bluuebunny/crossref_metadata_2025 huggingface dataset:
A calibration rig for multi-component internal strain gauge balance using the new design-of-experiment (DOE) approach
Authors: Nouri N. M. , Mostafapour K. , Kamran M.
Published: February 2018

In a closed water-tunnel circuit, the multi-component strain gauge force and moment sensor (also known as balance) are generally used to measure hydrodynamic forces and moments acting on scaled models. These balances are periodically calibrated by static loading. Their performance and accuracy depend significantly on the rig and the method of calibration. In this research, a new calibration rig was designed and constructed to calibrate multi-component internal strain gauge balances. The calibration rig has six degrees of freedom and six different component-loading structures that can be applied separately and synchronously. The system was designed based on the applicability of formal experimental design techniques, using gravity for balance loading and balance positioning and alignment relative to gravity. To evaluate the calibration rig, a six-component internal balance developed by Iran University of Science and Technology was calibrated using response surface methodology. According to the results, calibration rig met all design criteria. This rig provides the means by which various methods of formal experimental design techniques can be implemented. The simplicity of the rig saves time and money in the design of experiments and in balance calibration while simultaneously increasing the accuracy of these activities.
Flow dynamics in a variable-spacing, three bluff-body flowfield
Authors: Meehan M. , Tyagi A. , O’Connor J.
Published: February 2018

This work explores the wake dynamics of systems with three bluff bodies with variable spacing. Studies of single-wake systems have shown that coherent wake vortices have a regular and predictable periodicity. A growing literature of dual-wake studies has shown that multi-wake systems are more stochastic than single-wake systems, and their dynamics are highly dependent on the spacing between the wakes. Here, we expand on this literature by investigating three-wake systems and find that the coherent dynamics of the wakes are highly intermittent. We use proper orthogonal decomposition to extract the most energetic modes of the three-wake system at six bluff-body spacings that span a range of dynamical “regimes.” After describing the time-dependent behavior of the interacting wakes in these regimes, we use a statistical approach to describe the relative phase between oscillations in each of the wakes, identifying regimes where oscillations are more or less random. Interestingly, the wake oscillations are less random when the bluff bodies are positioned very close and relatively far from each other. In between these two extremes, an intermediary regime is identified where the wake oscillations are almost completely random; this finding parallels data from the dual-wake literature. Finally, we discuss the implications of the observed behaviors and possible future directions for this work.
Determining the spring constant of arbitrarily shaped cantilevers in viscous environments
Authors: Payam A. F. , Trewby W. , Voïtchovsky K.
Published: February 2018

Accurate calibration of the flexural spring constant of microcantilevers is crucial for sensing devices, microactuators, and atomic force microscopy (AFM). Existing methods rely on precise knowledge of cantilever geometry, make significant simplifications, or require potentially damaging contact with the sample. Here, we develop a simple equation to calculate the flexural spring constants of arbitrarily shaped cantilevers in fluid. Our approach, verified here with AFM, only requires the measurement of two resonance frequencies of the cantilever in air and in a liquid, with no need for additional input or knowledge about the system. We validate the method with cantilevers of different shapes and compare its predictions with existing models. We also show how the method's accuracy can be considerably improved, especially in more viscous liquids, if the effective width of the cantilever is known. Significantly, the developed equations can be extended to calculate the spring constants of the cantilever's higher eigenmodes.
Excited-state dissociation dynamics of phenol studied by a new time-resolved technique
Authors: Lin Yen-Cheng , Lee Chin , Lee Shih-Huang , Lee Yin-Yu , Lee Yuan T. , Tseng Chien-Ming , Ni Chi-Kung
Published: February 2018

Phenol is an important model molecule for the theoretical and experimental investigation of dissociation in the multistate potential energy surfaces. Recent theoretical calculations [X. Xu et al., J. Am. Chem. Soc. 136, 16378 (2014)] suggest that the phenoxyl radical produced in both the X and A states from the O–H bond fission in phenol can contribute substantially to the slow component of photofragment translational energy distribution. However, current experimental techniques struggle to separate the contributions from different dissociation pathways. A new type of time-resolved pump-probe experiment is described that enables the selection of the products generated from a specific time window after molecules are excited by a pump laser pulse and can quantitatively characterize the translational energy distribution and branching ratio of each dissociation pathway. This method modifies conventional photofragment translational spectroscopy by reducing the acceptance angles of the detection region and changing the interaction region of the pump laser beam and the molecular beam along the molecular beam axis. The translational energy distributions and branching ratios of the phenoxyl radicals produced in the X, A, and B states from the photodissociation of phenol at 213 and 193 nm are reported. Unlike other techniques, this method has no interference from the undissociated hot molecules. It can ultimately become a standard pump-probe technique for the study of large molecule photodissociation in multistates.
Generation of multiple vortex beam by means of active diffraction gratings
Authors: Muelas-Hurtado Ruben D. , Ealo Joao L. , Pazos-Ospina Jhon F. , Volke-Sepúlveda Karen
Published: February 2018

Acoustic vortices have attracted a great deal of attention in recent years due to their numerous applications. We introduce a highly efficient method for the generation of acoustic Bessel vortices in air, using spiral-shaped active diffraction gratings, which can be operated within a broad spectral range of ultrasonic frequencies. Using a single-arm active spiral source, we achieve the simultaneous generation of vortices of different topological charges, well separated among each other along the propagation axis. With a theoretical analysis, numerical simulations, and experiments, we demonstrate some features about spiral diffraction gratings, such as the equivalence between specific diffraction orders of an m-armed spiral and a single-arm spiral, and the annihilation of prescribed diffraction orders by tuning the width to pitch ratio.
Formation and identification of borane radical anions isolated in solid argon
Authors: Lin Meng-Yeh , Huang Tzu-Ping , Chin Chih-Hao , Wu Yu-Jong
Published: February 2018

The infrared (IR) spectrum of borane(3) anions (BH3−) isolated in solid Ar was recorded; two vibrational modes were observed at 2259.4 and 606.6 cm−1, which were assigned to the BH2 stretching (ν3) and out-of-plane large-amplitude (ν2) modes, respectively. These anions were produced by the electron bombardment of an Ar matrix sample containing a small proportion of B2H6 and H2 during matrix deposition or by the photolysis of single-bridged-B2H5− in an Ar matrix with the selected ultraviolet light. The band positions, relative intensity ratios, isotopic splitting pattern, and isotopic shift ratios of the observed IR features of BH3− are generally in good agreement with those predicted by the B2PLYP/aug-cc-pVTZ method.
Experimental research on time-resolved evolution of cathode plasma expansion velocity in a long pulsed magnetically insulated coaxial diode
Authors: Zhu Danni , Zhang Jun , Zhong Huihuang , Ge Xingjun , Gao Jingming
Published: February 2018

Unlike planar diodes, separate research of the axial and radial plasma expansion velocities is difficult for magnetically insulated coaxial diodes. Time-resolved electrical diagnostic which is based on the voltage-ampere characteristics has been employed to study the temporal evolution of the axial and radial cathode plasma expansion velocities in a long pulsed magnetically insulated coaxial diode. Different from a planar diode with a “U” shaped profile of temporal velocity evolution, the temporal evolution trend of the axial expansion velocity is proved to be a “V” shaped profile. Apart from the suppression on the radial expansion velocity, the strong magnetic field is also conducive to slowing down the axial expansion velocity. Compared with the ordinary graphite cathode, the carbon velvet and graphite composite cathode showed superior characteristics as judged by the low plasma expansion velocity and long-term electrical stability as a promising result for applications where long-pulsed and reliable operation at high power is required.
Peculiar behavior of magnetoresistance in HgSe single crystal with low electron concentration
Authors: Lonchakov A. T. , Bobin S. B. , Deryushkin V. V. , Okulov V. I. , Govorkova T. E. , Neverov V. N.
Published: February 2018

Magnetoresistive properties of the single crystal of HgSe with a low electron concentration were studied in a wide range of temperatures and magnetic fields. Some fundamental parameters of the spectrum and scattering of electrons were experimentally determined. Two important features of magnetic transport were found—strong transverse magnetoresistance (MR) and negative longitudinal MR, which can indicate the existence of the topological phase of the Weyl semimetal (WSM) in HgSe. Taking this hypothesis into account, we suggest a modified band diagram of mercury selenide at low electron energies. The obtained results are essential for the deeper understanding of both physics of gapless semiconductors and WSMs—promising materials for various applications in electronics, spintronics, computer, and laser technologies.
Using monomer vibrational wavefunctions to compute numerically exact (12D) rovibrational levels of water dimer
Authors: Wang Xiao-Gang , Carrington Tucker
Published: February 2018

We compute numerically exact rovibrational levels of water dimer, with 12 vibrational coordinates, on the accurate CCpol-8sf ab initio flexible monomer potential energy surface [C. Leforestier et al., J. Chem. Phys. 137, 014305 (2012)]. It does not have a sum-of-products or multimode form and therefore quadrature in some form must be used. To do the calculation, it is necessary to use an efficient basis set and to develop computational tools, for evaluating the matrix-vector products required to calculate the spectrum, that obviate the need to store the potential on a 12D quadrature grid. The basis functions we use are products of monomer vibrational wavefunctions and standard rigid-monomer basis functions (which involve products of three Wigner functions). Potential matrix-vector products are evaluated using the F matrix idea previously used to compute rovibrational levels of 5-atom and 6-atom molecules. When the coupling between inter- and intra-monomer coordinates is weak, this crude adiabatic type basis is efficient (only a few monomer vibrational wavefunctions are necessary), although the calculation of matrix elements is straightforward. It is much easier to use than an adiabatic basis. The product structure of the basis is compatible with the product structure of the kinetic energy operator and this facilitates computation of matrix-vector products. Compared with the results obtained using a [6 + 6]D adiabatic approach, we find good agreement for the inter-molecular levels and larger differences for the intra-molecular water bend levels.
Chaotic behaviors of one dimensional wave equations with van der Pol nonlinear boundary conditions
Authors: Chen Zhijing , Huang Tingwen , Huang Yu , Liu Xin
Published: February 2018

For one-dimensional linear wave equations with van der Pol boundary conditions, there have existed several different ways in the literature to characterize the complexity of their solutions. In this paper, we give a new way to characterize the dynamical behaviors of the systems, including almost equicontinuity and Devaney chaos. In order to do this, we consider a one-dimensional system (I, f) and its functional envelope (L1(I,I),Hf) and show that Hf is weakly mixing if and only if f is; Hf is Devaney chaotic if f is weakly mixing; Hf is almost equicontinuous if f has an attracting 2-period orbit. Those abstract results have their own significance and can be applied to the linear wave equations with van der Pol boundary conditions.
Decay of the compressible magneto-micropolar fluids
Authors: Zhang Peixin
Published: February 2018

This paper considers the large-time behavior of solutions to the Cauchy problem on the compressible magneto-micropolar fluid system under small perturbation in regular Sobolev space. Based on the time-weighted energy estimate, the asymptotic stability of the steady state with the strictly positive constant density, vanishing velocity, micro-rotational velocity, and magnetic field is established.
Linking root traits to superior phosphorus uptake and utilisation efficiency in three Fabales in the Core Cape Subregion, South Africa
Authors: MacAlister Dunja , Muasya A. Muthama , Chimphango Samson B. M.
Published: February 2018

In the low-P soil of the fynbos biome, plants have evolved several morphological and physiological P acquisition and use mechanisms, leading to variable uptake and use efficiencies. We expected that plants grown in low-P soils would exhibit greater P acquisition traits and hypothesised that Aspalathus linearis (Burm. f.) R. Dahlgren, a cluster-root-forming species adapted to drier and infertile soils, would be the most efficient at P acquisition compared with other species. Three fynbos Fabales species were studied: A. linearis and Podalyria calyptrata (Retz.) Willd, both legumes, and Polygala myrtifolia L., a nonlegume. A potted experiment was conducted where the species were grown in two soil types with high P (41.18 mg kg–1) and low P (9.79 mg kg–1). At harvest, biomass accumulation, foliar nutrients and P acquisition mechanisms were assessed. Polygala myrtifolia developed a root system with greater specific root length, root hair width and an average root diameter that exuded a greater amount of citrate and, contrary to the hypothesis, exhibited greater whole-plant P uptake efficiency. However, P. calyptrata had higher P use efficiency, influenced by N availability through N2 fixation. Specific root length, root length and root : shoot ratio were promising morphological traits for efficient foraging of P, whereas acid phosphatase exudation was the best physiological trait for solubilisation of P.
Forest connectivity is important for sustaining Admiralty cuscus (Spilocuscus kraemeri) in traditional terrestrial no-take areas on Manus Island, Papua New Guinea
Authors: Lamaris John , Whitmore Nathan
Published: February 2018

Tambu is a well respected concept in Melanesian societies and represents a periodic cultural restriction on harvesting for the purpose of fulfilling customary obligations and restocking resources. As a result it has been suggested as the basis for conservation and sustainability in Melanesia. One species subject to tambu management is the Admiralty cuscus (Spilocuscus kraemeri), an arboreal marsupial endemic to Manus Island, Papua New Guinea, where it is a major source of terrestrial protein for forest-dwelling villagers. We investigated the denning home range and movement patterns of 10 cuscus using radio-telemetry in and around a 21-ha forested tambu area over a 28-day period. Home-range sizes were estimated using a 95% minimum convex polygon method and possible contributing factors to home-range size were assessed through model selection. Home-range size was highly variable, log-normally distributed (back-transformed mean = 2.9 ha, mean ±1 s.d.: 0.6–13.8 ha, n = 8), and was not associated with body mass, age or sex. Additional telemetry data collected from three S. kraemeri over 74 days appeared to support the stable nature of the home ranges. Through application of Laplace’s extension of the Buffon’s needle problem we conclude that, despite potentially high growth rates and short juvenile dispersal distances, tambu areas are unlikely to be self-sustaining. We hypothesise that the apparent efficacy of tambu areas is a consequence of forest connectivity that allows the immigration of adult founders to offset losses in reproductive stock coming as a result of periodic harvest and juvenile dispersal.
Post-fire surface fuel dynamics in California forests across three burn severity classes
Authors: Eskelson Bianca N. I. , Monleon Vicente J.
Published: February 2018

Forest wildfires consume fuel and are followed by post-fire fuel accumulation. This study examines post-fire surface fuel dynamics over 9 years across a wide range of conditions characteristic of California fires in dry conifer and hardwood forests. We estimated post-fire surface fuel loadings (Mgha−1) from 191 repeatedly measured United States national inventory plots in dry conifer and hardwood stands of 49 California forest wildfires and identified differences across fire severity classes – low, moderate and high. No significant change in duff load was detected within the first 9 years post-fire across all forest types and fire severities. Litter, 1-h and 10-h fuels exhibited a quadratic trend over time in dry conifer stands, peaking ~6 years after fire, whereas hardwood stands displayed a constant rate of increase in those fuel types. For 100- and 1000-h fuels, the annual rate of change was constant for dry conifer and hardwood stands with differing rates of change across fire severity classes. This study was based on an extensive, spatially balanced sample across burned dry conifer and hardwood forests of California. Therefore, the estimated patterns of fuel accumulation are generally applicable to wildfires within this population.
Tim-3 co-stimulation promotes short-lived effector T cells, restricts memory precursors, and is dispensable for T cell exhaustion
Authors: Avery Lyndsay , Filderman Jessica , Szymczak-Workman Andrea L. , Kane Lawrence P.
Published: February 2018

Significance

During a chronic viral infection, prolonged exposure to viral antigens leads to dysfunction or “exhaustion” of T cells specific to the virus, a condition also observed in T cells that infiltrate tumors. The exhausted state is associated with poor T cell memory and expression of specific cell-surface proteins, some of which may inhibit T cell activation. Expression of Tim-3 is associated with acquisition of T cell exhaustion, although it is also expressed transiently during acute infection. We have found that a major function of Tim-3 is to enhance T cell activation during either acute or chronic viral infection, and that Tim-3 is not required for the development of T cell exhaustion.
Rocaglates as dual-targeting agents for experimental cerebral malaria
Authors: Langlais David , Cencic Regina , Moradin Neda , Kennedy James M. , Ayi Kodjo , Brown Lauren E. , Crandall Ian , Tarry Michael J. , Schmeing Martin , Kain Kevin C. , Porco John A. , Pelletier Jerry , Gros Philippe
Published: February 2018

Significance

Severe complications of malaria, such as anemia and cerebral malaria (CM) (neuroinflammation), are responsible for ∼25% of infant mortality in certain regions of Africa. Notwithstanding current effective antiplasmodial treatment, drug resistance is on the increase in the
Plasmodium
parasites, and therapy to treat CM is nonexistent. Here, we show that rocaglates derived from a natural product originally identified from plants of the
Aglaia
species, effectively block blood-stage parasite replication in several mouse models and in infected human RBCs. Importantly, neurological inflammation is mitigated and survival is promoted in experimental CM, highlighting the strong potential of this class of compounds to treat complicated malaria.
Massive crossover elevation via combination of
HEI10
and
recq4a recq4b
during
Arabidopsis
meiosis
Authors: Serra Heïdi , Lambing Christophe , Griffin Catherine H. , Topp Stephanie D. , Nageswaran Divyashree C. , Underwood Charles J. , Ziolkowski Piotr A. , Séguéla-Arnaud Mathilde , Fernandes Joiselle B. , Mercier Raphaël , Henderson Ian R.
Published: February 2018

Significance

The majority of eukaryotes reproduce sexually, creating genetic variation within populations. Sexual reproduction requires gamete production via meiotic cell division. During meiosis, homologous chromosomes pair and undergo exchange, called crossover. Crossover is vital for crop breeding and remains a major tool to combine useful traits. Despite the importance of crossovers for breeding, their levels are typically low, with one to two forming per chromosome, irrespective of physical chromosome size. Here we genetically engineer superrecombining
Arabidopsis
, via boosting the major procrossover pathway (using additional copies of the
HEI10
E3-ligase gene), and simultaneously removing a major antirecombination pathway (using mutations in
RECQ4A
and
RECQ4B
helicase genes). This strategy has the potential to drive massive crossover elevations in crop genomes and accelerate breeding.
Fundamental limits on dynamic inference from single-cell snapshots
Authors: Weinreb Caleb , Wolock Samuel , Tusi Betsabeh K. , Socolovsky Merav , Klein Allon M.
Published: February 2018

Significance

Seeing a snapshot of individuals at different stages of a dynamic process can reveal what the process would look like for a single individual over time. Biologists apply this principle to infer temporal sequences of gene expression states in cells from measurements made at a single moment in time. However, the sparsity and high dimensionality of single-cell data have made inference difficult using formal approaches. Here, we apply recent innovations in spectral graph theory to devise a simple and asymptotically exact algorithm for inferring the unique dynamic solution under defined approximations and apply it to data from bone marrow stem cells.
Algorithms in the historical emergence of word senses
Authors: Ramiro Christian , Srinivasan Mahesh , Malt Barbara C. , Xu Yang
Published: February 2018

Significance

How do words develop new senses? Unlike changes in sound or grammar where there are rich formal characterizations, semantic change is poorly understood. Changes in meaning are often considered intractable, with sparse attempts at formalizing and evaluating the principles against historical data at scale. We present a data-enriched formal approach that explores the time-varying lexicon. Motivated by prominent work in cognitive science and linguistics, we develop computational algorithms that predict the historical order in which the senses of a word have emerged, and we test these predictions against records of English over the past millennium. Our findings suggest that word senses emerge in ways that minimize cognitive costs, providing an efficient mechanism for expressing new ideas via a compact lexicon.
Axogenic mechanism enhances retinal ganglion cell excitability during early progression in glaucoma
Authors: Risner Michael L. , Pasini Silvia , Cooper Melissa L. , Lambert Wendi S. , Calkins David J.
Published: February 2018

Significance

Identifying new therapies for neurodegenerative disease requires understanding how neurons respond to stress and whether this response includes adaptation to slow progression. Because neurodegeneration affects both axons and dendrites, with their synaptic contacts, adaptation could involve both compartments. We investigated this question in experimental glaucoma, the world’s leading cause of irreversible vision loss. Glaucoma attacks retinal ganglion cell neurons and their axons, which comprise the optic nerve. We found that elevations in ocular pressure, a prominent risk factor for glaucoma, caused a paradoxical increase in ganglion cell excitability, including response to light, even in cells with substantial dendritic pruning. This adaptation arose from voltage-dependent mechanisms in the axon and may help maintain signaling to the brain to preserve vision.
A comprehensive model for the proliferation–quiescence decision in response to endogenous DNA damage in human cells
Authors: Heldt Frank S. , Barr Alexis R. , Cooper Sam , Bakal Chris , Novák Béla
Published: February 2018

Significance

Controlled transitions of human cells between proliferating and nonproliferating states are essential for normal development and tissue homeostasis. To understand how the decision to proliferate is made in response to positive input from growth factors and negative input from the DNA damage response, we have built a mathematical model of the underlying molecular network, based on data from live cell-imaging experiments. Our model suggests that two major cell-cycle transitions are crucial for decision making: the restriction point, which integrates pro- and antiproliferative signals, and the G1/S transition, which temporarily insulates cells from some aspects of the DNA damage response. Together, our model gives mechanistic insight into how cells maintain both sensitivity and robustness to external signals.
Crop intensification, land use, and on-farm energy-use efficiency during the worldwide spread of the green revolution
Authors: Pellegrini Pedro , Fernández Roberto J.
Published: February 2018

Significance

Global crop production tripled during the last 50 years, mainly by an increase in yield (production/area). We show that the energy embedded in the main oil-based inputs (machinery, fuel, and fertilizers) increased worldwide at a rate at first larger, but in the last decades slower, than crop production, resulting in a recent overall improved energy-use efficiency (EUE). This was explained by advances in the nitrogen fertilizer industry, irrigation, and other technologies and perhaps some environmental changes. Our results fit the “Jevons paradox”: Efficiency gains, both for EUE and land (yield), did not lead to resource savings. Just as increasing production does not guarantee alleviating hunger, technologies make land (and biodiversity) savings possible, but realizing them depends on bold political decisions.
Translational control in the tumor microenvironment promotes lung metastasis: Phosphorylation of eIF4E in neutrophils
Authors: Robichaud Nathaniel , Hsu Brian E. , Istomine Roman , Alvarez Fernando , Blagih Julianna , Ma Eric H. , Morales Sebastian V. , Dai David L. , Li Glenn , Souleimanova Margarita , Guo Qianyu , del Rincon Sonia V. , Miller Wilson H. , Ramón y Cajal Santiago , Park Morag , Jones Russell G. , Piccirillo Ciriaco A. , Siegel Peter M. , Sonenberg Nahum
Published: February 2018

Significance

Our findings document mRNA translation in cells of the tumor microenvironment (TME) as a crucial factor in metastatic progression. The results underscore the importance of understanding how translation-targeting therapies affect different cell types within the TME. We provide a rationale for targeting eIF4E phosphorylation in both cancer cells and cells that comprise the TME to halt metastasis and demonstrate the efficacy of this strategy using merestinib, a small molecule targeting the mitogen-activated protein kinase integrating kinases (MNKs). Our findings raise the possibility that a combination of MNK inhibitors with immunotherapy represents a therapeutic opportunity worthy of further investigation for treating cancer metastasis.
Robo and Ror function in a common receptor complex to regulate Wnt-mediated neurite outgrowth in
Caenorhabditis elegans
Authors: Wang Jiaming , Ding Mei
Published: February 2018

Significance

How a limited repertoire of secreted molecules pattern a large number of axon trajectories is an enduring mystery. Both Slit-Robo and Wnt-Ror pathways are involved in proper neurite extension, but whether and how these two signaling pathways are interacted is largely unknown. Here, we found that instead of mediating Slit signaling, Robo could bind and respond to Wnt ligand. By forming a complex with the Ror receptor and Dsh effector, the Robo receptor promotes signal transduction from Wnt to Dsh. The mechanistic link between the Robo receptor and Wnt-Ror-Dsh signaling revealed here will markedly advance our understanding of how guidance molecules interact in space and time to orchestrate the dynamic process of growth cone navigation through a complex cellular environment.
Membrane protein MHZ3 stabilizes OsEIN2 in rice by interacting with its Nramp-like domain
Authors: Ma Biao , Zhou Yang , Chen Hui , He Si-Jie , Huang Yi-Hua , Zhao He , Lu Xiang , Zhang Wan-Ke , Pang Jin-Huan , Chen Shou-Yi , Zhang Jin-Song
Published: February 2018

Significance

The ethylene signaling pathway has been extensively investigated in
Arabidopsis
, and EIN2 is the central component. Rice is a monocotyledonous model plant that exhibits different features in many aspects compared with the dicotyledonous
Arabidopsis
. Thus, rice provides an alternative system for identification of novel components of ethylene signaling. In this study, we identified a stabilizer of OsEIN2 through analysis of the rice ethylene-insensitive mutant
mhz3
. We found that MHZ3 stabilizes OsEIN2 likely by binding to its Nramp-like transmembrane domain and impeding protein ubiquitination, blocking proteasome-mediated protein degradation. This study reveals that MHZ3 is required for ethylene signaling and identifies how MHZ3 binds to OsEIN2 via the OsEIN2 N-terminal Nramp-like domain.
Synthetic addiction extends the productive life time of engineered
Escherichia coli
populations
Authors: Rugbjerg Peter , Sarup-Lytzen Kira , Nagy Mariann , Sommer Morten Otto Alexander
Published: February 2018

Significance

Bioproduction of chemicals offers a sustainable alternative to petrochemical synthesis routes by using genetically engineered microorganisms to convert waste and simple substrates into higher-value products. However, efficient high-yield production commonly introduces a metabolic burden that selects for subpopulations of nonproducing cells in large fermentations. To postpone such detrimental evolution, we have synthetically addicted production cells to production by carefully linking signals of product presence to expression of nonconditionally essential genes. We addict
Escherichia coli
cells to their engineered biosynthesis of mevalonic acid by fine-tuned control of essential genes using a product-responsive transcription factor. Over the course of a long-term fermentation equivalent to industrial 200-m
3
bioreactors such addicted cells remained productive, unlike the control, in which evolution fully terminated production.
Functional and physical interaction between yeast Hsp90 and Hsp70
Authors: Kravats Andrea N. , Hoskins Joel R. , Reidy Michael , Johnson Jill L. , Doyle Shannon M. , Genest Olivier , Masison Daniel C. , Wickner Sue
Published: February 2018

Significance

The Hsp90 molecular chaperone remodels and activates a large variety of client proteins. Its activity requires collaboration with the more than 25 Hsp90 cochaperone proteins, including the Hsp70 chaperone. In higher eukaryotes, Hsp90 collaborates with Hsp70 through a bridging protein, the Hop cochaperone. We show that yeast Hsp90 (Hsp82) and Hsp70 (Ssa1) directly interact in vitro in the absence of yeast Hop (Sti1) and identify a region in the middle domain of yeast Hsp90 that is important for interaction with Hsp70. This region of Hsp90 is also important for interactions with several cochaperones and client proteins, suggesting that collaboration between Hsp70 and Hsp90 in protein remodeling may be modulated through competition between Hsp70 and Hsp90 cochaperones for the interaction surface.
MHC-mismatched mixed chimerism restores peripheral tolerance of noncross-reactive autoreactive T cells in NOD mice
Authors: Zhang Mingfeng , Racine Jeremy J. , Lin Qing , Liu Yuqing , Tang Shanshan , Qin Qi , Qi Tong , Riggs Arthur D. , Zeng Defu
Published: February 2018

Significance

Mixed chimerism has shown good potential to cure some autoimmune diseases and prevent tissue rejection. It is known that MHC-mismatched but not -matched mixed chimerism effectively tolerizes autoreactive T cells, even those noncross-reactive T cells that do not directly recognize donor-type antigen presenting cells [i.e., dendritic cells (DCs)]. How this is accomplished remains unknown. These studies have shown that tolerizing peripheral residual host-type noncross-reactive autoreactive T cells requires engraftment of donor-type DCs and involves a host-type DC-mediated increase in donor-type Treg cells, which associates with restoration of tolerogenic features of host-type plasmacytoid DCs and expansion of host-type Treg cells. This study suggests a previously unrecognized tolerance network among donor- and host-type DCs and Treg cells in MHC-mismatched mixed chimeras.
Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane
Authors: Salanenka Yuliya , Verstraeten Inge , Löfke Christian , Tabata Kaori , Naramoto Satoshi , Glanc Matouš , Friml Jiří
Published: February 2018

Significance

This study identifies and outlines a nontranscriptional branch of the canonical GA signaling pathway that redirects protein traffic from the vacuolar degradation route to the plasma membrane. As a result, the amount of receptors and transporters, such as PIN transporters for the plant hormone auxin, is functionally regulated at the cell surface. The identified branching occurs at the level of DELLA proteins that, besides transcriptional regulation, also target the microtubule (MT) network and protein trafficking. In this work, we provide multiple lines of evidence that DELLA proteins act via their interacting partners Prefoldins and that a downstream MT/CLASP1 module regulates the activity of the retromer complex that directs protein trafficking at the intersection of the vacuolar and recycling pathways.
Gi- and Gs-coupled GPCRs show different modes of G-protein binding
Authors: Van Eps Ned , Altenbach Christian , Caro Lydia N. , Latorraca Naomi R. , Hollingsworth Scott A. , Dror Ron O. , Ernst Oliver P. , Hubbell Wayne L.
Published: February 2018

Significance

Activation of G protein-coupled receptors (GPCRs) initiates conformational shifts that trigger interaction with a specific G-protein subtype from a structurally homologous set. A major unsolved problem is the mechanism by which this selectivity is achieved. Structures of GPCR–G protein complexes so far fail to reveal the origin of selectivity because they all involve one G-protein subtype (Gs). In this work, we report a structural model of the activated GPCR rhodopsin in complex with another G-protein subtype (Gi) derived from intermolecular distance mapping with DEER-EPR and refinement with modeling. Comparison of the model with structures of complexes involving Gsreveals distinct GPCR–G protein-binding modes, the differences of which suggest key features of the structural selectivity filter.
Structure of full-length human TRPM4
Authors: Duan Jingjing , Li Zongli , Li Jian , Santa-Cruz Ana , Sanchez-Martinez Silvia , Zhang Jin , Clapham David E.
Published: February 2018

Significance

Ion channels are proteins that mediate the flow of ions across cell membranes. Human genetic mutations of one type of ion channel, called hTRPM4, underlie a form of progressive familial heart block. Its distribution among many tissues, however, suggests that its functions are broad. We have solved the atomic structure of hTRPM4 to an overall resolution of 3.7 Å. The channel is composed of four identical subunits surrounding a central pore. We show the path of Na
+
ions through the channel and point out aspects of the channel’s internal machinery that may affect its function. The structure will enable more directed experiments to understand the physiological function of this channel.
Optically functional isoxanthopterin crystals in the mirrored eyes of decapod crustaceans
Authors: Palmer Benjamin A. , Hirsch Anna , Brumfeld Vlad , Aflalo Eliahu D. , Pinkas Iddo , Sagi Amir , Rosenne Shaked , Oron Dan , Leiserowitz Leslie , Kronik Leeor , Weiner Steve , Addadi Lia
Published: February 2018

Significance

Some aquatic animals use reflectors in their eyes either to form images or to increase photon capture. Guanine is the most widespread molecular component of these reflectors. Here, we show that crystals of isoxanthopterin, a pteridine analog of guanine, form both the image-forming “distal” mirror and the intensity-enhancing tapetum reflector in the compound eyes of some decapod crustaceans. The crystal structure of isoxanthopterin was determined, providing an explanation for why these crystals are so well suited for efficient reflection. Pteridines were previously known only as pigments, and our discovery raises the question of which other organic molecules may be used to form crystals with superior reflective properties either in organisms or in artificial optical devices.
Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120
Authors: Yolitz Jason , Schwing Catherine , Chang Julia , Van Ryk Donald , Nawaz Fatima , Wei Danlan , Cicala Claudia , Arthos James , Fauci Anthony S.
Published: February 2018

Significance

Significant heterogeneity exists in the structure and antigenicity of HIV-1 envelope protein (Env) gp120 due, in part, to various posttranslational modifications. Using glycan and antigenic analysis, we show that the signal peptide (SP) of HIV Env can impact the glycan profile of gp120, which in turn impacts antigenicity of the mature protein. Thus, although the SP is not present in the mature gp120 protein, it is likely subject to immune pressure. Moreover, to the extent that glycan content impacts transmission fitness, variation in the SP may influence transmission. These observations potentially help us better understand both the early events in HIV transmission as well as the mechanisms whereby HIV evades humoral immune responses, providing additional information for HIV vaccine design.
Structural basis and energy landscape for the Ca
2+
gating and calmodulation of the Kv7.2 K
+
channel
Authors: Bernardo-Seisdedos Ganeko , Nuñez Eider , Gomis-Perez Carolina , Malo Covadonga , Villarroel Álvaro , Millet Oscar
Published: February 2018

Significance

Ion channels are sophisticated proteins that exert control over a plethora of body functions. Specifically, the members of the Kv7 family are prominent components of the nervous systems, responsible for the ion fluxes that regulate the electrical signaling in neurons and cardiac myocytes. Albeit its relevance, there are still several questions, including the Ca
2+
/calmodulin (CaM)-mediated gating mechanism. We found that Ca
2+
binding to CaM triggers a segmental rotation that allosterically transmits the signal from the cytosol up to the transmembrane region. NMR-derived analysis of the dynamics demonstrates that it occurs through a conformational selection mechanism. Energetically, CaM association with the channel tunes the affinities of the CaM lobes (calmodulation) so that the channel can sense the specific changes in [Ca
2+
] resulting after an action potential.
Derivative culpability
Authors: Montminy Martin
Published: February 2018

I explore the question of when an agent isderivatively, rather thandirectly, culpable for an undesirable outcome. The undesirable outcome might be a harmful incompetent or unwitting act, or it might be a harmful event. By examining various cases, I develop a sophisticated account of indirect culpability that is neutral about controversies regarding normative ethical issues and the condition on direct culpability.
Effect of flow on solidification structure of pure aluminium under pulse magneto-oscillation
Authors: Cheng Shumin , Zhong Yuyi , Xu Zhishuai , Pei Ning , Zhai Qijie , Gong Yongyong
Published: February 2018

This paper reports on the processing of aluminium melt by pulse magneto-oscillation (PMO) technology. The melt is divided into five layers using a layered isolation device and, after grinding and corrosion, the refining effects of equiaxed crystals are observed to decrease from the centre outwards. The electromagnetic force and flow velocity of the melt were simulated using the ANSYS package, and found to decrease in the same manner as crystal size; i.e. from the centre outwards. It was also found that the melt, treated by PMO, possessed an optimum characteristic length at which the flow velocity reaches a maximum value, thus improving the refining effect of the solidification structure of the melt.
Single-molecule imaging reveals dynamic biphasic partition of RNA-binding proteins in stress granules
Authors: Niewidok Benedikt , Igaev Maxim , Pereira da Graca Abel , Strassner Andre , Lenzen Christine , Richter Christian P. , Piehler Jacob , Kurre Rainer , Brandt Roland
Published: February 2018

Stress granules (SGs) are cytosolic, nonmembranous RNA–protein complexes. In vitro experiments suggested that they are formed by liquid–liquid phase separation; however, their properties in mammalian cells remain unclear. We analyzed the distribution and dynamics of two paradigmatic RNA-binding proteins (RBPs), Ras GTPase-activating protein SH3-domain–binding protein (G3BP1) and insulin-like growth factor II mRNA-binding protein 1 (IMP1), with single-molecule resolution in living neuronal cells. Both RBPs exhibited different exchange kinetics between SGs. Within SGs, single-molecule localization microscopy revealed distributed hotspots of immobilized G3BP1 and IMP1 that reflect the presence of relatively immobile nanometer-sized nanocores. We demonstrate alternating binding in nanocores and anomalous diffusion in the liquid phase with similar characteristics for both RBPs. Reduction of low-complexity regions in G3BP1 resulted in less detectable mobile molecules in the liquid phase without change in binding in nanocores. The data provide direct support for liquid droplet behavior of SGs in living cells and reveal transient binding of RBPs in nanocores. Our study uncovers a surprising disconnect between SG partitioning and internal diffusion and interactions of RBPs.
Another way of seeing things
Authors: Sedwick Caitlin
Published: February 2018

JGP study explores a novel photoreception pathway in a marine mollusk.
Handgrip Strength and Blood Pressure in Children and Adolescents: Evidence From NHANES 2011 to 2014
Authors: Zhang Rui , Li Changwei , Liu Tingting , Zheng Liqiang , Li Shengxu
Published: February 2018

BACKGROUND

Previous studies have reported that handgrip strength, a measure of muscular fitness, is associated with cardiovascular risk factors. However, the association of handgrip strength with blood pressure (BP) in children has been inconsistent. We tested the association of handgrip strength with systolic and diastolic BP in children and adolescents from the National Health and Nutrition Examination Survey (NHANES) 2011–2014.

METHODS

The study included 3,929 participants aged 8–19 years who underwent a handgrip test. The sum of the maximum handgrip strength from both hands was used. General linear models were used to examine the associations between handgrip strength and the outcome variables.

RESULTS

After adjustment for age, race, sex, body mass index, and physical activities, handgrip strength was significantly and positively associated with systolic (P < 0.0001) and diastolic (P = 0.01) BP. There was an increasing trend in systolic BP as handgrip strength increased from the bottom quartile to the top quartile, with 2.1 mm Hg difference between the top and the bottom quartiles (P for trend <0.0001). Similar results were observed for diastolic BP.

CONCLUSIONS

Muscular fitness is positively associated with BP in children and adolescents. The implications and underlying mechanisms for these results need further examinations.
ViCTree: an automated framework for taxonomic classification from protein sequences
Authors: Modha Sejal , Thanki Anil S , Cotmore Susan F , Davison Andrew J , Hughes Joseph
Published: February 2018

Motivation

The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualization tool that enables the tree to be explored interactively in the context of pairwise distance data.

Results

To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus.

Availability and implementation

ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/.

Supplementary information

Supplementary data are available at Bioinformatics online.
EPIC-CoGe: managing and analyzing genomic data
Authors: Nelson Andrew D L , Haug-Baltzell Asher K , Davey Sean , Gregory Brian D , Lyons Eric
Published: February 2018

The EPIC-CoGe browser is a web-based genome visualization utility that integrates the GMOD JBrowse genome browser with the extensive CoGe genome database (currently containing over 30 000 genomes). In addition, the EPIC-CoGe browser boasts many additional features over basic JBrowse, including enhanced search capability and on-the-fly analyses for comparisons and analyses between all types of functional and diversity genomics data. There is no installation required and data (genome, annotation, functional genomic and diversity data) can be loaded by following a simple point and click wizard, or using a REST API, making the browser widely accessible and easy to use by researchers of all computational skill levels. In addition, EPIC-CoGe and data tracks are easily embedded in other websites and JBrowse instances.

Availability and implementation

EPIC-CoGe Browser is freely available for use online through CoGe (https://genomevolution.org). Source code (MIT open source) is available: https://github.com/LyonsLab/coge.

Supplementary information

Supplementary data are available at Bioinformatics online.