bluuebunny/crossref_metadata_2025 huggingface dataset:
Manipulating duckweed through genome duplication
Authors: Vunsh R. , Heinig U. , Malitsky S. , Aharoni A. , Avidov A. , Lerner A. , Edelman M.
Published: July 2014

Significant inter‐ and intraspecific genetic variation exists in duckweed, thus the potential for genome plasticity and manipulation is high. Polyploidy is recognised as a major mechanism of adaptation and speciation in plants. We produced several genome‐duplicated lines of Landoltia punctata (Spirodela oligorrhiza) from both whole plants and regenerating explants using a colchicine‐based cocktail. These lines stably maintained an enlarged frond and root morphology. DNA ploidy levels determined by florescence‐activated cell sorting indicated genome duplication. Line A4 was analysed after 75 biomass doublings. Frond area, fresh and dry weights, rhizoid number and length were significantly increased versus wild type, while the growth rate was unchanged. This resulted in accumulation of biomass 17–20% faster in the A4 plants. We sought to determine if specific differences in gene products are found in the genome duplicated lines. Non‐targeted ultra performance LC‐quadrupole time of flight mass spectrometry was employed to compare some of the lines and the wild type to seek identification of up‐regulated metabolites. We putatively identified differential metabolites in Line A65 as caffeoyl hexoses. The combination of directed genome duplication and metabolic profiling might offer a path for producing stable gene expression, leading to altered production of secondary metabolites.
The Potential for Public Empowerment through Government‐Organized Participation
Authors: Buckwalter Neal D.
Published: July 2014

This article develops a better theoretical understanding of the linkage between the processes and outcomes associated with government‐organized public participation, including its potential to empower citizens in guiding administrative decisions. Special focus is given to those factors that shape the development and maintenance of the citizen–administrator relationship. To this end, the research examines the work of federally mandated citizen review panels and their interactions with state child protection agency administrators. Based on 52 in‐depth interviews conducted with citizens and administrators in three U.S. states, a grounded theory approach is employed to derive a series of testable theoretical propositions. The insights gained are of importance not only to public administration scholars but also to citizens and administrators who engage one another through formally organized channels of participation.
Base Salaries, Bonus Payments, and Work Absence among Managers in a German Company
Authors: Pfeifer Christian
Published: July 2014

This paper provides scarce insider econometric evidence on the structure of management compensation and on the incentive effects of fixed base salaries and bonus payments. Six years of personnel data of 177 managers in a German company are analyzed with special emphasis on the highest achievable bonuses under a Management‐by‐Objectives (MBO) incentive scheme. The main finding of panel negative binomial regressions is that higher achievable bonus payments are correlated with fewer absent working days, which supports the incentive effect of performance pay for managers. The fixed base salary component is, however, not significantly correlated with managers’ work absence.
Dynamic, high precision targeting of growth modulating agents is able to trigger pollen tube growth reorientation
Authors: Sanati Nezhad Amir , Packirisamy Muthukumaran , Geitmann Anja
Published: July 2014

The pollen tube is the most rapidly growing cell in the plant kingdom and has the function to deliver the sperm cells for fertilization. The growing tip region of the cell behaves in a chemotropic manner to respond to the guidance cues emitted by the pistil and the female gametophyte, but how it perceives and responds to these directional triggers is virtually unknown. Quantitative assessment of chemotropic behavior can greatly be enhanced by the administration of pharmacological or other biologically active agents at subcellular precision, which is a technical challenge when the target area moves as it grows. We developed a laminar flow based microfluidic device that allows for continuous administration of two different solutions with a movable interface that permits the dynamic targeting of the growing pollen tube apex over prolonged periods of time. Asymmetric administration of calcium revealed that rather than following the highest calcium concentration as would be expected with simple chemotropic behavior, the pollen tube of Camellia targets an optimal concentration suggesting the presence of two superimposed mechanisms. Subcellular application of pectin methyl esterase (PME), an enzyme that modifies the growth behavior by rigidifying the pollen tube cell wall, caused the tube to turn away from the agent – providing important evidence for a previously proposed conceptual model of the growth mechanism.
RCN1/OsABCG5, an ATP‐binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice (Oryza sativa)
Authors: Shiono Katsuhiro , Ando Miho , Nishiuchi Shunsaku , Takahashi Hirokazu , Watanabe Kohtaro , Nakamura Motoaki , Matsuo Yuichi , Yasuno Naoko , Yamanouchi Utako , Fujimoto Masaru , Takanashi Hideki , Ranathunge Kosala , Franke Rochus B. , Shitan Nobukazu , Nishizawa Naoko K. , Takamure Itsuro , Yano Masahiro , Tsutsumi Nobuhiro , Schreiber Lukas , Yazaki Kazufumi , Nakazono Mikio , Kato Kiyoaki
Published: July 2014

Suberin is a complex polymer composed of aliphatic and phenolic compounds. It is a constituent of apoplastic plant interfaces. In many plant species, including rice (Oryza sativa), the hypodermis in the outer part of roots forms a suberized cell wall (the Casparian strip and/or suberin lamellae), which inhibits the flow of water and ions and protects against pathogens. To date, there is no genetic evidence that suberin forms an apoplastic transport barrier in the hypodermis. We discovered that a rice reduced culm number1 (rcn1) mutant could not develop roots longer than 100 mm in waterlogged soil. The mutated gene encoded an ATP‐binding cassette (ABC) transporter named RCN1/OsABCG5. RCN1/OsABCG5 gene expression in the wild type was increased in most hypodermal and some endodermal roots cells under stagnant deoxygenated conditions. A GFP‐RCN1/OsABCG5 fusion protein localized at the plasma membrane of the wild type. Under stagnant deoxygenated conditions, well suberized hypodermis developed in wild types but not in rcn1 mutants. Under stagnant deoxygenated conditions, apoplastic tracers (periodic acid and berberine) were blocked at the hypodermis in the wild type but not in rcn1, indicating that the apoplastic barrier in the mutant was impaired. The amount of the major aliphatic suberin monomers originating from C28 and C30 fatty acids or ω‐OH fatty acids was much lower in rcn1 than in the wild type. These findings suggest that RCN1/OsABCG5 has a role in the suberization of the hypodermis of rice roots, which contributes to formation of the apoplastic barrier.
Measurement of salivary adiponectin concentrations in dogs
Authors: Tvarijonaviciute Asta , Carrillo‐Sanchez Juana D. , García‐Martinez Juan D. , Tecles Fernando , Martinez‐Subiela Silvia , German Alexander J. , Ceron Jose J.
Published: July 2014

Background

Measurement of salivary adiponectin could improve understanding of this adipokine's physiology, and its role in various clinical conditions.

Objectives

The purpose of the study was to evaluate the utility of a human adiponectin ELISA kit for measurement of salivary adiponectin in dogs, to compare serum and salivary adiponectin concentrations in a healthy dog population, and to evaluate possible effects of tooth‐cleaning on serum and salivary adiponectin concentrations in dogs.

Methods

For analytical validation, precision, accuracy, and lower limit of quantification of the assay were determined with saliva samples. In addition, adiponectin concentrations were quantified in serum and saliva samples from 24 healthy dogs, and from 7 dogs with mild gingivitis before and after a tooth‐cleaning procedure.

Results

The validation assays for salivary adiponectin had all coefficients of variation <15%, and recovery ranged from 85% to 120%. In the linearity test, interference was observed when measuring adiponectin in saliva, but this was solved by diluting samples 1:4. In healthy dogs, salivary and serum adiponectin concentrations were positively correlated (r = .650; P = .009). After the tooth‐cleaning procedure, salivary adiponectin concentration increased on day 0 (P = .004), but by day 14, concentrations were less than prior to the procedure (P = .041).

Conclusions

The human adiponectin ELISA kit can be used for precise and accurate salivary adiponectin measurement in dogs. Salivary adiponectin increased 24 hours after tooth‐cleaning, possibly due to acute inflammation or adiponectin leakage from the blood after gingival trauma.
Analysis of Sinusoidal Interfacial Wrinkling of an Anisotropic Film Sandwiched Between Two Compliant Layers
Authors: Yang J. W. , Nie G. H.
Published: July 2014

When a stiff film is bonded to a compliant layer and meanwhile encapsulated by another compliant layer on top, the film may form wrinkles under applied compressive stress. Inspired by the recent development of foldable circuit sealed in an encapsulating layer to improve bendability, unlike the wide study of surface wrinkling in a bilayer system, this paper presents a study of possible sinusoidal interfacial wrinkling in such sandwich system. The film is assumed to be anisotropic with arbitrary orientation of elastic axis while both layers are isotropic. A linear perturbation analysis is performed to predict critical membrane stress, wave number and equilibrium amplitude for the onset of interfacial wrinkles. The effect of parameters such as elastic axis orientation of the film and moduli, thicknesses, and Poisson's ratios of the layers on the wrinkling is evaluated in detail. The results show that compared to two compliant layers, the stiffer and thinner the film is, the smaller the values of both the critical stress and wave number for wrinkling will be. Especially, we illustrate three limiting cases: two layers both reach thick-layer limit, two layers both reach thin-layer limit and one layer reaches thick-layer limit while the other layer reaches thin-layer limit. Analytical solutions are obtained for first two cases and numerical solutions are plotted for the third case. It is found that as long as the thin-layer is near incompressible, the interfacial wrinkles can be suppressed. In addition, the equilibrium wave modes for the three limiting cases are also given. The resulting solutions for the sandwich system can be reduced to the classic solutions for a bilayer system.
Experiential Conjoint Analysis: An Experience-Based Method for Eliciting, Capturing, and Modeling Consumer Preference
Authors: Tovares Noah , Boatwright Peter , Cagan Jonathan
Published: July 2014

Traditionally, consumer preference is modeled in terms of preference for the aesthetic and functional features of a product. This paper introduces a new means to model consumer preference that accounts for not only for how a product looks and functions but also how it feels to interact with it. Traditional conjoint-based approaches to preference modeling require a participant to judge preference for a product based upon a static 2D visual representation or a feature list. While the aesthetic forms and functional features of a product are certainly important, the decision to buy or not to buy a product often depends on more, namely, the experience or feel of use. To address the importance of the product experience, we introduce the concept of experiential conjoint analysis, a method to mathematically capture preference for a product through experience-based (experiential) preference judgments. Experiential preference judgments are made based upon the use, or simulated use, of a product. For many products, creating enough physical prototypes to generate a preference model is cost prohibitive. In this work, virtual reality (VR) technologies are used to allow the participant an interactive virtual product experience, provided at little investment. The results of this work show that providing additional interaction-based (interactional) information about a product through a product experience does not affect the predictive ability of the resulting preference models. This work additionally demonstrates that the preference judgments of virtual product representations are more similar to preference judgments of real products than preference judgments of 2D product representations are. When examining similarity of modeled preference, experiential conjoint is found to be superior to visual conjoint with respect to mean absolute error (MAE), but with respect to correlation no significant difference between visual and experiential is found.
A Novel Nonlinear Modeling and Dynamic Analysis of Solenoid Actuated Butterfly Valves Coupled in Series
Authors: Naseradinmousavi Peiman
Published: July 2014

In this paper, we focus on a novel nonlinear modeling and dynamic analysis of the actuated butterfly valves coupled in series. The actuated valves used in the chilled water systems of the U.S. Navy and commercial ships, namely, “smart valves,” recently have received much attention when many of them are operating in a complex network. The network regulates the pressure of the pipeline, while several nonlinear torques/forces including the hydrodynamic and bearing torques and the magnetomotive force affect the performance of each set individually and subsequently the whole system via the couplings among the valves. The contribution of this work is to model such couplings in the presence of the nonlinearities and an applied periodic noise and then carry out dynamic analysis of the valves. We examine the model developed with/without actuation by applying a periodic noise on the upstream valve to capture the couplings among the parameters of both the actuators and valves. This would help us predict the behavior of a particular valve in the network subject to motions of other valves.
On-Chip Power Generation Using Ultrathin Thermoelectric Generators
Authors: Sullivan Owen , Gupta Man Prakash , Mukhopadhyay Saibal , Kumar Satish
Published: July 2014

Thermoelectric generators (TEGs) can significantly improve the net power consumption and battery life of the low power mobile devices or high performance devices by generating power from their waste heat. Recent advancements also show that the ultrathin thermoelectric devices can be fabricated and integrated within a micro-electronic package. This work investigates the power generation by an ultrathin TEG embedded within a micro-electronic package considering several key parameters such as load resistance, chip heat flux, and proximity of the TEG to chip. The analysis shows that the power generation from TEGs increases with increasing background heat flux on chip or when TEGs are moved closer to the chip. An array of embedded TEGs is considered in order to analyze the influence of multiple TEGs on total power generation and conversion efficiency. Increasing the number of TEGs from one to nine increases the useful power generation from 72.9 mW to 378.4 mW but decreases the average conversion efficiency from 0.47% to 0.32%. The average power generated per TEG gradually decrease from 72.9 mW to 42.0 mW when number of TEGs is increased from one to nine, but the total useful power generated using nine TEGs is significant and emphasize the benefits of using embedded TEGs to reduce net power consumption in electronics packages.
A Technological Effect Modeling on Complex Turbomachinery Applications With an Overset Grid Numerical Method
Authors: Castillon Lionel , Billonnet Gilles , Riou Jacques , Péron Stéphanie , Benoit Christophe
Published: July 2014

This paper presents an overview of numerical simulations performed at ONERA on turbomachinery configurations which include technological effects, such as tip clearance, hub disk leakage, circumferential and noncircumferential casing treatments (CTs), blade fillets, and cooling holes. An overset grid approach (Chimera technique) is used to simulate these geometrical effects with ONERA's structured computational fluid dynamics (CFD) solver elsA. Calculations performed on the different configurations enable to quantify the impact of these technological effects on the flow solution.
Māori and community news constructions of Meningococcal B: The promotion of a moral obligation to vaccinate
Authors: Groot Shiloh , Ngata Ronald , Hodgetts Darrin , Waimarie Nikora Linda , Karapu Rolinda , Chamberlain Kerry
Published: July 2014

Māori and community news constructions of Meningococcal B: The promotion of a moral obligation to vaccinate
Media Interactivity and Fantasy Sport
Authors: Jutel Thierry , Schirato Tony
Published: July 2014

Media Interactivity and Fantasy Sport
Review: The Romance of Transgression in Canada: Queering Sexualities, Nations, Cinemas by Thomas Waugh (Montreal & Kingston: McGill-Queen’s University Press 2006)
Authors: Alemany-Galway Mary
Published: July 2014

Review: The Romance of Transgression in Canada: Queering Sexualities, Nations, Cinemas by Thomas Waugh (Montreal & Kingston: McGill-Queen’s University Press 2006)
Conscientious dissident or radical eccentric: Negotiation of mediated protest images in New Zealand
Authors: Kenix Linda Jean
Published: July 2014

Conscientious dissident or radical eccentric: Negotiation of mediated protest images in New Zealand
Ethically Framed or Framed Ethnically? A Study of the Coverage of Immigrants, Refugees and Asylum Seekers in New Zealand’s Print Media from 2004­-2007
Authors: Miller Trudy
Published: July 2014

Ethically Framed or Framed Ethnically? A Study of the Coverage of Immigrants, Refugees and Asylum Seekers in New Zealand’s Print Media from 2004-­2007
Mass densification and defect restoration in chemical vapor deposition silicon dioxide film using Ar plasma excited by microwave
Authors: Kawase Kazumasa , Motoya Tsukasa , Uehara Yasushi , Teramoto Akinobu , Suwa Tomoyuki , Ohmi Tadahiro
Published: July 2014

Silicon dioxide (SiO2) films formed by chemical vapor deposition (CVD) have been treated with Ar plasma excited by microwave. The changes of the mass densities, carrier trap densities, and thicknesses of the CVD-SiO2 films with the Ar plasma treatments were investigated. The mass density depth profiles were estimated with X-Ray Reflectivity (XRR) analysis using synchrotron radiation. The densities of carrier trap centers due to defects of Si-O bond network were estimated with X-ray Photoelectron Spectroscopy (XPS) time-dependent measurement. The changes of the thicknesses due to the oxidation of Si substrates were estimated with the XRR and XPS. The mass densities of the CVD-SiO2 films are increased by the Ar plasma treatments. The carrier trap densities of the films are decreased by the treatments. The thicknesses of the films are not changed by the treatments. It has been clarified that the mass densification and defect restoration in the CVD-SiO2 films are caused by the Ar plasma treatments without the oxidation of the Si substrates.
2-D Material Molybdenum Disulfide Analyzed by XPS
Authors: Ganta D. , Sinha S. , Haasch Richard T.
Published: July 2014

Molybdenum disulfide (MoS2), a two-dimensional material purchased from SPI supplies, was analyzed using high-resolution X-ray photoelectron spectroscopy (XPS). A flake was mechanically exfoliated from a MoS2 bulk single crystal for the study. The XPS spectra of MoS2 obtained using monochromatic Al Kα radiation at 0.83401 nm include a survey scan, high-resolution spectra of O 1s, Mo 3p, C 1s, Mo 3d, S 2s, S 2p, Mo 4s, Mo 4p, S 3s, and valance band. Extended energy ranges were collected in the vicinity of the Mo 3d/S 2s, S 2p, and Mo 4s/Mo 4p/S 3s/Valence band regions allowing for fitting of surface plasmon features and determination of Tougaard scattering cross-section parameters. Quantitative analysis indicates a surface composition of MoS1.9.
The Variance Needed to Accurately Describe Jump Height from Vertical Ground Reaction Force Data
Authors: Richter Chris , McGuinness Kevin , O’Connor Noel E. , Moran Kieran
Published: July 2014

In functional principal component analysis (fPCA) a threshold is chosen to define the number of retained principal components, which corresponds to the amount of preserved information. A variety of thresholds have been used in previous studies and the chosen threshold is often not evaluated. The aim of this study is to identify the optimal threshold that preserves the information needed to describe a jump height accurately utilizing vertical ground reaction force (vGRF) curves. To find an optimal threshold, a neural network was used to predict jump height from vGRF curve measures generated using different fPCA thresholds. The findings indicate that a threshold from 99% to 99.9% (6–11 principal components) is optimal for describing jump height, as these thresholds generated significantly lower jump height prediction errors than other thresholds.
The Effects of a Lateral In-flight Perturbation on Lower Extremity Biomechanics During Drop Landings
Authors: Yom Jae P. , Simpson Kathy J. , Arnett Scott W. , Brown Cathleen N.
Published: July 2014

One potential ACL injury situation is due to contact with another person or object during the flight phase, thereby causing the person to land improperly. Conversely, athletes often have flight-phase collisions but do land safely. Therefore, to better understand ACL injury causation and methods by which people typically land safely, the purpose of this study was to determine the effects of an in-flight perturbation on the lower extremity biomechanics displayed by females during typical drop landings. Seventeen collegiate female recreational athletes performed baseline landings, followed by either unexpected laterally-directed perturbation or sham (nonperturbation) drop landings. We compared baseline and perturbation trials using paired-samples t tests (P < .05) and 95% confidence intervals for lower-extremity joint kinematics and kinetics and GRF. The results demonstrated that perturbation landings compared with baseline landings exhibited more extended joint positions of the lower extremity at initial contact; and, during landing, greater magnitudes for knee abduction and hip adduction displacements; peak magnitudes of vertical and medial GRF; and maximum moments of ankle extensors, knee extensors, and adductor and hip adductors. We conclude that a lateral in-flight perturbation leads to abnormal GRF and angular motions and joint moments of the lower extremity.
Kinematic Differences Between Those With and Without Medial Knee Displacement During a Single-leg Squat
Authors: Mauntel Timothy C. , Frank Barnett S. , Begalle Rebecca L. , Blackburn J. Troy , Padua Darin A.
Published: July 2014

A greater knee valgus angle is a risk factor for lower extremity injuries. Visually observed medial knee displacement is used as a proxy for knee valgus motion during movement assessments in an attempt to identify individuals at heightened risk for injury. The validity of medial knee displacement as an indicator of valgus motion has yet to be determined during a single-leg squat. This study compared three-dimensional knee and hip angles between participants who displayed medial knee displacement (MKD group) during a single-leg squat and those who did not (control group). Participants completed five single-leg squats. An electromagnetic motion tracking system was used to quantify peak knee and hip joint angles during the descent phase of each squat. MANOVA identified a difference between the MKD and control group kinematics. ANOVA post hoc testing revealed greater knee valgus angle in the MKD (12.86 ± 5.76) compared with the control (6.08 ± 5.23) group. There were no other differences between groups. Medial knee displacement is indicative of knee valgus motion; however, it is not indicative of greater knee or hip rotation, or hip adduction. These data indicate that clinicians can accurately identify individuals with greater knee valgus angle through visually observed medial knee displacement.
Comment on “Quantifying long-term scientific impact”
Authors: Wang Jian , Mei Yajun , Hicks Diana
Published: July 2014

Wang
et al
. (Reports, 4 October 2013, p. 127) claimed high prediction power for their model of citation dynamics. We replicate their analysis but find discouraging results: 14.75% papers are estimated with unreasonably large μ (>5) and λ (>10) and correspondingly enormous prediction errors. The prediction power is even worse than simply using short-term citations to approximate long-term citations.
A Doppler effect in embryonic pattern formation
Authors: Soroldoni Daniele , Jörg David J. , Morelli Luis G. , Richmond David L. , Schindelin Johannes , Jülicher Frank , Oates Andrew C.
Published: July 2014

Observing an embryonic Doppler effect

The sound of an oncoming train changes as it passes you, a phenomenon termed the Doppler effect. Soroldoni
et al.
propose a similar event during the formation of vertebrate embryo body segments. It is generally thought that the internal timing of a genetic oscillator called the “segmentation clock” sets the rhythm of body segments called somites. However, time-lapse microscopy of the spatial waves of oscillations and the timing of body segment formation showed segments forming faster than spatial genetic oscillations. This “Doppler effect” occurs because the end of the oscillating tissue moves steadily into the oncoming waves. Thus, the rhythm of sequential body segmentation is a function of genetic oscillations, their changing wave pattern, and tissue shortening.

Science
, this issue p.
222
Assessing the reliability of calculated catalytic ammonia synthesis rates
Authors: Medford Andrew J. , Wellendorff Jess , Vojvodic Aleksandra , Studt Felix , Abild-Pedersen Frank , Jacobsen Karsten W. , Bligaard Thomas , Nørskov Jens K.
Published: July 2014

Assessing calculated DFT properties

Density functional theory (DFT) is now widely used to calculate molecular and material properties. DFT's reliability is usually assessed by comparison with experimental values and higher-level theoretical methods. Medford
et al.
used the BEEFvdW, an exchange-correlation density functional tailored for surface chemistry, and looked at uncertainties with ensembles of functionals. For the specific case of ammonia synthesis catalyzed by transition-metal surfaces, relative rates between different catalysts had lower errors than the absolute rates.

Science
, this issue p.
197
Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase
Authors: Casadei Cecilia M. , Gumiero Andrea , Metcalfe Clive L. , Murphy Emma J. , Basran Jaswir , Concilio Maria Grazia , Teixeira Susana C. M. , Schrader Tobias E. , Fielding Alistair J. , Ostermann Andreas , Blakeley Matthew P. , Raven Emma L. , Moody Peter C. E.
Published: July 2014

Peroxidase proton placement

Heme enzymes catalyze a variety of biochemical oxidations through the activation of oxygen by iron. Casadei
et al.
used neutron crystallography to elucidate the mechanism of cytochrome c peroxidase (see the perspective by Groves and Boaz). In the highly reactive intermediate state termed compound I, the iron(IV) oxo, or ferryl, fragment was not protonated, whereas a nearby histidine residue was protonated. The sensitivity of neutron scattering to proton locations revealed these protonation states, where more common techniques, such as x-ray diffraction, have yielded more ambiguous results.

Science
, this issue p.
193
; see also p.
142
MurJ is the flippase of lipid-linked precursors for peptidoglycan biogenesis
Authors: Sham Lok-To , Butler Emily K. , Lebar Matthew D. , Kahne Daniel , Bernhardt Thomas G. , Ruiz Natividad
Published: July 2014

Building the cell wall is flipping difficult

The cell wall of bacteria is constructed from a polysaccharide called peptidoglycan (PG). It forms a matrix that surrounds cells and is essential for the integrity of the cytoplasmic membrane. Many of our most successful antibiotics target PG synthesis. The synthetic pathway involves the assembly of sugar building blocks on a lipid carrier at the inner face of the cytoplasmic membrane. The reactions that produce this so-called lipid II precursor and the enzymes that catalyze them have been known for decades. However, the identity of the flippase enzyme that “flips” lipid II in the membrane to expose the sugar building blocks on the cell surface for polymerization has remained highly controversial. Sham
et al.
now show that the essential protein MurJ is the long sought-after flippase responsible for the translocation of lipid-linked cell wall precursors across the bacterial cytoplasmic membrane (see the Perspective by Young). The work completes the cell wall biogenesis pathway and defines the function of an attractive target for new antibiotics.

Science
, this issue p.
220
; see also p.
139
Taking the pulse of ocean microbes
Authors: Armbrust E. Virginia
Published: July 2014

Gene expression patterns of open-ocean microbes are tightly coupled.

[Also see Report by

Ottesen
et al.

]
Fishing for peroxidase protons
Authors: Groves John T. , Boaz Nicholas C.
Published: July 2014

Where are the protons in heme protein catalysis?

[Also see Report by

Casadei
et al.

]
A focus on child development
Authors: Silver Karlee L. , Singer Peter A.
Published: July 2014

By September 2014, the United Nations (UN) Open Working Group will present its final report on the Sustainable Development Goals to the UN Secretary General and President of the General Assembly, who will finalize these goals by September 2015. Because these goals (the successors to the Millennium Development Goals) will guide global action through 2030, it is unfortunate that early child development is not yet effectively addressed in this framework. Investing in child development is the foundation for improved health, economic, and social outcomes. Not getting the early years “right” is linked to violent behavior, depression, higher rates of noncommunicable disease, and lower wages, and it negatively affects a nation's gross domestic product. Unless early child development is addressed effectively in the UN Sustainable Development Goals, countries will be locked into poverty, and sustainable development will not be achieved.
Conflict erupts over landmark E.U. neuroscience plan
Authors: Enserink Martin , Kupferschmidt Kai
Published: July 2014

Scientists threaten to boycott the Human Brain Project.
Monkey fever unbound
Authors: Stone Richard
Published: July 2014

The spread of an emerging disease from its forest stronghold is sounding alarm bells in India.
Validation of an Enzyme-Linked Immunosorbent Assay That Detects Histoplasma capsulatum Antigenuria in Colombian Patients with AIDS for Diagnosis and Follow-Up during Therapy
Authors: Caceres Diego H. , Scheel Christina M. , Tobón Ángela M. , Ahlquist Cleveland Angela , Restrepo Ángela , Brandt Mary E. , Chiller Tom , Gómez Beatriz L.
Published: July 2014

We validated an antigen capture enzyme-linked immunosorbent assay (ELISA) in Colombian persons with AIDS and proven histoplasmosis and evaluated the correlation between antigenuria and clinical improvement during follow-up. The sensitivity of theHistoplasma capsulatumELISA was 86%, and the overall specificity was 94%. The antigen test successfully monitored the response to therapy.
Autographa californica Multiple Nucleopolyhedrovirus DNA Polymerase C Terminus Is Required for Nuclear Localization and Viral DNA Replication
Authors: Feng Guozhong , Krell Peter J.
Published: July 2014

The DNA polymerase (DNApol) of the baculovirus
Autographa californica
multiple nucleopolyhedrovirus (AcMNPV) is essential for viral DNA replication. The DNApol exonuclease and polymerase domains are highly conserved and are considered functional in DNA replication. However, the role of the DNApol C terminus has not yet been characterized. To identify whether only the exonuclease and polymerase domains are sufficient for viral DNA replication, several DNApol C-terminal truncations were cloned into a
dnapol
-null AcMNPV bacmid with a green fluorescent protein (GFP) reporter. Surprisingly, most of the truncation constructs, despite containing both exonuclease and polymerase domains, could not rescue viral DNA replication and viral production in bacmid-transfected Sf21 cells. Moreover, GFP fusions of these same truncations failed to localize to the nucleus. Truncation of the C-terminal amino acids 950 to 984 showed nuclear localization but allowed for only limited and delayed viral spread. The C terminus contains a typical bipartite nuclear localization signal (NLS) motif at residues 804 to 827 and a monopartite NLS motif at residues 939 to 948. Each NLS, as a GFP fusion peptide, localized to the nucleus, but both NLSs were required for nuclear localization of DNApol. Alanine substitutions in a highly conserved baculovirus DNApol sequence at AcMNPV DNApol amino acids 972 to 981 demonstrated its importance for virus production and DNA replication. Collectively, the data indicated that the C terminus of AcMNPV DNApol contains two NLSs and a conserved motif, all of which are required for nuclear localization of DNApol, viral DNA synthesis, and virus production.

IMPORTANCE
The baculovirus DNA polymerase (DNApol) is a highly specific polymerase that allows viral DNA synthesis and hence virus replication in infected insect cells. We demonstrated that the exonuclease and polymerase domains of
Autographa californica
multiple nucleopolyhedrovirus (AcMNPV) alone are insufficient for viral DNA synthesis and virus replication. Rather, we identified three features, including two nuclear localization signals and a highly conserved 10-amino-acid sequence in the AcMNPV DNApol C terminus, all three of which are important for both nuclear localization of DNApol and for DNApol activity, as measured by viral DNA synthesis and virus replication.
Diverse Specificities, Phenotypes, and Antiviral Activities of Cytomegalovirus-Specific CD8+T Cells
Authors: Jackson S. E. , Mason G. M. , Okecha G. , Sissons J. G. P. , Wills M. R.
Published: July 2014

CD8+T cells specific for pp65, IE1, and IE2 are present at high frequencies in human cytomegalovirus (HCMV)-seropositive individuals, and these have been shown to have phenotypes associated with terminal differentiation, as well as both cytokine and proliferative dysfunctions, especially in the elderly. However, more recently, T cell responses to many other HCMV proteins have been described, but little is known about their phenotypes and functions. Consequently, in this study, we chose to determine the diversity of HCMV-specific CD8+T cell responses to the products of 11 HCMV open reading frames (ORFs) in a cohort of donors aged 20 to 80 years old as well as the ability of the T cells to secrete gamma interferon (IFN-γ). Finally, we also tested their functional antiviral capacity using a novel viral dissemination assay. We identified substantial CD8+T cell responses by IFN-γ enzyme-linked immunospot (ELISPOT) assays to all 11 of these HCMV proteins, and across the cohort, individuals displayed a range of responses, from tightly focused to highly diverse, which were stable over time. CD8+T cell responses to the HCMV ORFs were highly differentiated and predominantly CD45RA+, CD57+, and CD28−, across the cohort. These highly differentiated cells had the ability to inhibit viral spread even following directex vivoisolation. Taken together, our data argue that HCMV-specific CD8+T cells have effective antiviral activity irrespective of the viral protein recognized across the whole cohort and despite viral immune evasion.

IMPORTANCEHuman cytomegalovirus (HCMV) is normally carried without clinical symptoms and is widely prevalent in the population; however, it often causes severe clinical disease in individuals with compromised immune responses. HCMV is never cleared after primary infection but persists in the host for life. In HCMV carriers, the immune response to HCMV includes large numbers of virus-specific immune cells, and the virus has evolved many mechanisms to evade the immune response. While this immune response seems to protect healthy people from subsequent disease, the virus is never eliminated. It has been suggested that this continuous surveillance by the immune system may have deleterious effects in later life. The study presented in this paper examined immune responses from a cohort of donors and shows that these immune cells are effective at controlling the virus and can overcome the virus' lytic cycle immune evasion mechanisms.
A Mutation in the DNA Polymerase Accessory Factor of Herpes Simplex Virus 1 Restores Viral DNA Replication in the Presence of Raltegravir
Authors: Zhou Bin , Yang Kui , Wills Elizabeth , Tang Liang , Baines Joel D.
Published: July 2014

Previous reports showed that raltegravir, a recently approved antiviral compound that targets HIV integrase, can inhibit the nuclease function of human cytomegalovirus (HCMV terminase)
in vitro
. In this study, subtoxic levels of raltegravir were shown to inhibit the replication of four different herpesviruses, herpes simplex virus 1 (HSV-1), HSV-2, HCMV, and mouse cytomegalovirus, by 30- to 700-fold, depending on the dose and the virus tested. Southern blotting and quantitative PCR revealed that raltegravir inhibits DNA replication of HSV-1 rather than cleavage of viral DNA. A raltegravir-resistant HSV-1 mutant was generated by repeated passage in the presence of 200 μM raltegravir. The genomic sequence of the resistant virus, designated clone 7, contained mutations in 16 open reading frames. Of these, the mutations F198S in unique long region 15 (U
L
15; encoding the large terminase subunit), A374V in U
L
32 (required for DNA cleavage and packaging), V296I in U
L
42 (encoding the DNA polymerase accessory factor), and A224S in U
L
54 (encoding ICP27, an important transcriptional regulator) were introduced independently into the wild-type HSV-1(F) genome, and the recombinant viruses were tested for raltegravir resistance. Viruses bearing both the U
L
15 and U
L
32 mutations inserted within the genome of the U
L
42 mutant were also tested. While the U
L
15, U
L
32, and U
L
54 mutant viruses were fully susceptible to raltegravir, any virus bearing the U
L
42 mutation was as resistant to raltegravir as clone 7. Overall, these results suggest that raltegravir may be a valuable therapeutic agent against herpesviruses and the antiviral activity targets the DNA polymerase accessory factor rather than the nuclease activity of the terminase.

IMPORTANCE
This paper shows that raltegravir, the antiretrovirus drug targeting integrase, is effective against various herpesviruses. Drug resistance mapped to the herpesvirus DNA polymerase accessory factor, which was an unexpected finding.
Age-Dependent Myeloid Dendritic Cell Responses Mediate Resistance to La Crosse Virus-Induced Neurological Disease
Authors: Taylor Katherine G. , Woods Tyson A. , Winkler Clayton W. , Carmody Aaron B. , Peterson Karin E.
Published: July 2014

La Crosse virus (LACV) is the major cause of pediatric viral encephalitis in the United States; however, the mechanisms responsible for age-related susceptibility in the pediatric population are not well understood. Our current studies in a mouse model of LACV infection indicated that differences in myeloid dendritic cell (mDC) responses between weanling and adult mice accounted for susceptibility to LACV-induced neurological disease. We found that type I interferon (IFN) responses were significantly stronger in adult than in weanling mice. Production of these IFNs required both endosomal Toll-like receptors (TLRs) and cytoplasmic RIG-I-like receptors (RLRs). Surprisingly, IFN expression was not dependent on plasmacytoid DCs (pDCs) but rather was dependent on mDCs, which were found in greater number and induced stronger IFN responses in adults than in weanlings. Inhibition of these IFN responses in adults resulted in susceptibility to LACV-induced neurological disease, whereas postinfection treatment with type I IFN provided protection in young mice. These studies provide a definitive mechanism for age-related susceptibility to LACV encephalitis, where mDCs in young mice are insufficiently activated to control peripheral virus replication, thereby allowing virus to persist and eventually cause central nervous system (CNS) disease.

IMPORTANCE
La Crosse virus (LACV) is the primary cause of pediatric viral encephalitis in the United States. Although the virus infects both adults and children, over 80% of the reported neurological disease cases are in children. To understand why LACV causes neurological disease primarily in young animals, we used a mouse model where weanling mice, but not adult mice, develop neurological disease following virus infection. We found that an early immune response cell type, myeloid dendritic cells, was critical for protection in adult animals and that these cells were reduced in young animals. Activation of these cells during virus infection or after treatment with type I interferon in young animals provided protection from LACV. Thus, this study demonstrates a reason for susceptibility to LACV infection in young animals and shows that early therapeutic treatment in young animals can prevent neurological disease.
New Small-Molecule Inhibitors Effectively Blocking Picornavirus Replication
Authors: Ford Siltz Lauren A. , Viktorova Ekaterina G. , Zhang Ben , Kouiavskaia Diana , Dragunsky Eugenia , Chumakov Konstantin , Isaacs Lyle , Belov George A.
Published: July 2014

Few drugs targeting picornaviruses are available, making the discovery of antivirals a high priority. Here, we identified and characterized three compounds from a library of kinase inhibitors that block replication of poliovirus, coxsackievirus B3, and encephalomyocarditis virus. Using an
in vitro
translation-replication system, we showed that these drugs inhibit different stages of the poliovirus life cycle. A4(1) inhibited both the formation and functioning of the replication complexes, while E5(1) and E7(2) were most effective during the formation but not the functioning step. Neither of the compounds significantly inhibited VPg uridylylation. Poliovirus resistant to E7(2) had a G5318A mutation in the 3A protein. This mutation was previously found to confer resistance to enviroxime-like compounds, which target a phosphatidylinositol 4-kinase IIIβ (PI4KIIIβ)-dependent step in viral replication. Analysis of host protein recruitment showed that E7(2) reduced the amount of GBF1 on the replication complexes; however, the level of PI4KIIIβ remained intact. E7(2) as well as another enviroxime-like compound, GW5074, interfered with viral polyprotein processing affecting both 3C- and 2A-dependent cleavages, and the resistant G5318A mutation partially rescued this defect. Moreover, E7(2) induced abnormal recruitment to membranes of the viral proteins; thus, enviroxime-like compounds likely severely compromise the interaction of the viral polyprotein with membranes. A4(1) demonstrated partial protection from paralysis in a murine model of poliomyelitis. Multiple attempts to isolate resistant mutants in the presence of A4(1) or E5(1) were unsuccessful, showing that effective broad-spectrum antivirals could be developed on the basis of these compounds.

IMPORTANCE
Diverse picornaviruses can trigger multiple human maladies, yet currently, only hepatitis A virus and poliovirus can be controlled with vaccination. The development of antipicornavirus therapeutics is also facing significant difficulties because these viruses readily generate resistance to compounds targeting either viral or cellular factors. Here, we describe three novel compounds that effectively block replication of distantly related picornaviruses with minimal toxicity to cells. The compounds prevent viral RNA replication after the synthesis of the uridylylated VPg primer. Importantly, two of the inhibitors are strongly refractory to the emergence of resistant mutants, making them promising candidates for further broad-spectrum therapeutic development. Evaluation of one of the compounds in an
in vivo
model of poliomyelitis demonstrated partial protection from the onset of paralysis.
TRIM13 Is a Negative Regulator of MDA5-Mediated Type I Interferon Production
Authors: Narayan Kavitha , Waggoner Lisa , Pham Serena T. , Hendricks Gabriel L. , Waggoner Stephen N. , Conlon Joseph , Wang Jennifer P. , Fitzgerald Katherine A. , Kang Joonsoo
Published: July 2014

Retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are essential intracellular detectors of viral RNA. They contribute to the type I interferon (IFN) response that is crucial for host defense against viral infections. Given the potent antiviral and proinflammatory activities elicited by the type I IFNs, induction of the type I IFN response is tightly regulated. Members of the tripartite motif (TRIM) family of proteins have recently emerged as key regulators of antiviral immunity. We show that TRIM13, an E3 ubiquitin ligase, is expressed in immune cells and is upregulated in bone marrow-derived macrophages upon stimulation with inducers of type I IFN. TRIM13 interacts with MDA5 and negatively regulates MDA5-mediated type I IFN production
in vitro
, acting upstream of IFN regulatory factor 3. We generated
Trim13
−/−
mice and show that upon lethal challenge with encephalomyocarditis virus (EMCV), which is sensed by MDA5,
Trim13
−/−
mice produce increased amounts of type I IFNs and survive longer than wild-type mice.
Trim13
−/−
murine embryonic fibroblasts (MEFs) challenged with EMCV or poly(I·C) also show a significant increase in beta IFN (IFN-β) levels, but, in contrast, IFN-β responses to the RIG-I-detected Sendai virus were diminished, suggesting that TRIM13 may play a role in positively regulating RIG-I function. Together, these results demonstrate that TRIM13 regulates the type I IFN response through inhibition of MDA5 activity and that it functions nonredundantly to modulate MDA5 during EMCV infection.

IMPORTANCE
The type I interferon (IFN) response is crucial for host defense against viral infections, and proper regulation of this pathway contributes to maintaining immune homeostasis. Retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are intracellular detectors of viral RNA that induce the type I IFN response. In this study, we show that expression of the gene tripartite motif 13 (
Trim13
) is upregulated in response to inducers of type I IFN and that TRIM13 interacts with both MDA5 and RIG-I
in vitro
. Through the use of multiple
in vitro
and
in vivo
model systems, we show that TRIM13 is a negative regulator of MDA5-mediated type I IFN production and may also impact RIG-I-mediated type I IFN production by enhancing RIG-I activity. This places TRIM13 at a key junction within the viral response pathway and identifies it as one of the few known modulators of MDA5 activity.