bluuebunny/crossref_metadata_2025 huggingface dataset:
Oxidative transformations of amino acids and peptides catalysed by Cytochromes P450
Authors: Cryle Max J. , Brieke Clara , Haslinger Kristina
Published: November 2013

Cytochromes P450 (P450s) are a superfamily of oxidoreductases that display not only a high degree of substrate diversity across xenobiotic and secondary metabolism but also show flexibility in the oxidation chemistry that they catalyse. The oxidative transformation of amino acids and peptides by P450s represents an important collection of transformations for this enzyme class: these transformations are used in Nature to diversify the limited range of monomers available for ribosomal peptide production, as well as altering peptides to afford desired biological properties. This chapter will highlight current examples of P450-catalysed transformations of amino acids and peptides, organised by the nature of the oxidative transformation performed by the P450.
Biofunctional peptide design
Authors: Ryadnov Maxim G.
Published: November 2013

De novo peptide design provides an efficient strategy to emulate native folding elements. Polypeptide sequences are arranged into secondary structure oligomers, which can be continuous, that is belonging to one sequence, non-covalent, but monodisperse and autonomously folded, and supramolecular leading to nanostructured assemblies, which are not necessarily discrete and uniform. Despite the diversity of sequences and functions they encode there exist relatively few arrangement types, with each being associated with a specific type of function. This forms the basis for the classification of polypeptide folds, which help provide a design framework for de novo peptides. Therefore, designed sequences that deliver particular biological functions can be referred to as bio-functional motifs, and strategies that are principally focused on providing such motifs constitute bio-functional peptide design. This report highlights recent developments in the field and sets out from generic design principles of conventional backbone secondary structures, both autonomously folded and self-assembling motifs, with a progress overview in designing unconventional alternative peptide backbones.
Integrating chemical cross-linking with mass spectrometric analysis of peptides and proteins
Authors: Henrion André
Published: November 2013

The report provides an overview of chemical cross-linking and mass spectrometry as an integral capability for the exploration of proximity or distance constraints of secondary-structure building blocks in proteins, individual or in complex. The use of cross-linkers is to chemically fix spatial relationships of such building blocks, with mass spectrometry helping identify partners by correlating amino-acid-sequence patterns. Distance constraints relate to the maximum span provided by a linker, and just a few of these may suffice to confirm a protein fold. Provided that interacting and contacting interfaces of given proteins are determined, proteins can be identified even in complex milieu such as cell lysates. The wide use of this efficient strategy is supported by the progress made in mass spectrometry and is developing with established and emerging technologies. In this chapter, an emphasis is made on the types of information this capability can provide and on the basic concepts of using ‘standard’ cross-linkers which are discussed along with mass-spectrometric analysis of cross-linked products. Principles and current tendencies in the development of novel cross-linkers are addressed in the light of analytical extraction of the cross-linked species and computer-based interpretation of their mass spectra.
Peptidome analysis: tools and technologies
Authors: Rakowska Paulina D. , Ryadnov Maxim G.
Published: November 2013

Among specialised “-omics” strategies developed to provide traceable biomolecular links at the cellular and systems level, peptidome analysis offers an information-rich and self-sufficient approach enabling the quantitative and systematic measurements of peptides in different biological media. Peptidome is usually referred to as an array of peptides present in a particular sampled pool or degradome of biomarkers (cells, plasma, cerebrospinal fluid). A clear distinction is made regarding the nature of the biomarkers, which are endogenous and are of low molecular weight, and can include peptidic factors, hormones and metabolic products. Exogenous peptides are of lesser emphasis in the literature, primarily due to molecular diagnostics approaches and nanoscale technologies that are developed in parallel and inter-relate with peptidomics at the point of mutual applications. Peptidomic profiles obtained for different conditions and diseases can vary greatly and require similarly varied tools, the development and optimisation of which are continuing from the traditional biochemical methods to advanced multidimensional separations and bioinformatics-empowered mass spectrometry. This report highlights mainstream tendencies in peptidome analysis exemplified by recent developments from the perspective of analytical tools and technologies
Rhoeo discolor leaf extract as a novel immobilizing matrix for the fabrication of an electrochemical glucose and hydrogen peroxide biosensor
Authors: Nandini Seetharamaiah , Nalini Seetharamaiah , Shanmugam Sangaraju , Niranjana Pathappa , Melo Jose Savio , Suresh Gurukar Shivappa
Published: November 2013

This work aims at using non-toxic, easily availableRhoeo discolor(Rd) leaf extract as a matrix for enzyme immobilization in the development of electrochemical biosensors.
Extraction of natural estrogens in environmental waters by dispersive multiwalled carbon nanotube-based agitation-assisted adsorption and ultrasound-assisted desorption
Authors: Zhu Hangcui , Chen Wanxin , Li Zhiling , He Jun , Tang Xuejiao , Wang Chengjun
Published: November 2013

Extraction of natural EDCs in waters by MWCNTs-based dispersive solid-phase microextraction prior to HPLC-DAD analysis.
Epoxy amino acids produced from allylglycines intramolecularly cyclised to yield four stereoisomers of 4-hydroxyproline derivatives
Authors: Krishnamurthy Suvratha , Arai Toru , Nakanishi Kanae , Nishino Norikazu
Published: November 2013

Intermolecular epoxide-opening generated stereoisomeric hydroxyprolines; cis-isomer formed lactone, being easily separable from trans-hydroxyproline ester.
Development and characterisation of (Mg, Mn) U‐type microwave absorbing materials and its application in radar cross sections reduction
Authors: Padhy Sankarsan , Sanyal Subrata , Meena Ram Swaroop , Chatterjee Rantamala , Bose Aniruddha
Published: November 2013

The preparation and complex permittivity and permeability measurement of a new U‐type of hexaferrite microwave absorbing material (Ba4 Mg2 − x MnxFe36 O60) is reported for different value of x in range 0 ≤ x ≤ 2. Complex permittivity and permeability values of hexaferrite pellets are measured using a vector network analyser (VNA) in X‐band. The reflection loss of the materials is computed for different values of x and thickness using the measured permittivity and permeability values. The optimum reflection loss is found to be −43 dB for hexaferrite pellet (x = 0.5) at a thickness of t = 1.7 mm. Microwave absorbing paint pellets are prepared by mixing hexaferrite powder with polyimide solution and their complex permeability and permittivity are also measured using a VNA. Using these measured values, radar cross‐section reduction simulation for artillery shells has been carried out using electromagnetic simulation software in the 8–10 GHz frequency range. A maximum radar cross‐section reduction of 15 dB has been observed for a 30 mm artillery shell at 9 GHz.
Reshaping the IT governance in Octo Telematics to gain IT–business alignment
Authors: Vaia Giovanni , Carmel Erran
Published: November 2013

The case shows how a technology services company shaped and reshaped – and reshaped again – its IT governance structure to better integrate the IT function with business clients. The company is a large Italian telematics provider – Octo Telematics – which is specialized in the provision of telematic services and systems for the insurance and automotive markets. During the period described in this case, the company was growing and globalizing rapidly. The desired alignment between IT and the business units is needed to promote behaviors consistent with the organization's mission and strategy. As Octo experimented with new processes, committees and reorganizations the company ‘traveled’ through several governance archetypes.
Biohydrogen production using anaerobic mixed bacteria: Process parameters optimization studies
Authors: Karthic P. , Joseph Shiny , Arun Naveenji , Varghese Lity Alen , Santhiagu A.
Published: November 2013

Process parameters optimization using response surface methodology (RSM) and artificial neural network (ANN) coupled with Genetic Algorithm (GA) were carried out to analyze the influence of process parameters on maximum hydrogen production and H2 yield using sucrose as a sole carbon source. Alkali pretreated mixed culture obtained from the food waste was used for fermentative hydrogen production. Box-Behnken design was applied to examine the interactive effect of the significant variables (sucrose concentration, initial pH, inoculum size, and peptone concentration). Characterization of culture indicated that the culture was gram-negative facultative anaerobe. Maximum experimental hydrogen yield of 2.36 mol H2/mol sucrose was achieved at the optimal points predicted by the RSM. Modified Gompertz model and logistic model adequately fitted well and described the fermentative hydrogen production and bacterial growth, respectively. Process modeling abilities of ANN and RSM were compared on the basis of parameters such as estimated values of root mean square error (RMSE), multiple correlation coefficients (R2), and standard error of prediction (SEP). GA couple with ANN was used to find the global optimum point and the maximum H2 yield of 2.39 mol H2/mol sucrose was found at sucrose concentration 15.5 g/l, pH 8, inoculum size (% v/v) 8.4, and peptone concentration 4.9 g/l. The estimated values of RMSE, R2, and SEP for ANN model and RSM model confirm that fitness and prediction accuracy of ANN model was higher when compared to RSM model. From this study, we confirmed that genetic algorithm coupled with ANN technique can be a powerful tool to obtain global optimization in biochemical systems.
Conjugate flow action functionals
Authors: Venturi Daniele
Published: November 2013

We present a new general framework to construct an action functional for a non-potential field theory. The key idea relies on representing the governing equations relative to a diffeomorphic flow of curvilinear coordinates which is assumed to be functionally dependent on the solution field. Such flow, which will be called the conjugate flow, evolves in space and time similarly to a physical fluid flow of classical mechanics and it can be selected in order to symmetrize the Gâteaux derivative of the field equations with respect to suitable local bilinear forms. This is equivalent to requiring that the governing equations of the field theory can be derived from a principle of stationary action on a Lie group manifold. By using a general operator framework, we obtain the determining equations of such manifold and the corresponding conjugate flow action functional. In particular, we study scalar and vector field theories governed by second-order nonlinear partial differential equations. The identification of transformation groups leaving the conjugate flow action functional invariant could lead to the discovery of new conservation laws in fluid dynamics and other disciplines.
Competition of the connectivity with the local and the global order in polymer melts and crystals
Authors: Bernini S. , Puosi F. , Barucco M. , Leporini D.
Published: November 2013

The competition between the connectivity and the local or global order in model fully flexible chain molecules is investigated by molecular-dynamics simulations. States with both missing (melts) and high (crystal) global order are considered. Local order is characterized within the first coordination shell (FCS) of a tagged monomer and found to be lower than in atomic systems in both melt and crystal. The role played by the bonds linking the tagged monomer to FCS monomers (radial bonds), and the bonds linking two FCS monomers (shell bonds) is investigated. The detailed analysis in terms of Steinhardt's orientation order parameters Ql (l = 2 − 10) reveals that increasing the number of shell bonds decreases the FCS order in both melt and crystal. Differently, the FCS arrangements organize the radial bonds. Even if the molecular chains are fully flexible, the distribution of the angle formed by adjacent radial bonds exhibits sharp contributions at the characteristic angles θ ≈ 70°, 122°, 180°. The fractions of adjacent radial bonds with θ ≈ 122°, 180° are enhanced by the global order of the crystal, whereas the fraction with 70° ≲ θ ≲ 110° is nearly unaffected by the crystallization. Kink defects, i.e., large lateral displacements of the chains, are evidenced in the crystalline state.
Charge steering of laser plasma accelerated fast ions in a liquid spray — creation of MeV negative ion and neutral atom beams
Authors: Schnürer M. , Abicht F. , Prasad R. , Borghesi M. , Priebe G. , Braenzel J. , Andreev A. , Nickles P. V. , Jequier S. , Tikhonchuk V. , Ter-Avetisyan S.
Published: November 2013

The scenario of “electron capture and loss” has been recently proposed for the formation of negative ion and neutral atom beams with up to MeV kinetic energy [S. Ter-Avetisyan, et al., Appl. Phys. Lett. 99, 051501 (2011)]. Validation of these processes and of their generic nature is here provided in experiments where the ion source and the interaction medium have been spatially separated. Fast positive ions accelerated from a laser plasma sourceare sent through a cold spray where their charge is changed. Such formed neutral atom or negative ion has nearly the same momentum as the original positive ion. Experiments are released for protons,carbon, and oxygen ions and corresponding beams of negative ions and neutral atoms have been obtained. The electron capture and loss phenomenon is confirmed to be the origin of the negative ion and neutral atom beams. The equilibrium ratios of different chargecomponents and cross sections have been measured. Our method is general and allows the creation of beamsof neutral atoms and negative ions for different species which inherit the characteristics of the positive ion source.
Oscillations of a sessile droplet in open air
Authors: Korenchenko A. E. , Beskachko V. P.
Published: November 2013

The open system consisting of a sessile drop, a neutral gas, and a substrate is analyzed by numerical methods. The mode with constant contact angle is considered. The model takes into account evaporation from drop surface, free and forced convection in gas, buoyancy, and Marangoni effect in the liquid phase. It was established that every considered mechanical and thermodynamical disturbance of the system leads to the drop surface oscillations, and thus a drop in an open air oscillates almost inevitably. The displacement of the liquid-gas interface due to oscillations is analyzed in terms of its impact on the accuracy of measurement of the surface tension by sessile drop method.
Chain conformations of ring polymers under theta conditions studied by Monte Carlo simulation
Authors: Suzuki Jiro , Takano Atsushi , Matsushita Yushu
Published: November 2013

We studied equilibrium conformations of trivial-, 31-knot, and 51-knot ring polymers with finite chain length at their θ-conditions using a Monte Carlo simulation. The polymer chains treated in this study were composed of beads and bonds on a face-centered-cubic lattice respecting the excluded volume. The Flory's critical exponent ν in Rg ∼ Nν relationship was obtained from the dependence of the radius of gyration, Rg, on the segment number of polymers, N. In this study, the temperatures at which ν equal 1/2 are defined as θ-temperatures of several ring molecules. The θ-temperatures for trivial-, 31-knot, and 51-knot ring polymers are lower than that for a linear polymer in N ⩽ 4096, where their topologies are fixed by their excluded volumes. The radial distribution functions of the segments in each molecule are obtained at their θ-temperatures. The functions of linear- and trivial-ring polymers have been found to be expressed by those of Gaussian and closed-Gaussian chains, respectively. At the θ-conditions, the excluded volumes of chains and the topological-constraints of trivial-ring polymers can be apparently screened by the attractive force between segments, and the \documentclass[12pt]{minimal}\begin{document}$\langle R_g^2 \rangle$\end{document}⟨Rg2⟩ values for trivial ring polymers are larger than the half of those for linear polymers. In the finite N region the topological-constraints of 31- and 51-knot rings are stronger than that of trivial-ring, and trajectories of the knotted ring polymers cannot be described as a closed Gaussian even though they are under θ-conditions.
A phenomenological model on the kink mode threshold varying with the inclination of sheath boundary
Authors: Sun X. , Intrator T. P. , Liu M. , Sears J. , Weber T.
Published: November 2013

In nature and many laboratory plasmas, a magnetic flux tube threaded by current or a flux rope has a footpoint at a boundary. The current driven kink mode is one of the fundamental ideal magnetohydrodynamic instabilities in plasmas. It has an instability threshold that has been found to strongly depend on boundary conditions (BCs). We provide a theoretical model to explain the transition of this threshold dependence between nonline tied and line tied boundary conditions. We evaluate model parameters using experimentally measured plasma data, explicitly verify several kink eigenfunctions, and validate the model predictions for boundary conditions BCs that span the range between NLT and LT BCs. Based on this model, one could estimate the kink threshold given knowledge of the displacement of a flux rope end, or conversely estimate flux rope end motion based on knowledge of it kink stability threshold.
Structural and optical characterization of Mg-doped GaAs nanowires grown on GaAs and Si substrates
Authors: Falcão B. P. , Leitão J. P. , Correia M. R. , Soares M. R. , Morales F. M. , Mánuel J. M. , Garcia R. , Gustafsson A. , Moreira M. V. B. , de Oliveira A. G. , González J. C.
Published: November 2013

We report an investigation on the morphological, structural, and optical properties of large size wurtzite GaAs nanowires, low doped with Mg, grown on GaAs(111)B and Si(111) substrates. A higher density of vertical nanowires was observed when grown upon GaAs(111)B. Very thin zinc-blende segments are observed along the axis of the nanowires with a slightly higher linear density being found on the nanowires grown on Si(111). Low temperature cathodoluminescence and photoluminescence measurements reveal an emission in the range 1.40–1.52 eV related with the spatial localization of the charge carriers at the interfaces of the two crystalline phases. Mg related emission is evidenced by cathodoluminescence performed on the GaAs epilayer. However, no direct evidence for a Mg related emission is found for the nanowires. The excitation power dependency on both peak energy and intensity of the photoluminescence gives a clear evidence for the type II nature of the radiative transitions. From the temperature dependence on the photoluminescence intensity, non-radiative de-excitation channels with different activation energies were found. The fact that the estimated energies for the escape of the electron are higher in the nanowires grown on Si(111) suggests the presence of wider zinc-blende segments.
Microscopic magnetic properties of an oxygen-doped Tb-Fe thin film by magnetic Compton scattering
Authors: Agui Akane , Unno Tomoya , Matsumoto Sayaka , Suzuki Kousuke , Koizumi Akihisa , Sakurai Hiroshi
Published: November 2013

The magnetic Compton scattering of a Tb32Fe55O13 film was measured in order to investigate the microscopic magnetization processes (i.e., the spin moment, orbital moment, and element specific moments). The trend of the spin magnetic moment was the same as that of the total magnetic moment but opposite to the orbital magnetic moment. In the low magnetic field region, the magnetic moments were not perfectly aligned perpendicular to the film surface, and the perpendicular components were found to mainly arise from the magnetic moment of Tb. Oxygen atoms hinder long range magnetic interaction and hence also affect the magnetization process of the magnetic moments of Tb and Fe.
Sire effects on neonatal lamb vigour and following-behaviour
Authors: Hergenhan R. L. , Hinch G. N. , Ferguson D. M.
Published: November 2013

The ability of the lamb to maintain contact with the ewe as she moves away from the birth site is critical to the lamb’s subsequent survival. If this contact is compromised then lamb loss is likely to occur due to starvation/mismothering. This study uses sires from the Sheep CRC Information Nucleus Flock to compare the effect of selection of sires within the Merino breed for high or low losses due to starvation/mismothering on neonatal lamb vigour. Lamb vigour was measured using conventional measures of time to perform early neonatal behaviours, early physiological measures (rectal temperatures and blood glucose), and performance in a modified barrier test while under physiological stress from cold exposure. Lambs were exposed to cold at a time (4–6 h after birth) when the ewe is likely to be moving away from the birth site and therefore when losses due to starvation/mismothering are likely to begin. Progeny from the high-loss sires were significantly (P < 0.05) slower to attempt to stand, and to stand, than progeny from the no-loss sires and tended to be slower to reach the udder and suckle (P = 0.07). Lambs from the no-loss group also had a significantly (P < 0.01) higher vigour score than the high-loss group. There was no effect of sire group on the performance of lambs in the modified barrier test; however, cold-treated lambs performed poorly in the test compared with control lambs. It was concluded that sire can have an effect on lamb vigour, but it does not necessarily translate into effects on later following-behaviour while under stressful conditions.
Mollie Elizabeth Holman 1930–2010
Authors: McLachlan Elspeth M. , Hirst G. David S.
Published: November 2013

Mollie Holman was a biophysicist whose work on the autonomic nervous system and the innervation of smooth muscle was seminal in advancing knowledge of its behaviour at a cellular level. She was particularly known for her technical expertise in microelectrode recording of membrane potential from single smooth muscle cells, and the interpretation of their electrical activity, both spontaneous and in response to transmitters released from their autonomic nerves.
Liebig’s Australian Connection: James King’s Scientific Viticulture
Authors: Rae Ian D. , Brock William H.
Published: November 2013

The pioneering New South Wales vigneron James King (1797–1857) took a technical approach to his winemaking as he did to the pottery he established near his Hunter Valley property, ‘Irrawang'. In the 1840s he began a correspondence with the famous German chemist and prominent advocate of a scientific approach to agriculture, Justus Liebig, whose ideas he promoted locally. Liebig analysed King's wines and compared them with European varieties. The two men later became personally acquainted when King journeyed to Europe in the mid–1850s. The Liebig connection was augmented by the presence at ‘Irrawang'of two members of the Muspratt family, alkali manufacturers of Liverpool, both of whom had studied with Liebig and espoused his principles. Thus the master's influence on winemaking in colonial New South Wales was exerted indirectly through them and directly through his correspondence with King.
Similarity increases altruistic punishment in humans
Authors: Mussweiler Thomas , Ockenfels Axel
Published: November 2013

Significance

Cooperation is a defining characteristic of human social behavior. More than any other species, humans entertain elaborate systems of cooperation that transcend genetic relatedness, geographic proximity, and temporal immediacy. Recent evidence has demonstrated that altruistic punishment is a key behavioral mechanism in the evolution of human cooperation. We show that interpersonal similarity increases reciprocal altruistic punishment. Importantly, this influence of similarity is not explained by group identity, which has the opposite effect on altruistic punishment. These findings illustrate how similarity and altruistic punishment are closely intertwined in encouraging human cooperation. Moreover, because perceived similarity triggers an altruistic response, our result provides a rationale for why similar people are more likely to build stable relationships and groups.
Arabidopsis thaliana
AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain
Authors: Zhao Jianfei , Favero David S. , Peng Hao , Neff Michael M.
Published: November 2013

Significance

Members of the
AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED
(
AHL
) family are involved in various plant biological processes. Our findings reveal a molecular model whereby the AHLs interact with each other via the plant and prokaryote conserved (PPC)/domain of unknown function #296 (DUF296) domain to form homo-/hetero-complexes, possibly trimers. The AHL complex also interacts with other nuclear proteins to form a macromolecular complex that modulates plant growth and development. The coordinated action of AHLs requires an AT-hook motif capable of binding AT-rich DNA, as well as a PPC/DUF296 domain containing a conserved six-amino-acid region. Our proposed model provides a better understanding of the roles of
AHL
genes in regulating plant growth and development, which may in turn lead to better seedling establishment and increased yield.
CDK10/cyclin M is a protein kinase that controls ETS2 degradation and is deficient in STAR syndrome
Authors: Guen Vincent J. , Gamble Carly , Flajolet Marc , Unger Sheila , Thollet Aurélie , Ferandin Yoan , Superti-Furga Andrea , Cohen Pascale A. , Meijer Laurent , Colas Pierre
Published: November 2013

Significance

STAR syndrome is an X-linked dominant developmental disorder caused by mutations in
FAM58A
, which codes for an orphan cyclin with undescribed functions. Here we demonstrate that cyclin M interacts with CDK10 (one of the last orphan CDKs) to form a novel cyclin-dependent kinase. CDK10 is known to be involved in the control of cell division and in the resistance of certain breast cancers to endocrine therapy. We show that CDK10/cyclin M phosphorylates and positively regulates the degradation of ETS2, a transcription factor that plays key roles in cancer and development. These results shed light on the molecular mechanisms underlying STAR syndrome, and they pave the way for the exploration of the functions of the CDK10/cyclin M kinase.
TREM2 governs Kupffer cell activation and explains
belr1
genetic resistance to malaria liver stage infection
Authors: Gonçalves Lígia Antunes , Rodrigues-Duarte Lurdes , Rodo Joana , Vieira de Moraes Luciana , Marques Isabel , Penha-Gonçalves Carlos
Published: November 2013

Significance

Current efforts in malaria therapeutics and vaccine development include strategies aimed at deterring infection at the liver stage, preventing subsequent clinical complications and malaria transmission. To elucidate response mechanisms operating during liver stage infection, we searched for host genetic factors that control parasite expansion in a mouse model of malaria liver stage resistance. Here we report that the cell surface receptor TREM2 is expressed in innate immune cell types residing in the liver and takes part in a mechanism enabling such cells to control the yield of hepatocyte infection. This work highlights the relevance of innate immunity mechanisms in controlling expansion of the malaria parasite in the liver.
Frequency-specific mechanism links human brain networks for spatial attention
Authors: Daitch Amy L. , Sharma Mohit , Roland Jarod L. , Astafiev Serguei V. , Bundy David T. , Gaona Charles M. , Snyder Abraham Z. , Shulman Gordon L. , Leuthardt Eric C. , Corbetta Maurizio
Published: November 2013

Significance

Humans have the remarkable ability to flexibly attend to stimuli in the environment and seamlessly shift behaviors, depending on sensory conditions and internal goals. Neuroimaging studies have shown that tasks involving particular cognitive domains consistently recruit specific broadly distributed functional brain networks. A fundamental question in neuroscience is how the brain flexibly manages communication within and between these brain networks, allowing task-relevant regions to interact while minimizing the influence of task-irrelevant activity. In this report we show that low-frequency neuronal oscillations, which reflect fluctuations in neuronal excitability, are modulated selectively within task-relevant, but not -irrelevant brain networks. This modulation of oscillatory activity may coordinate the selective routing of neuronal information within the brain during everyday behavior.
Lkb1/Stk11 regulation of mTOR signaling controls the transition of chondrocyte fates and suppresses skeletal tumor formation
Authors: Lai Lick Pui , Lilley Brendan N. , Sanes Joshua R. , McMahon Andrew P.
Published: November 2013

Significance

The transition from a mitotic to a postmitotic, hypertrophic chondrocyte is a key regulatory event in the growing vertebrate skeleton. By using genetic approaches, cell culture, and cell transplantation models, we provide compelling evidence that attenuating the energy-sensing mammalian target of rapamycin complex 1 (mTORC1) pathway is critical for switching chondrocyte states. A failure of mTORC1 suppression in
Lkb1
mutants leads to a dramatic disruption of the skeletal growth plate and the formation of cartilage tumors comprising undifferentiated chondrocytes that display differential sensitivity to two key cartilage growth regulators, Indian hedgehog and Igf. The study highlights the interconnection between energy sensing pathways, normal growth control, and tumorigenesis in the skeletal program.
Differential effects of global versus local testosterone on singing behavior and its underlying neural substrate
Authors: Alward Beau A. , Balthazart Jacques , Ball Gregory F.
Published: November 2013

Significance

Steroid hormones coordinate multiple behaviors into a functional response (reproduction, stress). It is easy to assess such coordination when comparing actions in different target tissues but is more of a challenge when numerous functions are combined in the brain. Our study illustrates how steroids act on distinct cell groups to regulate separate components of a testosterone-dependent behavior, learned birdsong. Testosterone in the medial preoptic nucleus (POM) increased singing but not optimal song performance. Moreover, testosterone in the POM enhanced volumes of forebrain regions that control song, presumably reflecting the effect of activity-dependent plasticity. Thus, optimal performance of a complex, learned behavior requires testosterone at multiple loci, and activity and/or transsynaptic influences may stimulate forebrain neuroplasticity.
Metabolically programmed quality control system for dolichol-linked oligosaccharides
Authors: Harada Yoichiro , Nakajima Kazuki , Masahara-Negishi Yuki , Freeze Hudson H. , Angata Takashi , Taniguchi Naoyuki , Suzuki Tadashi
Published: November 2013

Significance

In mammals, asparagine (
N
)-linked glycosylation of nascent polypeptides synthesized in the endoplasmic reticulum regulates folding, degradation, and intracellular trafficking of the glycoproteins. The normal
N
-glycosylation requires the completely-assembled dolichol-linked oligosaccharide (DLO) as the optimal glycan donor substrate; however, a low-glucose environment causes arrest of the DLO assembly, which results in the synthesis of extensively truncated premature DLOs, thereby increasing a risk of abnormal
N
-glycosylation. Here, we report that under low-glucose conditions, the premature DLOs are efficiently degraded by unidentified pyrophosphatase, catabolizing them to singly phosphorylated oligosaccharides. Our results suggest that the pyrophosphatase-mediated degradation of premature DLOs functions as a quality control system to avoid abnormal
N
-glycosylation under conditions that impair efficient DLO biosynthesis.
Exploring network scaling through variations on optimal channel networks
Authors: Briggs Lily A. , Krishnamoorthy Mukkai
Published: November 2013

Significance

Optimal Channel Networks (OCNs) model the drainage of a river basin through river channels, minimizing the energy expended in draining the basin. At local optima of this energy functional, OCNs accurately model many characteristics of real river networks, and thus are useful in studying river processes such as channel evolution and flooding. Efficient transportation networks have been studied more generally, with application to blood or metabolite distribution networks in organisms as well as to rivers. We extend the OCN model to three dimensions, toward a goal of a better understanding of efficient transportation networks. We focus on the scaling behaviors of several properties, and find that three-dimensional OCNs exhibit predictable scaling behavior similar to that of metabolite distribution networks.
Gene amplification and microsatellite polymorphism underlie a recent insect host shift
Authors: Bass Chris , Zimmer Christoph T. , Riveron Jacob M. , Wilding Craig S. , Wondji Charles S. , Kaussmann Martin , Field Linda M. , Williamson Martin S. , Nauen Ralf
Published: November 2013

Significance

Insect host shifts may lead to sympatric speciation and can create new crop pests, however identifying the genetic changes involved has proved elusive. We studied a subspecies of the aphid
Myzus persicae
that has recently host shifted to tobacco and are resistant to the plant alkaloid nicotine. We found these races overexpress a cytochrome P450 enzyme (CYP6CY3) that allows them to detoxify nicotine and also certain synthetic insecticides. Overexpression of CYP6CY3 is caused by gene amplification (up to 100 copies) and expansion of a dinucleotide microsatellite in the promoter. Our findings provide insights into the molecular drivers of insect host shifts.
Exchange protein directly activated by cAMP plays a critical role in bacterial invasion during fatal rickettsioses
Authors: Gong Bin , Shelite Thomas , Mei Fang C. , Ha Tuha , Hu Yaohua , Xu Guang , Chang Qing , Wakamiya Maki , Ksiazek Thomas G. , Boor Paul J. , Bouyer Donald H. , Popov Vsevolod L. , Chen Ju , Walker David H. , Cheng Xiaodong
Published: November 2013

Significance

Our studies combining genetic and pharmacological manipulations provide convincing evidence that exchange protein directly activated by cAMP (Epac) 1 plays a critical role in fatal spotted fever group rickettsioses. Inhibition of Epac1 suppresses bacterial adhesion and/or invasion. Most importantly, we show that a small-molecule Epac inhibitor can prevent and suppress rickettsial infection. Our results demonstrate that Epac1-mediated signaling represents a mechanism for host–pathogen interactions and that Epac1 is a potential target for the prevention and treatment of fatal rickettsioses. This is significant from the biodefense viewpoint because it suggests that Epac1 inhibitor can be potentially used as a prophylaxis to thwart initial bacterial infection in the event of a bioterrorism threat.
Quantifying the dynamic interactions between a clathrin-coated pit and cargo molecules
Authors: Weigel Aubrey V. , Tamkun Michael M. , Krapf Diego
Published: November 2013

Significance

Clathrin-mediated endocytosis is the primary pathway of cargo internalization in mammalian cells. However, little is known about the time-dependent interactions between the endocytic machinery and cargo molecules. Nevertheless, these interactions are known to regulate the maturation of a clathrin-coated pit. In this study, we attain a quantitative understanding of the interactions between clathrin-coated pits and cargo using a combination of imaging techniques, single-molecule tracking, and stochastic modeling. We observe that the binding times of cargo molecules are much shorter than the overall endocytic process, albeit they exhibit a very broad distribution. Our modeling explains the measured statistics of cargo captures and binding times. This work further identifies a mechanism for the large diversity in the dynamic behavior of clathrin structures.
Deep ocean communities impacted by changing climate over 24 y in the abyssal northeast Pacific Ocean
Authors: Smith Kenneth L. , Ruhl Henry A. , Kahru Mati , Huffard Christine L. , Sherman Alana D.
Published: November 2013

Significance

Global warming is now a well-documented phenomenon that is influencing every aspect of our world, from increased storm intensity to melting of polar ice sheets and rising sea level. The impact of such changes in climate is least known for the deep ocean, which covers over 60% of the earth’s surface. An unprecedented 24-y time series measuring changes in food supply and utilization by benthic communities at 4,000-m depth in the deep northeast Pacific reveal strong connectivity with changing surface ocean conditions, which have broad implications for the global carbon cycle.
Phototropic growth control of nanoscale pattern formation in photoelectrodeposited Se–Te films
Authors: Sadtler Bryce , Burgos Stanley P. , Batara Nicolas A. , Beardslee Joseph A. , Atwater Harry A. , Lewis Nathan S.
Published: November 2013

Significance

Phototropism, in which plants grow toward a source of illumination, uses dynamic feedback between the light source and photosensitive hormones within the plant to direct the curvature of the plant as it grows. In this manuscript, we describe an adaptive inorganic system that dynamically alters its emergent nanoscale morphology in response to changes in the illumination conditions during growth. Phototropic growth control of nanoscale pattern formation in photoelectrodeposited selenium–tellurium films provides the ability to grow nanostructures of entirely different geometries, periods, and directions abruptly on top of one another, and the ability to change the physical growth direction of the material by changing the direction of the incident light beam.
Sleep deprivation increases dorsal nexus connectivity to the dorsolateral prefrontal cortex in humans
Authors: Bosch Oliver G. , Rihm Julia S. , Scheidegger Milan , Landolt Hans-Peter , Stämpfli Philipp , Brakowski Janis , Esposito Fabrizio , Rasch Björn , Seifritz Erich
Published: November 2013

Significance

Major depressive disorder is a significant contributor to the global burden of disease, affecting 350 million people according to an estimation of the World Health Organization. Today, no valid biomarkers of depression, which could predict the efficacy of a certain treatment in a certain group of patients, exist. Sleep deprivation is an effective and rapid-acting antidepressive treatment. However, the biomechanism of this effect is largely unknown. This study shows the effects of sleep deprivation on human brain functional connectivity alterations via the dorsal nexus, an area which is crucial in major depressive disorder. Here, we offer a neurobiological explanation for the known antidepressive action of sleep deprivation.
Three-dimensional textures and defects of soft material layering revealed by thermal sublimation
Authors: Yoon Dong Ki , Kim Yun Ho , Kim Dae Seok , Oh Seong Dae , Smalyukh Ivan I. , Clark Noel A. , Jung Hee-Tae
Published: November 2013

Significance

Techniques that enable direct visualization in three dimensions of internal nanometer- to micrometer-scale structure are highly prized in materials research and engineering. Here, we demonstrate an effective method for the 3D imaging of soft materials, revealing the alignment, textures, and defects in the organization of their internal interfaces: in this case, of a soft crystal and liquid crystal phase. This method employs combinations of quenching and sublimation generating surface topography that reflects the internal structure, exposing it for visualization using standard techniques.
Fungal-derived semiochemical 1-octen-3-ol disrupts dopamine packaging and causes neurodegeneration
Authors: Inamdar Arati A. , Hossain Muhammad M. , Bernstein Alison I. , Miller Gary W. , Richardson Jason R. , Bennett Joan Wennstrom
Published: November 2013

Significance

Poor air quality from fungal growth in water-damaged, moldy buildings/residences is correlated with a negative impact on human health. The volatile organic compound 1-octen-3-ol is commonly emitted by molds and is responsible for much of the distinctive moldy odor associated with fungal colonization. Using a
Drosophila
model, we demonstrate via genetic, biochemical, and immunological studies that 1-octen-3-ol causes dopamine neuron degeneration through disruption of dopamine handling. These data demonstrate that 1-octen-3-ol exerts toxicity via disruption of dopamine homeostasis and may represent a naturally occurring environmental agent involved in parkinsonism. Moreover, it provides possible insights into reported movement disorders associated with human exposure to fungi and their volatile organic compounds.
Foretinib is a potent inhibitor of oncogenic ROS1 fusion proteins
Authors: Davare Monika A. , Saborowski Anna , Eide Christopher A. , Tognon Cristina , Smith Rebecca L. , Elferich Johannes , Agarwal Anupriya , Tyner Jeffrey W. , Shinde Ujwal P. , Lowe Scott W. , Druker Brian J.
Published: November 2013

Significance

ROS1 fusion kinases are critical oncogenes in several malignancies, suggesting that ROS1 inhibitors are likely to be effective molecularly targeted therapies in these patients. Although phase I/II clinical trials using the ALK/ROS1 inhibitor crizotinib to treat ROS1 fusion-harboring non–small-cell lung cancer patients demonstrate early success, evidence of clinical resistance to crizotinib due to the acquired ROS1
G2032R
mutation was recently reported. Here, we demonstrate that foretinib is a more potent ROS1 inhibitor than crizotinib in vitro and in vivo and remains effective against crizotinib-resistant ROS1 kinase domain mutations, including ROS1 G2032R. Taken together, our findings establish foretinib as a highly promising therapeutic candidate for treating patients with ROS1-driven malignancies and provide rationale for rapid clinical translation.
Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation
Authors: Zhang Huakun , Bian Yao , Gou Xiaowan , Dong Yuzhu , Rustgi Sachin , Zhang Bangjiao , Xu Chunming , Li Ning , Qi Bao , Han Fangpu , von Wettstein Diter , Liu Bao
Published: November 2013

Significance

This paper discusses speciation by allopolyploidy of tetraploid wheat, which in turn is a milestone event in establishing hexaploid bread wheat. The results suggested that karyotype stabilization together with variation in copy number of coding genes and localized changes in genomic repeats may have contributed to the establishment of tetraploid wheat as successful species. These observations are of relevance to the plant-breeding community for developing unique wheat cultivars by wide-hybridization and chromosomal engineering.
Beyond Intensity: Spectral Features Effectively Predict Music-Induced Subjective Arousal
Authors: Gingras Bruno , Marin Manuela M. , Fitch W. Tecumseh
Published: November 2013

Emotions in music are conveyed by a variety of acoustic cues. Notably, the positive association between sound intensity and arousal has particular biological relevance. However, although amplitude normalization is a common procedure used to control for intensity in music psychology research, direct comparisons between emotional ratings of original and amplitude-normalized musical excerpts are lacking.

In this study, 30 nonmusicians retrospectively rated the subjective arousal and pleasantness induced by 84 six-second classical music excerpts, and an additional 30 nonmusicians rated the same excerpts normalized for amplitude. Following the cue-redundancy and Brunswik lens models of acoustic communication, we hypothesized that arousal and pleasantness ratings would be similar for both versions of the excerpts, and that arousal could be predicted effectively by other acoustic cues besides intensity.

Although the difference in mean arousal and pleasantness ratings between original and amplitude-normalized excerpts correlated significantly with the amplitude adjustment, ratings for both sets of excerpts were highly correlated and shared a similar range of values, thus validating the use of amplitude normalization in music emotion research. Two acoustic parameters, spectral flux and spectral entropy, accounted for 65% of the variance in arousal ratings for both sets, indicating that spectral features can effectively predict arousal. Additionally, we confirmed that amplitude-normalized excerpts were adequately matched for loudness. Overall, the results corroborate our hypotheses and support the cue-redundancy and Brunswik lens models.
Islamists in power: the case of the Muslim Brotherhood in Egypt
Authors: Al-Awadi Hesham
Published: November 2013

The article examines the Muslim Brotherhood in power in Egypt, 2012–2013, and how they dealt with the multifaceted challenges. The main argument is that the Brotherhood benefited from their past populist legitimacy to fill the vacuum created by the collapse of the Mubarak regime, but that this legitimacy waned when they did not consolidate this legitimacy with a tangible national achievement. The Brotherhood were unable to count on Egyptians’ sympathy for their endurance of rough treatment at the hands of the previous regime over many years, because the 25 January Revolution changed the Egyptian people’s expectations and spread knowledge of how to punish rulers who fail to meet these expectations: with sit-ins and street demonstrations. Despite Muhammad Morsi’s victory in the presidential elections, and the forceful curtailment of his four-year term by the army, this leading member of the Muslim Brotherhood failed to translate his legal legitimacy into a wider populist legitimacy based on tangible achievements.
Authoritarianism and the precariat
Authors: Jordan Bill
Published: November 2013

This article traces present-day policy debates on precarious employment to the nineteenth century. Liberal and paternalist versions of state authority emerged as responses to early capitalist development, and precariousness was an issue that contributed to the differentiation between them. The author argues that these connections with the bases of state power help explain why radical alternative approaches to today’s challenges find it so hard to get a hearing in mainstream political circles.