scale.

Results A total of 169 participants provided self‐report adherence data; 151 also provided urine samples. Adherence rates were 111/151 (68%) according to self‐report and 90/151 (60%) according to urine analysis, but the two measures were not correlated (χ2 = 0.12,P = 0.725). Logistic regression identified a significant association between self‐reported non‐adherence and younger age [odds ratio (OR) for increased age 0.954, 95% confidence interval (CI) 0.932–0.976] and also doubts about personal need for medication (OR for BMQ – Specific Necessity scores 0.578, 95% CI 0.366–0.913). For non‐adherence based on urine analysis, only South Asian ethnicity was independently associated with non‐adherence (OR 2.940, 95% CI 1.303–6.638).

Conclusions Our observations confirm the difficulty of accurately assessing medication adherence. Nonmodifiable (younger age, South Asian ethnicity) and potentially modifiable (medication beliefs) predictors of non‐adherence were identified.
Effects of DGAT1 and GHR on milk yield and milk composition in the Chinese dairy population
Authors: Sun D. , Jia J. , Ma Y. , Zhang Y. , Wang Y. , Yu Y. , Zhang Y.
Published: September 2009

Previous studies have demonstrated that the p.Lys232Ala substitution in the acylCoA: diacylglycerol acyltransferase (DGAT1) gene and the p.Phe279Tyr mutation in the growth hormone receptor (GHR) gene are the causative quantitative trait loci underlying milk yield and composition on BTA14 and BTA20 respectively. To examine their applications in the genetic improvement of Chinese dairy cattle productivity, we herein investigated the effects of the DGAT1 p.Lys232Ala and GHR p.Phe279Tyr mutations on milk, fat and protein yield, as well as fat and protein percentage in the milk of 1222 Holstein cows. Genotyping was performed using PCR‐RFLP for DGAT1 or primer‐introduced restriction analysis (PCR‐PIRA) for GHR. With a mixed animal model, the significant associations of the DGAT1 p.Lys232Ala substitution with 305‐day milk, fat and protein yield were identified (P = 0.0001). The DGAT1 allele that encode lysine at position 232 was associated with increased 305‐day milk fat yield, but with decreased 305‐day milk and protein yield, whereas the GHR p.Phe279Tyr mutation was found to be significantly associated with protein percentage (P = 0.0014). The allele substitution effect of p.279Phe by p.279Tyr may lead to a significant increase in protein percentage. Our findings indicate that DGAT1 p.232Ala and GHR p.279Phe could be used to increase milk yield and protein yield of Chinese Holstein cows.