bluuebunny/crossref_metadata_2025 huggingface dataset:
Cdc42-dependent Modulation of Tight Junctions and Membrane Protein Traffic in Polarized Madin-Darby Canine Kidney Cells
Authors: Rojas Raul , Ruiz Wily G. , Leung Som-Ming , Jou Tzuu-Shuh , Apodaca Gerard
Published: July 2013

Polarized epithelial cells maintain the asymmetric composition of their apical and basolateral membrane domains by at least two different processes. These include the regulated trafficking of macromolecules from the biosynthetic and endocytic pathway to the appropriate membrane domain and the ability of the tight junction to prevent free mixing of membrane domain-specific proteins and lipids. Cdc42, a Rho family GTPase, is known to govern cellular polarity and membrane traffic in several cell types. We examined whether this protein regulated tight junction function in Madin-Darby canine kidney cells and pathways that direct proteins to the apical and basolateral surface of these cells. We used Madin-Darby canine kidney cells that expressed dominant-active or dominant-negative mutants of Cdc42 under the control of a tetracycline-repressible system. Here we report that expression of dominant-active Cdc42V12 or dominant-negative Cdc42N17 altered tight junction function. Expression of Cdc42V12 slowed endocytic and biosynthetic traffic, and expression of Cdc42N17 slowed apical endocytosis and basolateral to apical transcytosis but stimulated biosynthetic traffic. These results indicate that Cdc42 may modulate multiple cellular pathways required for the maintenance of epithelial cell polarity.
A Conserved Mechanism of Synaptogyrin Localization
Authors: Zhao Hongjuan , Nonet Michael L.
Published: July 2013

We have studied the localization of synaptogyrin family members in vivo. Both native and green fluorescent protein (GFP)-taggedCaenorhabditis elegans synaptogyrin (SNG-1) are expressed in neurons and synaptically localized. Deletion and mutational analysis with the use of GFP-tagged SNG-1 has defined a 38 amino acid sequence within the C terminus of SNG-1 and a single arginine in the cytoplasmic loop between transmembrane domain 2 and 3 that are required for SNG-1 localization. These domains may represent components of signals that target synaptogyrin for endocytosis from the plasma membrane and direct synaptogyrin to synaptic vesicles, respectively. In chimeric studies, these regions were sufficient to relocalize cellugyrin, a nonneuronal form of synaptogyrin, from nonsynaptic regions such as the sensory dendrites and the cell body to synaptic vesicles. Furthermore, GFP-tagged rat synaptogyrin is synaptically localized in neurons of C. elegans and in cultured hippocampal neurons. Similarly, the C-terminal domain of rat synaptogyrin is necessary for localization in hippocampal neurons. Our study suggests that the mechanisms for synaptogyrin localization are likely to be conserved from C. elegans to vertebrates.
The Proteasomal Substrate Stm1 Participates in Apoptosis-like Cell Death in Yeast
Authors: Ligr Martin , Velten Iris , Fröhlich Eleonore , Madeo Frank , Ledig Matthias , Fröhlich Kai-Uwe , Wolf Dieter H. , Hilt Wolfgang
Published: July 2013

We have identified the yeast gene STM1 in an overexpression screen for new proteasomal substrates. Stm1 is unstable in wild-type cells and stabilized in cells with defective proteasomal activity and thus a bona fide substrate of the proteasome. It is localized in the perinuclear region and is required for growth in the presence of mutagens. Overexpression in cells with impaired proteasomal degradation leads to cell death accompanied with cytological markers of apoptosis: loss of plasma membrane asymmetry, chromatin condensation, and DNA cleavage. Cells lacking Stm1 display deficiency in the apoptosis-like cell death process induced by treatment with low concentrations of H2O2. We suggest that Stm1 is involved in the control of the apoptosis-like cell death in yeast. Survival is increased when Stm1 is completely missing from the cells or when inhibition of Stm1 synthesis permits proteasomal degradation to decrease its amount in the cell. Conversely, Stm1 accumulation induces cell death. In addition we identified five other genes whose overexpression in proteasomal mutants caused similar apoptotic phenotypes.
Actin Polymerization Is Essential for Pollen Tube Growth
Authors: Vidali Luis , McKenna Sylvester T. , Hepler Peter K.
Published: July 2013

Actin microfilaments, which are prominent in pollen tubes, have been implicated in the growth process; however, their mechanism of action is not well understood. In the present work we have used profilin and DNAse I injections, as well as latrunculin B and cytochalasin D treatments, under quantitatively controlled conditions, to perturb actin microfilament structure and assembly in an attempt to answer this question. We found that a ∼50% increase in the total profilin pool was necessary to half-maximally inhibit pollen tube growth, whereas a ∼100% increase was necessary for half-maximal inhibition of cytoplasmic streaming. DNAse I showed a similar inhibitory activity but with a threefold more pronounced effect on growth than streaming. Latrunculin B, at only 1–4 nM in the growth medium, has a similar proportion of inhibition of growth over streaming to that of profilin. The fact that tip growth is more sensitive than streaming to the inhibitory substances and that there is no correlation between streaming and growth rates suggests that tip growth requires actin assembly in a process independent of cytoplasmic streaming.
Proteasome Inhibitors Block a Late Step in Lysosomal Transport of Selected Membrane but not Soluble Proteins
Authors: van Kerkhof Peter , dos Santos Cristina M. Alves , Sachse Martin , Klumperman Judith , Bu Guojun , Strous Ger J.
Published: July 2013

The ubiquitin-proteasome pathway acts as a regulator of the endocytosis of selected membrane proteins. Recent evidence suggests that it may also function in the intracellular trafficking of membrane proteins. In this study, several models were used to address the role of the ubiquitin-proteasome pathway in sorting of internalized proteins to the lysosome. We found that lysosomal degradation of ligands, which remain bound to their receptors within the endocytic pathway, is blocked in the presence of specific proteasome inhibitors. In contrast, a ligand that dissociates from its receptor upon endosome acidification is degraded under the same conditions. Quantitative electron microscopy showed that neither the uptake nor the overall distribution of the endocytic marker bovine serum albumin-gold is substantially altered in the presence of a proteasome inhibitor. The data suggest that the ubiquitin-proteasome pathway is involved in an endosomal sorting step of selected membrane proteins to lysosomes, thereby providing a mechanism for regulated degradation.
Dynamin GTPase Domain Mutants Block Endocytic Vesicle Formation at Morphologically Distinct Stages
Authors: Damke Hanna , Binns Derk D. , Ueda Hideho , Schmid Sandra L. , Baba Takeshi
Published: July 2013

Abundant evidence has shown that the GTPase dynamin is required for receptor-mediated endocytosis, but its exact role in endocytic clathrin-coated vesicle formation remains to be established. Whereas dynamin GTPase domain mutants that are defective in GTP binding and hydrolysis are potent dominant-negative inhibitors of receptor-mediated endocytosis, overexpression of dynamin GTPase effector domain (GED) mutants that are selectively defective in assembly-stimulated GTPase-activating protein activity can stimulate the formation of constricted coated pits and receptor-mediated endocytosis. These apparently conflicting results suggest that a complex relationship exists between dynamin's GTPase cycle of binding and hydrolysis and its role in endocytic coated vesicle formation. We sought to explore this complex relationship by generating dynamin GTPase mutants predicted to be defective at distinct stages of its GTPase cycle and examining the structural intermediates that accumulate in cells overexpressing these mutants. We report that the effects of nucleotide-binding domain mutants on dynamin's GTPase cycle in vitro are not as predicted by comparison to other GTPase superfamily members. Specifically, GTP and GDP association was destabilized for each of the GTPase domain mutants we analyzed. Nonetheless, we find that overexpression of dynamin mutants with subtle differences in their GTPase properties can lead to the accumulation of distinct intermediates in endocytic coated vesicle formation.
ADY1, A Novel Gene Required for Prospore Membrane Formation at Selected Spindle Poles inSaccharomyces cerevisiae
Authors: Deng Changchun , Saunders William S.
Published: July 2013

ADY1 is identified in a genetic screen for genes on chromosome VIII of Saccharomyces cerevisiae that are required for sporulation. ADY1 is not required for meiotic recombination or meiotic chromosome segregation, but it is required for the formation of four spores inside an ascus. In the absence of ADY1, prospore formation is restricted to mainly one or two spindle poles per cell. Moreover, the two spores in the dyads of the ady1 mutant are predominantly nonsisters, suggesting that the proficiency to form prospores is not randomly distributed to the four spindle poles in theady1 mutant. Interestingly, the meiosis-specific spindle pole body component Mpc54p, which is known to be required for prospore membrane formation, is localized predominantly to only one or two spindle poles per cell in the ady1 mutant. A partially functional Myc-Pfs1p is localized to the nucleus of mononucleate meiotic cells but not to the spindle pole body or prospore membrane. These results suggest that Pfs1p is specifically required for prospore formation at selected spindle poles, most likely by ensuring the functionality of all four spindle pole bodies of a cell during meiosis II.
Involvement of Integrin αvβ3and Cell Adhesion Molecule L1 in Transendothelial Migration of Melanoma Cells
Authors: Voura Evelyn B. , Ramjeesingh Ravi A. , Montgomery Anthony M.P. , Siu Chi-Hung
Published: July 2013

Tumor metastasis involves many stage-specific adhesive interactions. The expression of several cell adhesion molecules, notably the integrin αvβ3, has been associated with the metastatic potential of tumor cells. In this study, we used a novel in vitro assay to examine the role of αvβ3in the transmigration of melanoma cells through a monolayer of human lung microvascular endothelial cells. Confocal microscopy revealed the presence of the integrin αvβ3on melanoma membrane protrusions and pseudopods penetrating the endothelial junction. αvβ3was also enriched in heterotypic contacts between endothelial cells and melanoma cells. Transendothelial migration of melanoma cells was inhibited by either a cyclic Arg-Gly-Asp peptide or the anti-αvβ3monoclonal antibody LM609. Although both platelet endothelial cell adhesion molecule-1 and L1 are known to bind integrin αvβ3, only L1 serves as a potential ligand for αvβ3during melanoma transendothelial migration. Also, polyclonal antibodies against L1 partially inhibited the transendothelial migration of melanoma cells. However, addition of both L1 and αvβ3antibodies did not show additive effects, suggesting that they are components of the same adhesion system. Together, the data suggest that interactions between the integrin αvβ3on melanoma cells and L1 on endothelial cells play an important role in the transendothelial migration of melanoma cells.
Alpha-Smooth Muscle Actin Expression Upregulates Fibroblast Contractile Activity
Authors: Hinz Boris , Celetta Giuseppe , Tomasek James J. , Gabbiani Giulio , Chaponnier Christine
Published: July 2013

To evaluate whether α-smooth muscle actin (α-SMA) plays a role in fibroblast contractility, we first compared the contractile activity of rat subcutaneous fibroblasts (SCFs), expressing low levels of α-SMA, with that of lung fibroblasts (LFs), expressing high levels of α-SMA, with the use of silicone substrates of different stiffness degrees. On medium stiffness substrates the percentage of cells producing wrinkles was similar to that of α-SMA–positive cells in each fibroblast population. On high stiffness substrates, wrinkle production was limited to a subpopulation of LFs very positive for α-SMA. In a second approach, we measured the isotonic contraction of SCF- and LF-populated attached collagen lattices. SCFs exhibited 41% diameter reduction compared with 63% by LFs. TGFβ1 increased α-SMA expression and lattice contraction by SCFs to the levels of LFs; TGFβ-antagonizing agents reduced α-SMA expression and lattice contraction by LFs to the level of SCFs. Finally, 3T3 fibroblasts transiently or permanently transfected with α-SMA cDNA exhibited a significantly higher lattice contraction compared with wild-type 3T3 fibroblasts or to fibroblasts transfected with α-cardiac and β- or γ-cytoplasmic actin. This took place in the absence of any change in smooth muscle or nonmuscle myosin heavy-chain expression. Our results indicate that an increased α-SMA expression is sufficient to enhance fibroblast contractile activity.
Dicentric Chromosome Stretching during Anaphase Reveals Roles of Sir2/Ku in Chromatin Compaction in Budding Yeast
Authors: Thrower Douglas A. , Bloom Kerry
Published: July 2013

We have used mitotic spindle forces to examine the role of Sir2 and Ku in chromatin compaction. Escherichia coli lac operator DNA was placed between two centromeres on a conditional dicentric chromosome in budding yeast cells and made visible by expression of a lac repressor–green fluorescent fusion protein. Centromeres on the same chromatid of a dicentric chromosome attach to opposite poles ∼50% of the time, resulting in chromosome bridges during anaphase. In cells deleted for yKU70,yKU80, or SIR2, a 10-kb region of the dicentric chromosome stretched along the spindle axis to a length of 6 μm during anaphase. On spindle disassembly, stretched chromatin recoiled to the bud neck and was partitioned to mother and daughter cells after cytokinesis and cell separation. Chromatin immunoprecipitation revealed that Sir2 localizes to the lacO region in response to activation of the dicentric chromosome. These findings indicate that Ku and Sir proteins are required for proper chromatin compaction within regions of a chromosome experiencing tension or DNA damage. The association of Sir2 with the affected region suggests a direct role in this process, which may include the formation of heterochromatic DNA.
Sequential Activities of Phosphoinositide 3-Kinase, PKB/Akt, and Rab7 during Macropinosome Formation inDictyostelium
Authors: Rupper Adam , Lee Kyung , Knecht David , Cardelli James
Published: July 2013

Macropinocytosis plays an important role in the internalization of antigens by dendritic cells and is the route of entry for many bacterial pathogens; however, little is known about the molecular mechanisms that regulate the formation or maturation of macropinosomes. Like dendritic cells, Dictyostelium amoebae are active in macropinocytosis, and various proteins have been identified that contribute to this process. As described here, microscopic analysis of null mutants have revealed that the class I phosphoinositide 3-kinases, PIK1 and PIK2, and the downstream effector protein kinase B (PKB/Akt) are important in regulating completion of macropinocytosis. Although actin-rich membrane protrusions form in these cell lines, they recede without forming macropinosomes. Imaging of cells expressing green fluorescent protein (GFP) fused to the pleckstrin homology domain (PH) of PKB (GFP-PHPKB) indicates that D3 phosphoinositides are enriched in the forming macropinocytic cup and remain associated with newly formed macropinosomes for <1 minute. A fusion protein, consisting of GFP fused to an F-actin binding domain, overlaps with GFP-PHPKB in the timing of association with forming macropinosomes. Although macropinocytosis is reduced in cells expressing dominant negative Rab7, microscopic imaging studies reveal that GFP-Rab7 associates only with formed macropinosomes at approximately the time that F-actin and D3 phosphoinositide levels decrease. These results support a model in which F-actin modulating proteins and vesicle trafficking proteins coordinately regulate the formation and maturation of macropinosomes.
MAP-1 and IAP-1, Two Novel AAA Proteases with Catalytic Sites on Opposite Membrane Surfaces in Mitochondrial Inner Membrane ofNeurospora crassa
Authors: Klanner Carola , Prokisch Holger , Langer Thomas
Published: July 2013

Eukaryotic AAA proteases form a conserved family of membrane-embedded ATP-dependent proteases but have been analyzed functionally only in the yeast Saccharomyces cerevisiae. Here, we have identified two novel members of this protein family in the filamentous fungus Neurospora crassa, which were termed MAP-1 and IAP-1. Both proteins are localized to the inner membrane of mitochondria. They are part of two similar-sized high molecular mass complexes, but expose their catalytic sites to opposite membrane surfaces, namely, the intermembrane and the matrix space. Disruption of iap-1 by repeat-induced point mutation caused a slow growth phenotype at high temperature and stabilization of a misfolded inner membrane protein against degradation. IAP-1 could partially substitute for functions of its yeast homolog Yme1, demonstrating functional conservation. However, respiratory growth at 37°C was not restored. Our results identify two components of the quality control system of the mitochondrial inner membrane in N. crassa and suggest that AAA proteases with catalytic sites exposed to opposite membrane surfaces are present in mitochondria of all eukaryotic cells.
Data-based filtering for replicated high-throughput transcriptome sequencing experiments
Authors: Rau Andrea , Gallopin Mélina , Celeux Gilles , Jaffrézic Florence
Published: July 2013

Motivation: RNA sequencing is now widely performed to study differential expression among experimental conditions. As tests are performed on a large number of genes, stringent false-discovery rate control is required at the expense of detection power. Ad hoc filtering techniques are regularly used to moderate this correction by removing genes with low signal, with little attention paid to their impact on downstream analyses.

Results: We propose a data-driven method based on the Jaccard similarity index to calculate a filtering threshold for replicated RNA sequencing data. In comparisons with alternative data filters regularly used in practice, we demonstrate the effectiveness of our proposed method to correctly filter lowly expressed genes, leading to increased detection power for moderately to highly expressed genes. Interestingly, this data-driven threshold varies among experiments, highlighting the interest of the method proposed here.

Availability: The proposed filtering method is implemented in the R package HTSFilter available on Bioconductor.

Contact:  andrea.rau@jouy.inra.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
First direct measurements of behavioural responses by Cuvier's beaked whales to mid-frequency active sonar
Authors: DeRuiter Stacy L. , Southall Brandon L. , Calambokidis John , Zimmer Walter M. X. , Sadykova Dinara , Falcone Erin A. , Friedlaender Ari S. , Joseph John E. , Moretti David , Schorr Gregory S. , Thomas Len , Tyack Peter L.
Published: July 2013

Most marine mammal­ strandings coincident with naval sonar exercises have involved Cuvier's beaked whales (Ziphius cavirostris). We recorded animal movement and acoustic data on two taggedZiphiusand obtained the first direct measurements of behavioural responses of this species to mid-frequency active (MFA) sonar signals. Each recording included a 30-min playback (one 1.6-s simulated MFA sonar signal repeated every 25 s); one whale was also incidentally exposed to MFA sonar from distant naval exercises. Whales responded strongly to playbacks at low received levels (RLs; 89–127 dB re 1 µPa): after ceasing normal fluking and echolocation, they swam rapidly, silently away, extending both dive duration and subsequent non-foraging interval. Distant sonar exercises (78–106 dB re 1 µPa) did not elicit such responses, suggesting that context may moderate reactions. The observed responses to playback occurred at RLs well below current regulatory thresholds; equivalent responses to operational sonars could elevate stranding risk and reduce foraging efficiency.
Deleterious consequences of antioxidant supplementation on lifespan in a wild-derived mammal
Authors: Selman Colin , McLaren Jane S. , Collins Andrew R. , Duthie Garry G. , Speakman John R.
Published: July 2013

While oxidative damage owing to reactive oxygen species (ROS) often increases with advancing age and is associated with many age-related diseases, its causative role in ageing is controversial. In particular, studies that have attempted to modulate ROS-induced damage, either upwards or downwards, using antioxidant or genetic approaches, generally do not show a predictable effect on lifespan. Here, we investigated whether dietary supplementation with either vitamin E (α-tocopherol) or vitamin C (ascorbic acid) affected oxidative damage and lifespan in short-tailed field voles,
Microtus agrestis
. We predicted that antioxidant supplementation would reduce ROS-induced oxidative damage and increase lifespan relative to unsupplemented controls. Antioxidant supplementation for nine months reduced hepatic lipid peroxidation, but DNA oxidative damage to hepatocytes and lymphocytes was unaffected. Surprisingly, antioxidant supplementation significantly shortened lifespan in voles maintained under both cold (7 ± 2°C) and warm (22 ± 2°C) conditions. These data further question the predictions of free-radical theory of ageing and critically, given our previous research in mice, indicate that similar levels of antioxidants can induce widely different interspecific effects on lifespan.
Prediction of fracture healing under axial loading, shear loading and bending is possible using distortional and dilatational strains as determining mechanical stimuli
Authors: Steiner Malte , Claes Lutz , Ignatius Anita , Niemeyer Frank , Simon Ulrich , Wehner Tim
Published: July 2013

Numerical models of secondary fracture healing are based on mechanoregulatory algorithms that use distortional strain alone or in combination with either dilatational strain or fluid velocity as determining stimuli for tissue differentiation and development. Comparison of these algorithms has previously suggested that healing processes under torsional rotational loading can only be properly simulated by considering fluid velocity and deviatoric strain as the regulatory stimuli. We hypothesize that sufficient calibration on uncertain input parameters will enhance our existing model, which uses distortional and dilatational strains as determining stimuli, to properly simulate fracture healing under various loading conditions including also torsional rotation. Therefore, we minimized the difference between numerically simulated and experimentally measured courses of interfragmentary movements of two axial compressive cases and two shear load cases (torsional and translational) by varying several input parameter values within their predefined bounds. The calibrated model was then qualitatively evaluated on the ability to predict physiological changes of spatial and temporal tissue distributions, based on respectivein vivodata. Finally, we corroborated the model on five additional axial compressive and one asymmetrical bending load case. We conclude that our model, using distortional and dilatational strains as determining stimuli, is able to simulate fracture-healing processes not only under axial compression and torsional rotation but also under translational shear and asymmetrical bending loading conditions.
Directional reflectance and milli-scale feather morphology of the African Emerald Cuckoo,Chrysococcyx cupreus
Authors: Harvey Todd Alan , Bostwick Kimberly S. , Marschner Steve
Published: July 2013

Diverse plumages have evolved among birds through complex morphological modifications. We investigate how the interplay of light with surface and subsurface feather morphology determines thedirectionof light propagation, an understudied aspect of avian visual signalling. We hypothesize that milli-scale modifications of feathers produce anisotropic reflectance, the direction of which may be predicted by the orientation of the milli-scale structure. The subject of this study is the African Emerald Cuckoo,Chrysococcyx cupreus, noted for its shimmering green iridescent appearance. Using a spherical gantry, we measured the change in the directional reflectance across the feather surface and over a hemisphere of incident lighting directions. Using a microCT scanner, we also studied the morphology of the structural branches of the barb. We tracked the changes in the directional reflectance to the orientation of the structural branches as observed in the CT data. We conclude that (i) the far-field signal of the feather consists of multiple specular components, each associated with a different structural branch and (ii) the direction of each specular component is correlated to the orientation of the corresponding structure.
Male clasping ability, female polymorphism and sexual conflict: fine-scale elytral morphology as a sexually antagonistic adaptation in female diving beetles
Authors: Karlsson Green Kristina , Kovalev Alexander , Svensson Erik I. , Gorb Stanislav N.
Published: July 2013

During sexual conflict, males and females are expected to evolve traits and behaviours with a sexually antagonistic function. Recently, sexually antagonistic coevolution was proposed to occur between male and female diving beetles (Dytiscidae). Male diving beetles possess numerous suction cups on their forelegs whereas females commonly have rough structures on their elytra. These rough structures have been suggested to obstruct adhesion from male suction cups during mating attempts. However, some diving beetle species are dimorphic, where one female morph has a rough elytra and the other has a smooth elytra. Here, we used biomechanics to study the adhesive performance of male suction cups on the female morphs in two diving beetle species:Dytiscus lapponicusandGraphoderus zonatus. We compared adhesion on the rough and the smooth female morphs to infer the function of the rough elytral modifications. We found that the adhesive force on the rough structures was much lower than on other surfaces. These findings support the suggestion of sexual conflict in diving beetles and a sexually antagonistic function of the rough female structures. In addition, males differed in their adhesive capacity on different female surfaces, indicating a male trade-off between adhering to smooth and rough female morphs.
Interactions between serotypes of dengue highlight epidemiological impact of cross-immunity
Authors: Reich Nicholas G. , Shrestha Sourya , King Aaron A. , Rohani Pejman , Lessler Justin , Kalayanarooj Siripen , Yoon In-Kyu , Gibbons Robert V. , Burke Donald S. , Cummings Derek A. T.
Published: July 2013

Dengue, a mosquito-borne virus of humans, infects over 50 million people annually. Infection with any of the four dengue serotypes induces protective immunity to that serotype, but does not confer long-term protection against infection by other serotypes. The immunological interactions between serotypes are of central importance in understanding epidemiological dynamics and anticipating the impact of dengue vaccines. We analysed a 38-year time series with 12 197 serotyped dengue infections from a hospital in Bangkok, Thailand. Using novel mechanistic models to represent different hypothesized immune interactions between serotypes, we found strong evidence that infection with dengue provides substantial short-term cross-protection against other serotypes (approx. 1–3 years). This is the first quantitative evidence that short-term cross-protection exists since human experimental infection studies performed in the 1950s. These findings will impact strategies for designing dengue vaccine studies, future multi-strain modelling efforts, and our understanding of evolutionary pressures in multi-strain disease systems.
Ruga
mechanics of creasing: from instantaneous to setback creases
Authors: Diab Mazen , Zhang Teng , Zhao Ruike , Gao Huajian , Kim Kyung-Suk
Published: July 2013

We present mechanics of surface creasing caused by lateral compression of a nonlinear neo-Hookean solid surface, with its elastic stiffness decaying exponentially with depth. Nonlinear bifurcation stability analysis reveals that neo-Hookean solid surfaces can develop instantaneous surface creasing under compressive strains greater than 0.272 but less than 0.456. It is found that instantaneous creasing is set off when the compressive strain is large enough, and the longest-admissible perturbation wavelength relative to the decay length of the elastic modulus is shorter than a critical value. A compressive strain smaller than 0.272 can only trigger bifurcation of a stable wrinkle that can prompt a setback crease upon further compression. The minimum compressive strain required to develop setback creasing is found to be 0.174. If the relative longest-admissible perturbation wavelength is long enough, then the wrinkle can fold before it creases, and the specimen can be compressed further beyond the Biot critical strain limit of 0.456. Various bifurcation branches on a plane of normalized longest-admissible wavelength versus compressive strain delineate different phases of corrugated surface configurations to form a
ruga
phase diagram. The phase diagram will be useful for understating surface crease, as well as for controlling
ruga
structures for various applications, such as designing stretchable electronics.
On a Boltzmann-type price formation model
Authors: Burger Martin , Caffarelli Luis , Markowich Peter A. , Wolfram Marie-Therese
Published: July 2013

In this paper, we present a Boltzmann-type price formation model, which is motivated by a parabolic free boundary model for the evolution of price presented by Lasry and Lions in 2007. We discuss the mathematical analysis of the Boltzmann-type model and show that its solutions converge to solutions of the model by Lasry and Lions as the transaction rate tends to infinity. Furthermore, we analyse the behaviour of the initial layer on the fast time scale and illustrate the price dynamics with various numerical experiments.
Making waves round a structured cloak: lattices, negative refraction and fringes
Authors: Colquitt D. J. , Jones I. S. , Movchan N. V. , Movchan A. B. , Brun M. , McPhedran R. C.
Published: July 2013

Using the framework of transformation optics, this paper presents a detailed analysis of a non-singular square cloak for acoustic, out-of-plane shear elastic and electromagnetic waves. Analysis of wave propagation through the cloak is presented and accompanied by numerical illustrations. The efficacy of the regularized cloak is demonstrated and an objective numerical measure of the quality of the cloaking effect is provided. It is demonstrated that the cloaking effect persists over a wide range of frequencies. As a demonstration of the effectiveness of the regularized cloak, a Young's double slit experiment is presented. The stability of the interference pattern is examined when a cloaked and uncloaked obstacle are successively placed in front of one of the apertures. This novel link with a well-known quantum mechanical experiment provides an additional method through which the quality of cloaks may be examined. In the second half of the paper, it is shown that an approximate cloak may be constructed using a discrete lattice structure. The efficiency of the approximate lattice cloak is analysed and a series of illustrative simulations presented. It is demonstrated that effective cloaking may be obtained by using a relatively simple lattice structure, particularly, in the low-frequency regime.
Chronobiology by moonlight
Authors: Kronfeld-Schor Noga , Dominoni Davide , de la Iglesia Horacio , Levy Oren , Herzog Erik D. , Dayan Tamar , Helfrich-Forster Charlotte
Published: July 2013

Most studies in chronobiology focus on solar cycles (daily and annual). Moonlight and the lunar cycle received considerably less attention by chronobiologists. An exception are rhythms in intertidal species. Terrestrial ecologists long ago acknowledged the effects of moonlight on predation success, and consequently on predation risk, foraging behaviour and habitat use, while marine biologists have focused more on the behaviour and mainly on reproduction synchronization with relation to the Moon phase. Lately, several studies in different animal taxa addressed the role of moonlight in determining activity and studied the underlying mechanisms. In this paper, we review the ecological and behavioural evidence showing the effect of moonlight on activity, discuss the adaptive value of these changes, and describe possible mechanisms underlying this effect. We will also refer to other sources of night-time light (‘light pollution’) and highlight open questions that demand further studies.
Latitudinal clines: an evolutionary view on biological rhythms,
Authors: Hut Roelof A. , Paolucci Silvia , Dor Roi , Kyriacou Charalambos P. , Daan Serge
Published: July 2013

Properties of the circadian and annual timing systems are expected to vary systematically with latitude on the basis of different annual light and temperature patterns at higher latitudes, creating specific selection pressures. We review literature with respect to latitudinal clines in circadian phenotypes as well as in polymorphisms of circadian clock genes and their possible association with annual timing. The use of latitudinal (and altitudinal) clines in identifying selective forces acting on biological rhythms is discussed, and we evaluate how these studies can reveal novel molecular and physiological components of these rhythms.
The nocturnal bottleneck and the evolution of activity patterns in mammals
Authors: Gerkema Menno P. , Davies Wayne I. L. , Foster Russell G. , Menaker Michael , Hut Roelof A.
Published: July 2013

In 1942, Walls described the concept of a ‘nocturnal bottleneck’ in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail.
Blue whales respond to simulated mid-frequency military sonar
Authors: Goldbogen Jeremy A. , Southall Brandon L. , DeRuiter Stacy L. , Calambokidis John , Friedlaender Ari S. , Hazen Elliott L. , Falcone Erin A. , Schorr Gregory S. , Douglas Annie , Moretti David J. , Kyburg Chris , McKenna Megan F. , Tyack Peter L.
Published: July 2013

Mid-frequency military (1–10 kHz) sonars have been associated with lethal mass strandings of deep-diving toothed whales, but the effects on endangered baleen whale species are virtually unknown. Here, we used controlled exposure experiments with simulated military sonar and other mid-frequency sounds to measure behavioural responses of tagged blue whales (Balaenoptera musculus) in feeding areas within the Southern California Bight. Despite using source levels orders of magnitude below some operational military systems, our results demonstrate that mid-frequency sound can significantly affect blue whale behaviour, especially during deep feeding modes. When a response occurred, behavioural changes varied widely from cessation of deep feeding to increased swimming speed and directed travel away from the sound source. The variability of these behavioural responses was largely influenced by a complex interaction of behavioural state, the type of mid-frequency sound and received sound level. Sonar-induced disruption of feeding and displacement from high-quality prey patches could have significant and previously undocumented impacts on baleen whale foraging ecology, individual fitness and population health.
The evolution of plant reproductive systems: how often are transitions irreversible?
Authors: Barrett Spencer C. H.
Published: July 2013

Flowering plants are characterized by striking variation in reproductive systems, and the evolutionary lability of their sexual traits is often considered a major driver of lineage diversification. But, evolutionary transitions in reproductive form and function are never entirely unconstrained and many changes exhibit strong directionality. Here, I consider why this occurs by examining transitions in pollination, mating and sexual systems, some of which have been considered irreversible. Among pollination systems, shifts from bee to hummingbird pollination are rarely reversible, whereas transitions from animal to wind pollination are occasionally reversed. Specialized pollination systems can become destabilized through a loss of pollinator service resulting in a return to generalized pollination, or more commonly a reliance on self-pollination. Homomorphic and heteromorphic self-incompatibility systems have multiple origins but breakdown to self-compatibility occurs much more frequently with little evidence for subsequent gains, at least over short time-spans. Similarly, numerous examples of the shift from outcrossing to predominant self-fertilization are known, but cases of reversal are very limited supporting the view that autogamy usually represents an evolutionary dead-end. The evolution of dioecy from hermaphroditism has also been considered irreversible, although recent evidence indicates that the occurrence of sex inconstancy and hybridization can lead to the origin of derived sexual systems from dioecy. The directionality of many transitions clearly refutes the notion of unconstrained reproductive flexibility, but novel adaptive solutions generally do not retrace earlier patterns of trait evolution.
Social monitoring via close calls in meerkats
Authors: Reber Stephan A. , Townsend Simon W. , Manser Marta B.
Published: July 2013

Social monitoring of the actions of group members is thought to be a key development associated with group living. Humans constantly monitor the behaviour of others and respond to them in a flexible way depending on past interactions and the current social context. While other primates have also been reported to change their behaviour towards other group members flexibly based on the current state of their relationship, empirical evidence is typically linked to contextually specific events such as aggressive or reproductive interactions. In the cooperatively breeding meerkat (
Suricata suricatta
), we investigated whether subordinate females use frequently emitted, non-agonistic close calls to monitor the location of the dominant female and whether they subsequently adjust their response based on recent social interactions during conflict and non-conflict periods. Subjects discriminated between the close calls of the dominant female and control playbacks, responding by approaching the loudspeaker and displaying submissive behaviour only if they were currently threatened by eviction. Our results suggest that meerkats assess the risk for aggressive interactions with close associates depending on social circumstances, and respond accordingly. We argue that social monitoring based on non-agonistic cues is probably a common mechanism in group-living species that allows the adjustment of behaviour depending on variation in relationships.
Phylogenetic correlates of extinction risk in mammals: species in older lineages are not at greater risk
Authors: Verde Arregoitia Luis Darcy , Blomberg Simon P. , Fisher Diana O.
Published: July 2013

Phylogenetic information is becoming a recognized basis for evaluating conservation priorities, but associations between extinction risk and properties of a phylogeny such as diversification rates and phylogenetic lineage ages remain unclear. Limited taxon-specific analyses suggest that species in older lineages are at greater risk. We calculate quantitative properties of the mammalian phylogeny and model extinction risk as an ordinal index based on International Union for Conservation of Nature Red List categories. We test for associations between lineage age, clade size, evolutionary distinctiveness and extinction risk for 3308 species of terrestrial mammals. We show no significant global or regional associations, and three significant relationships within taxonomic groups. Extinction risk increases for evolutionarily distinctive primates and decreases with lineage age when lemurs are excluded. Lagomorph species (rabbits, hares and pikas) that have more close relatives are less threatened. We examine the relationship between net diversification rates and extinction risk for 173 genera and find no pattern. We conclude that despite being under-represented in the frequency distribution of lineage ages, species in older, slower evolving and distinct lineages are not more threatened or extinction-prone. Their extinction, however, would represent a disproportionate loss of unique evolutionary history.
When should a trophically and vertically transmitted parasite manipulate its intermediate host? The case ofToxoplasma gondii
Authors: Lélu Maud , Langlais Michel , Poulle Marie-Lazarine , Gilot-Fromont Emmanuelle , Gandon Sylvain
Published: July 2013

Parasites with complex life cycles are expected to manipulate the behaviour of their intermediate hosts (IHs), which increase their predation rate and facilitate the transmission to definitive hosts (DHs). This ability, however, is a double-edged sword when the parasite can also be transmitted vertically in the IH. In this situation, as the manipulation of the IH behaviour increases the IH death rate, it conflicts with vertical transmission, which requires healthy and reproducing IHs. The protozoanToxoplasma gondii, a widespread pathogen, combines both trophic and vertical transmission strategies. Is parasite manipulation of host behaviour still adaptive in this situation? We model the evolution of the IH manipulation byT. gondiito study the conflict between these two routes of transmission under different epidemiological situations. Model outputs show that manipulation is particularly advantageous for virulent strains and in epidemic situations, and that different levels of manipulation may evolve depending on the sex of the IH and the transmission routes considered. These results may help to understand the variability of strain characteristics encountered forT. gondiiand may extend to other trophically transmitted parasites.
STAU1 binding 3′ UTR IRAlus complements nuclear retention to protect cells from PKR-mediated translational shutdown
Authors: Elbarbary Reyad A. , Li Wencheng , Tian Bin , Maquat Lynne E.
Published: July 2013

For a number of human genes that encode transcripts containing inverted repeat Alu elements (IRAlus) within their 3′ untranslated region (UTR), product mRNA is efficiently exported to the cytoplasm when the IRAlus, which mediate nuclear retention, are removed by alternative polyadenylation. Here we report a new mechanism that promotes gene expression by targeting mRNAs that maintain their 3′ UTR IRAlus: Binding of the dsRNA-binding protein Staufen1 (STAU1) to 3′ UTR IRAlus inhibits nuclear retention so as to augment the nuclear export of 3′ UTR IRAlus-containing mRNAs (IRAlus mRNAs). Moreover, we found that 3′ UTR IRAlus-bound STAU1 enhances 3′ UTR IRAlus mRNA translation by precluding protein kinase R (PKR) binding, which obviates PKR activation, eukaryotic translation initiation factor 2α (eIF2α) phosphorylation, and repression of global cell translation. Thus, STAU1 binding to 3′ UTR IRAlus functions along with 3′ UTR IRAlus-mediated nuclear retention to suppress the shutdown of cellular translation triggered by PKR binding to endogenous cytoplasmic dsRNAs. We also show that a changing STAU1/PKR ratio contributes to myogenesis via effects on the 3′ UTR IRAlus of mRNA encoding the microRNA-binding protein LIN28.
Identification of a New Class of Lipid Droplet-Associated Proteins in Plants
Authors: Horn Patrick J. , James Christopher N. , Gidda Satinder K. , Kilaru Aruna , Dyer John M. , Mullen Robert T. , Ohlrogge John B. , Chapman Kent D.
Published: July 2013

Lipid droplets in plants (also known as oil bodies, lipid bodies, or oleosomes) are well characterized in seeds, and oleosins, the major proteins associated with their surface, were shown to be important for stabilizing lipid droplets during seed desiccation and rehydration. However, lipid droplets occur in essentially all plant cell types, many of which may not require oleosin-mediated stabilization. The proteins associated with the surface of nonseed lipid droplets, which are likely to influence the formation, stability, and turnover of this compartment, remain to be elucidated. Here, we have combined lipidomic, proteomic, and transcriptomic studies of avocado (Persea americana) mesocarp to identify two new lipid droplet-associated proteins, which we named LDAP1 and LDAP2. These proteins are highly similar to each other and also to the small rubber particle proteins that accumulate in rubber-producing plants. An Arabidopsis (Arabidopsis thaliana) homolog to LDAP1 and LDAP2, At3g05500, was localized to the surface of lipid droplets after transient expression in tobacco (Nicotiana tabacum) cells that were induced to accumulate triacylglycerols. We propose that small rubber particle protein-like proteins are involved in the general process of binding and perhaps the stabilization of lipid-rich particles in the cytosol of plant cells and that the avocado and Arabidopsis protein members reveal a new aspect of the cellular machinery that is involved in the packaging of triacylglycerols in plant tissues.
Evolution of order in amorphous-to-crystalline phase transformation of MgF2
Authors: Mu Xiaoke , Neelamraju Sridhar , Sigle Wilfried , Koch Christoph T. , Totò Nico , Schön J. Christian , Bach Andreas , Fischer Dieter , Jansen Martin , van Aken Peter A.
Published: July 2013

Structural disorder and distortion play a significant role in phase transformations. Experimentally, electron diffraction in the transmission electron microscope offers the ability to characterize disorderviathe pair distribution function (PDF) at high spatial resolution. In this work, energy-filteredin situelectron diffraction is applied to measure PDFs of different phases of MgF2from the amorphous deposit through metastable modifications to the thermodynamically stable phase. Despite the restriction of thick specimens resulting in multiple electron scattering, elaborate data analysis enabled experimental and molecular dynamics simulation data to be matched, thus allowing analysis of the evolution of short-range ordering. In particular, it is possible to explain the theoretically not predicted existence of a metastable phase by the presence of atomic disorder and distortion. The short-range ordering in the amorphous and crystalline phases is elucidated as three steps: (i) an initial amorphous phase exhibiting CaCl2-type short-range order which acts as a crystallization nucleus to guide the phase transformation to the metastable CaCl2-type phase and thus suppresses the direct appearance of the rutile-type phase; (ii) a metastable CaCl2-type phase containing short-range structural features of the stable rutile type; and (iii) the formation of a large volume fraction of disordered intergranular regions which stabilize the CaCl2-type phase. The structure evolution is described within the energy landscape concept.