bluuebunny/crossref_metadata_2025 huggingface dataset:
A first-principles investigation of spintronics of nitrophosphorene doped with 3d transition metals
Authors: Shi Lawrence , Luo Xuan
Published: June 2019

There has been search for materials with spintronic properties as they have potential advantages in data transfer and storage over their conventional electronics counterparts. Notably, phosphorene is at the center of such material search with its widely tunable bandgap and high carrier mobility. Nitrophosphorene (PN), a newly discovered material in 2017, is known for its superior electronic properties as a semiconductor. However, little is known or has been studied in the existing literature about PN as a spintronic material. In this study, we present strong evidence that many PN impurities have excellent spintronic potential. Specifically, we used first-principles calculations to investigate the electronic and magnetic properties of 3d transition metal interstitially doped PN with dopants from Sc to Ni and an 11.1% dopant concentration. Sc, Cr, and Co doping result in a dilute magnetic semiconductor, with magnetizations ranging from 1.00 μB to 3.08 μB and total bandgaps ranging from 0.36 eV to 0.50 eV, indicating that they are practical materials for spintronics. V, Mn, and Fe doping result in a half-metal, and Ti and Ni doping result in a standard semiconductor with no magnetization. Overall, we find that spintronic properties can be induced in certain PN impurities.
Towards quantum phase slip based standard of electric current
Authors: Wang Zhiming M. , Lehtinen J. S. , Arutyunov K. Yu.
Published: June 2019

An accurate standard of electric current is a long-standing challenge of modern metrology. It has been predicted that a superconducting nanowire in the regime of quantum fluctuations can be considered as the dynamic equivalent of a chain of conventional Josephson junctions. In full analogy with the quantum standard of electric voltage based on the Josephson effect, the quantum phase slip phenomenon in ultrathin superconducting nanowires could be used for building the quantum standard of electric current. This work presents advances toward this ultimate goal.
On the role of the pre-ionization mechanism in the optical breakdown of molecular oxygen induced by CO2 laser: Numerical investigation
Authors: Gamal Yosr E. E.-D. , Nassef O. Aied , Salama A. S.
Published: June 2019

A numerical study is presented to investigate the threshold intensity dependence on the gas pressure in the breakdown of molecular oxygen induced by CO2 laser radiation with a wavelength of 10.591 μm and a pulse FWHM of 64 ns [Camacho et al., J. Phys. D: Appl. Phys. 41, 105201 (2008)]. This experiment allowed for a new method of providing an adequate density of the seed electrons required to ignite the breakdown mechanism. The investigations are based on a modification of a previously developed model [Gamal and Omar, Radiat. Phys. Chem. 62(5), 361–370 (2001)], which solves a differential equation and designates the time evolution of the electron energy distribution numerically and a set of rate equations that describe the change of the excited state population. The model considered inverse bremsstrahlung absorption as the main electron energy gain process leading to oxygen breakdown. As an interesting finding, in comparing the calculated and measured thresholds as a function of gas pressure, computations could precisely reveal the densities of the created seed electrons at each value of the tested pressures. The unsystematic variation of these densities with the gas pressure clarified the origin of the slight oscillations observed in the measured thresholds. Analyzing the electron energy distribution function and its parameters in three gas pressure regions could determine the correlation between the gas pressure and the electron gain and loss processes responsible for oxygen breakdown. This analysis explained the violation from the simple p−1 law observed experimentally in the relation between threshold intensity and gas pressure.
Dual approach for effective potentials that accurately model structure and energetics
Authors: Lebold Kathryn M. , Noid W. G.
Published: June 2019

Because they eliminate unnecessary degrees of freedom, coarse-grained (CG) models enable studies of phenomena that are intractable with more detailed models. For the same reason, the effective potentials that govern CG degrees of freedom incorporate entropic contributions from the eliminated degrees of freedom. Consequently, these effective potentials demonstrate limited transferability and provide a poor estimate of atomic energetics. Here, we propose a simple dual-potential approach that combines “structure-based” and “energy-based” variational principles to determine effective potentials that model free energies and potential energies, respectively, as a function of the CG configuration. We demonstrate this approach for 1-site CG models of water and methanol. We accurately sample configuration space by performing simulations with the structure-based potential. We accurately estimate average atomic energies by postprocessing the sampled configurations with the energy-based potential. Finally, the difference between the two potentials predicts a qualitatively accurate estimate for the temperature dependence of the structure-based potential.
High performance transistors and photodetectors based on self-catalyzed zinc-blende InP nanowires
Authors: Yan Xin , Li Bang , Lin Qimin , Liu Peng , Luo Yanbin , Lu Qichao , Zhang Xia , Ren Xiaomin
Published: June 2019

InP nanowires are an important material for nanoscale electronic and optical devices. However, the crystal phase mixing and stacking faults severely degrade the device's performance. Here, we demonstrate high performance field-effect transistors and photodetectors based on high-quality InP nanowires. The ⟨110⟩-oriented InP nanowires, which are formed by spontaneous kinking from the original ⟨111⟩ nanowire roots, exhibit a stacking-faults-free zinc blende crystal structure. Based on the high-quality nanowire, the field-effect transistor exhibits a high electron mobility of 1438 cm2 V−1 s−1, much higher than that with stacking faults. A high responsivity of 5495 A/W is obtained from the photodetector, among the highest values reported for InP nanowire photodetectors. Moreover, the response/recovery time of the device is only 0.6/2.2 ms, 2–3 orders of magnitude shorter than other InP nanowire photodetectors. The high crystal quality and excellent electrical and optical properties make the zinc blende ⟨110⟩ InP nanowire a promising candidate for high performance electronic and optoelectronic devices.
Nonlinear frequency conversion of vectorial optical fields with a Mach-Zehnder interferometer
Authors: Li Hui , Liu Haigang , Chen Xianfeng
Published: June 2019

Vectorial optical fields with inhomogeneous polarization states have attracted great interest for their unique properties in both quantum and classical physics. In this paper, we propose a method to realize such nonlinear frequency conversion of the vectorial optical fields, which is by using a Mach–Zehnder interferometer. The separated arms enable two nonlinear processes to simultaneously proceed in two vertical directions. In our experiment, nonlinear frequency conversion of fundamental frequency vectorial optical fields with topological charge l=3 is studied. To illustrate the flexibility of this method, Taiji and clover patterns with inhomogeneous polarization distribution are also generated at second harmonic wavelengths. This research proposes a more flexible method to realize nonlinear frequency conversion of the vectorial optical fields and may have potential applications in the generation of ultrafast vectorial optical fields.
Is water one liquid or two?
Authors: Soper A. K.
Published: June 2019

The idea that water is a mixture of two distinct states is analyzed in some detail. It is shown that the known compressibility of water is in fact sufficiently small that for a volume of water of size 1 nm3, the density fluctuations are of order 4% of the average density. This is much smaller than the ≈25% density fluctuations that would be required for significant regions of high and low density water to occur on this volume scale. It is also pointed out that the density fluctuations in water are, if anything, smaller than those that occur in other common liquids which do not have the anomalous properties of water. It is shown that if the distribution of density fluctuations is unimodal, the system is in the one-phase region, and if bimodal, it is in the two-phase region. None of the liquid or amorphous phases of water explored in this work give any sign of being in the two-phase region. Existing neutron and X-ray scattering data on water in the amorphous phases, and in the stable liquid phases as a function pressure and temperature, are subject to a new set of empirical potential structure refinement simulations. These simulations are interrogated for their configurational entropy, using a spherical harmonic reconstruction of the full orientational pair correlation function. It is shown that the excess pair entropy derived from this function, plus the known perfect gas contributions, give a reasonable account of the total entropy of water, within the likely errors. This estimated entropy follows the expected declining trend with decreasing temperature. Evidence that higher density water will have higher entropy than lower density water emerges, in accordance with what is expected from the negative thermal expansion coefficient of water at low temperatures. However, this entropy increase is not large and goes through a maximum before declining at yet higher densities and pressures, in a manner reminiscent of what has been previously observed in the diffusion coefficient as a function of pressure. There is no evidence that ambient water can be regarded as patches of high density, high entropy and low density, low entropy liquid, as some have claimed, since high density water has a similar entropy to low density water. There is some evidence that the distinction between these two states will become more pronounced as the temperature is lowered. Extensive discussion of the use of order parameters to describe water structure is given, and it is pointed out that these indices generally cannot be used to infer two-state behavior.
Three-dimensional flow dynamics and mixing in a gas-centered liquid-swirl coaxial injector at supercritical pressure
Authors: Wang Xingjian , Wang Yanxing , Yang Vigor
Published: June 2019

Three-dimensional flow dynamics and mixing in a gas-centered liquid-swirl coaxial injector at supercritical pressure is numerically studied using the large-eddy-simulation technique. In this class of injectors, typical of liquid-fueled propulsion engines, high-temperature gaseous oxygen (GOX) is axially delivered into the center tube and kerosene is tangentially injected through discrete orifices into the coaxial annulus. The operating conditions and geometry mimic those of the main injector elements used in staged-combustion propulsion engines. The present work details the full three-dimensional flow evolution over the entire injector configuration, including axial and circumferential dynamics that are essential for small-scale mixing between GOX and kerosene. Various key flow structures and instability mechanisms in the injector, including axial and azimuthal shear-layer instabilities, secondary instabilities (baroclinic torque and volume dilatation), centrifugal instability, flow recirculation, and acoustic motion, are identified. The significance of these instability mechanisms is explored in the context of streamwise and azimuthal vorticity transport. The GOX core is found to exhibit a hexagonal shape, mainly due to the interactions of vortex rings detached from the center post and coaxial annulus. For comparison, a cylindrical sector of the configuration is also simulated. The results of the present study will support the design and development of high-performance injectors for future propulsion applications.
Asymmetric magneto-transport in a Dirac semimetal heterostructure
Authors: Song Hua-Ding , Kong Ling-Jian , Wu Yan-Fei , Zhang Liang , Li Cai-Zhen , Liao Zhi-Min , Yu Da-Peng
Published: June 2019

A three-dimensional (3D) Dirac semimetal is known as a 3D analog of graphene; its Fermi-arc-like surface states are attractive for spintronic applications and can potentially modulate graphene via interface engineering. Here, we report the asymmetric magnetotransport in graphene/Cd3As2 heterostructure devices. The electron transfer occurring at the graphene/Cd3As2 interface results in a strong n-type doping of graphene. The interfacial coupling between graphene and Cd3As2 also enables us to selectively pin the chemical potential of graphene. The asymmetrical magnetotransport near the zero Landau level in graphene suggests that the interfacial coupling between Cd3As2 and graphene can be modulated by the magnetic field.
A microsphere molecule: The interaction of two charged microspheres in a magneto-gravitational trap
Authors: Slezak Bradley R. , D'Urso Brian
Published: June 2019

Optomechanical systems composed of levitated particles in vacuum provide excellent conditions to test the predictions of both classical and quantum physics. While similar in approach, differing experimental setups used to achieve levitation and trapping provide unique parameter regimes for study. In this work, we show that the highly anisotropic and deep potential well provided by a magnetogravitational trap allows the creation of a micrometer-scale “molecule” consisting of two like-charged microspheres in a harmonic potential. We demonstrate the detection and manipulation (excitation and cooling) of two distinct modes of the microsphere molecule motion along the weakest trap axis.
Dephasing and relaxational polarized sub-Ohmic baths acting on a two-level system
Authors: Palm T. , Nalbach P.
Published: June 2019

We study a quantum two-level system under the influence of two independent baths, i.e., a sub-Ohmic pure dephasing bath and an Ohmic or sub-Ohmic relaxational bath. We show that cooling such a system invariably polarizes one of the two baths. A polarized relaxational bath creates an effective asymmetry. This asymmetry can be suppressed by additional dephasing noise. This being less effective, the more dominant low frequencies are in the dephasing noise. A polarized dephasing bath generates a large shift in the coherent oscillation frequency of the two-level system. This frequency shift is little affected by additional relaxational noise nor by the frequency distribution of the dephasing noise itself. As our model reflects a typical situation for superconducting phase qubits, our findings can help optimize cooling protocols for future quantum electronic devices.
Dynamic structure factor of strongly coupled Yukawa plasmas with dissipation
Authors: Kählert Hanno
Published: June 2019

The dynamic structure factor (DSF) of the three-dimensional Yukawa one-component plasma is studied with molecular and Langevin dynamics simulations at moderate and strong coupling. The focus of the investigation is on the dependence of the DSF on the friction coefficient in different frequency and wavenumber regimes. At small to intermediate wavenumbers, frictional damping reduces the strength of the sound peak and leads to a red-shift of its frequency. In an intermediate range of friction coefficients, reducing the wavenumber leads to the vanishing of the sound peak at a finite frequency and the formation of a maximum at zero frequency. This is in contrast to simulations without friction, where the characteristic Rayleigh and Brillouin peaks are observed. The Rayleigh peak around zero frequency for systems without dissipation is generally weak. The simulations show that a small amount of friction can initially decrease its height even further before a strong single maximum is formed at strong damping. At large wavenumbers, the DSF of moderately coupled Yukawa plasmas with dissipation is well described by a single-particle model without interactions, provided frictional damping is taken into account.
Single-charge band-to-band tunneling via multiple-dopant clusters in nanoscale Si Esaki diodes
Authors: Prabhudesai Gaurang , Muruganathan Manoharan , Anh Le The , Mizuta Hiroshi , Hori Masahiro , Ono Yukinori , Tabe Michiharu , Moraru Daniel
Published: June 2019

The electrostatic potential of p+-n+ junctions, as in Esaki (tunnel) diodes, originates from the Coulomb potentials of ionized dopants in the depletion-layer, but it has been modeled so far based on uniform space-charge regions, ignoring the discrete and random dopant distribution. This model can explain well the band-to-band tunneling (BTBT) between the opposite bands of the quasineutral regions (conduction band in the n+-region and valence band in the p+-region). In this letter, we show that a BTBT transport model should contain the mechanism of tunneling via “inherent” localized bandgap-states, created by dopant-induced potential fluctuation, which becomes detectable as a parallel transport mechanism in nanoscale Esaki diodes. This is manifested by the observation of single-charge (SC) BTBT at 5.5 K in nanoscale Si Esaki diodes. Numerical analysis of nanoscale p+-n+ junctions with random dopant-atom distributions suggests that SC-BTBT is mediated by a potential dip created by a number of dopants “clustered” near each other, i.e., by a multiple-dopant cluster.
The purported square ice in bilayer graphene is a nanoscale, monolayer object
Authors: Pascal Tod A. , Schwartz Craig P. , Lawler Keith V. , Prendergast David
Published: June 2019

The phase diagram of water is complex, and interfacial effects can stabilize unusual structures at the nanoscale. Here, we employ bond order accelerated molecular dynamics simulations to show that upon encapsulation within bilayer graphene, water can spontaneously adopt a two-dimensional (monomolecular) layer of “square ice” at ambient conditions, instead of an encapsulated water droplet. Free energy calculations show that this motif is thermodynamically stable up to diameters of approximately 15 nm due to enhanced hydrogen bonding and favorable binding to the graphene sheets. Entropic losses due to solidification and reduced graphene–graphene binding enthalpy are opposing thermodynamic forces that conspire to limit the maximum size, but modification of any of these thermodynamic factors should change the range of stability. Simulated core-level spectroscopy reveals unambiguous orientation dependent signatures of square ice that should be discernable in experiments.
Infrared luminescence from N-polar InN quantum dots and thin films grown by metal organic chemical vapor deposition
Authors: Reilly Caroline E. , Lund Cory , Nakamura Shuji , Mishra Umesh K. , DenBaars Steven P. , Keller Stacia
Published: June 2019

N-polar InN quantum dots and thin layers grown by metal organic chemical vapor deposition were shown to exhibit tunable emission from around 1.00 μm to longer than 1.55 μm at room temperature. The emission wavelength was dependent on both the growth temperature and quantum dot size or InN layer thickness. No measurable change in InN quantum dot emission wavelength or intensity was observed after capping of the InN quantum dots with GaN, paving the way for incorporating N-polar InN quantum dots into buried regions of device structures.
Neutral gas in complex plasmas causes friction and affects the dynamics of dust particle systems
Authors: Jaycen Amelia
Published: June 2019

Particle simulations of a dust-infused plasma show how friction affects the motion of dust particles in the plasma and highlight regimes that are most affected by dissipation.
Indium nitride quantum dots could shine the light for next-generation fiber optics
Authors: Berkowitz Jacob
Published: June 2019

Researchers demonstrate the first wavelength-tunable photoluminescence from N-polar InN quantum dots from 1.00 µm to longer than 1.55 µm.
Cost effectiveness of fire management strategies in southern Australia
Authors: Penman T. D. , Cirulis B. A.
Published: June 2019

Fire-management agencies invest significant resources to reduce the impacts of future fires. There has been increasing public scrutiny over how agencies allocate fire-management budgets and, in response, agencies are looking to use quantitative risk-based approaches to make decisions about expenditure in a more transparent manner. Advances in fire-simulation software and computing capacity of fire-agency staff have meant that fire simulators have been increasingly used for quantitative fire-risk analysis. Here we analyse the cost trade-offs of future fire management in the Australian Capital Territory (ACT) and surrounding areas by combining fire simulation with Bayesian Decision Networks. We compare potential future-management approaches considering prescribed burning, suppression and fire exclusion. These data combined costs of treatment and impacts on assets to undertake a quantitative risk analysis. The proposed approach for fuel treatment in ACT and New South Wales (NSW) provided the greatest reduction in risk and the most cost-effective approach to managing fuels in this landscape. Past management decisions have reduced risk in the landscape and the legacy of these treatments will last for at least 3 years. However, an absence of burning will result in an increased risk from fire in this landscape.
Outflanking immunodominance to target subdominant broadly neutralizing epitopes
Authors: Angeletti Davide , Kosik Ivan , Santos Jefferson J. S. , Yewdell William T. , Boudreau Carolyn M. , Mallajosyula Vamsee V. A. , Mankowski Madeleine C. , Chambers Michael , Prabhakaran Madhu , Hickman Heather D. , McDermott Adrian B. , Alter Galit , Chaudhuri Jayanta , Yewdell Jonathan W.
Published: June 2019

Significance

The most promising target for a universal influenza A vaccine is the conserved hemagglutinin (HA) stem domain. However, in infected or immunized individuals, the response to HA stem is limited due to HA head immunodominance. To understand factors hampering the development of stem B cells, we have immunized mice with full-length HA and HA stem alone or in different combinations and shown that physical attachment of HA head to stem severely hinders stem responses. By increasing local antigen concentration of full-length HA, we were able to rescue stem-specific B cells and serum antibodies. Our results provide a template for improving vaccination by overcoming immunodominance.
Intracellular mechanisms of fungal space searching in microenvironments
Authors: Held Marie , Kašpar Ondřej , Edwards Clive , Nicolau Dan V.
Published: June 2019

Significance

Many filamentous fungi colonizing animal or plant tissue, waste matter, or soil must find optimal paths through the constraining geometries of their microenvironment. Imaging of live fungal growth in custom-built microfluidics structures revealed the intracellular mechanisms responsible for this remarkable efficiency. In meandering channels, the Spitzenkörper (an assembly of vesicles at the filament tip) acted like a natural gyroscope, conserving the directional memory of growth, while the fungal cytoskeleton organized along the shortest growth path. However, if an obstacle could not be negotiated, the directional memory was lost due to the disappearance of the Spitzenkörper gyroscope. This study can impact diverse environmental, industrial, and medical applications, from fungal pathogenicity in plants and animals to biology-inspired computation.
Role of cerebellar GABAergic dysfunctions in the origins of essential tremor
Authors: Zhang Xu , Santaniello Sabato
Published: June 2019

Significance

We investigated the mechanisms of tremor generation in essential tremor (ET). Using computational modeling we show that tremor-related activity can originate from the olivocerebellar loop in response to a dysfunction and compensatory up-regulation of GABA receptors in the dentate nucleus of cerebellum. The emerging tremor-related activity then projects to thalamus and reaches the corticothalamic motor loop. Consistent with clinical observations, the study shows that the tremor frequency decreases as the up-regulation becomes stronger and increases as high-frequency stimulation is delivered to the thalamus. Our results provide an explanation of how local synaptic abnormalities would lead to widespread tremor-related neural activity in ET and suggest that compensatory processes in degenerative diseases may underlie brain dysfunction.
Intrinsically reversible superglues via shape adaptation inspired by snail epiphragm
Authors: Cho Hyesung , Wu Gaoxiang , Christopher Jolly Jason , Fortoul Nicole , He Zhenping , Gao Yuchong , Jagota Anand , Yang Shu
Published: June 2019

Significance

Achieving both superstrong adhesion and reversibility is challenging, particularly for hydrogels. Here, we report a hydrogel-based, reversible, superglue-like adhesive by combining the benefits of both liquid and dry adhesives in a single material while overcoming their respective limitations. When hydrated, the softened gel conformally adapts to the target surface by low-energy deformation, which is then locked upon drying as the elastic modulus is raised from hundreds of kilopascals to a few gigapascals, analogous to the action of the epiphragm of snails. We show that reversible superstrong adhesion could be achieved from a nonstructured material when the criterion of shape adaption is met, with minimal residual strain energy stored in the system.
Gating modules of the AMPA receptor pore domain revealed by unnatural amino acid mutagenesis
Authors: Poulsen Mette H. , Poshtiban Anahita , Klippenstein Viktoria , Ghisi Valentina , Plested Andrew J. R.
Published: June 2019

Significance

Glutamate receptors are membrane proteins that incorporate an ion channel domain. Binding of the neurotransmitter glutamate opens the ion channel, a key event in neurotransmission, but also triggers other dynamic changes in protein structure. We have probed these changes in the membrane domain using light-sensitive unnatural amino acids at 30 sites. This approach allowed us to use ultraviolet light to progressively perturb receptor structure local to specified sites. We identify the collar domain and the selectivity filter, a structure that determines the permeant ion species, as exerting unexpectedly broad control over the gating and desensitization of the receptor. This work supports the idea of a dynamic selectivity filter, which in turn, may facilitate pharmacological intervention at this essential receptor.
Restoring universality to the pinch-off of a bubble
Authors: Pahlavan Amir A. , Stone Howard A. , McKinley Gareth H. , Juanes Ruben
Published: June 2019

Significance

We observe the formation of bubbles and drops on a daily basis, from dripping faucets to raindrops entraining bubbles on the surface of a lake. The ubiquity of the phenomenon masks the fascinating underlying nonlinear dynamics that is such an important aspect of modern physics. Here, we report on the surprising observation that confinement makes the pinch-off of a bubble a universal process, as opposed to the unconfined case, where pinch-off is sensitive to the details of the experimental setting. We explain how the motion of the contact line, where the liquid, gas, and solid phases meet, leads to self-similar dynamics that effectively erase the memory of the system. Our observations have implications for immiscible flow phenomena from microfluidics to geophysical flows, where confinement, together with fluid–solid physicochemical interactions, play a key role.
Reactive school closure weakens the network of social interactions and reduces the spread of influenza
Authors: Litvinova Maria , Liu Quan-Hui , Kulikov Evgeny S. , Ajelli Marco
Published: June 2019

School-closure policies are considered one of the most promising nonpharmaceutical interventions for mitigating seasonal and pandemic influenza. However, their effectiveness is still debated, primarily due to the lack of empirical evidence about the behavior of the population during the implementation of the policy. Over the course of the 2015 to 2016 influenza season in Russia, we performed a diary-based contact survey to estimate the patterns of social interactions before and during the implementation of reactive school-closure strategies. We develop an innovative hybrid survey-modeling framework to estimate the time-varying network of human social interactions. By integrating this network with an infection transmission model, we reduce the uncertainty surrounding the impact of school-closure policies in mitigating the spread of influenza. When the school-closure policy is in place, we measure a significant reduction in the number of contacts made by students (14.2 vs. 6.5 contacts per day) and workers (11.2 vs. 8.7 contacts per day). This reduction is not offset by the measured increase in the number of contacts between students and nonhousehold relatives. Model simulations suggest that gradual reactive school-closure policies based on monitoring student absenteeism rates are capable of mitigating influenza spread. We estimate that without the implemented reactive strategies the attack rate of the 2015 to 2016 influenza season would have been 33% larger. Our study sheds light on the social mixing patterns of the population during the implementation of reactive school closures and provides key instruments for future cost-effectiveness analyses of school-closure policies.
PFKFB3-mediated endothelial glycolysis promotes pulmonary hypertension
Authors: Cao Yapeng , Zhang Xiaoyu , Wang Lina , Yang Qiuhua , Ma Qian , Xu Jiean , Wang Jingjing , Kovacs Laszlo , Ayon Ramon J. , Liu Zhiping , Zhang Min , Zhou Yaqi , Zeng Xianqiu , Xu Yiming , Wang Yong , Fulton David J. , Weintraub Neal L. , Lucas Rudolf , Dong Zheng , Yuan Jason X.-J. , Sullivan Jennifer C. , Meadows Louise , Barman Scott A. , Wu Chaodong , Quan Junmin , Hong Mei , Su Yunchao , Huo Yuqing
Published: June 2019

Significance

Lung endothelial cells express high levels of glucose metabolic enzymes, such as PFKFB3, and consequently produce large amounts of glucose metabolites. These metabolites are able to stabilize the cell signaling molecule HIF2A, similar to that which occurs under hypoxic conditions. This stabilization of HIF2A by glucose metabolites in lung endothelial cells stimulates production of growth and inflammatory factors, thereby enhancing proliferation and inflammation of the pulmonary vessels and exacerbating pulmonary hypertension (PH). In this study, blockade of endothelial PFKFB3 inhibits PH development in rodent models, suggesting that targeting glucose metabolic enzymes is a promising strategy for the treatment of PH.
Compartmentalized biosynthesis of mycophenolic acid
Authors: Zhang Wei , Du Lei , Qu Zepeng , Zhang Xingwang , Li Fengwei , Li Zhong , Qi Feifei , Wang Xiao , Jiang Yuanyuan , Men Ping , Sun Jingran , Cao Shaona , Geng Ce , Qi Fengxia , Wan Xiaobo , Liu Changning , Li Shengying
Published: June 2019

Significance

Here, we elucidate the full biosynthetic pathway of the fungal natural product mycophenolic acid (MPA). Besides the intriguing enzymatic mechanisms, we reveal that the MPA biosynthetic enzymes are elegantly compartmentalized; the oxygenase MpaB′ is the long-sought enzyme responsible for initiating the oxidative cleavage of the farnesyl side chain; and the subcellular localization of the acyl-coenzyme A hydrolase MpaH′ in peroxisomes is required for the unique cooperation between biosynthetic and β-oxidation catabolism machineries. This work highlights the importance of a cell biology perspective for understanding the underexplored organelle-associated essential catalytic mechanisms in natural product biosynthesis of fungi and other higher organisms. The insights gained in our study will benefit future efforts for both industrial strain improvement and novel drug development.
I-branched carbohydrates as emerging effectors of malignant progression
Authors: Dimitroff Charles J.
Published: June 2019

Cell surface carbohydrates, termed “glycans,” are ubiquitous posttranslational effectors that can tune cancer progression. Often aberrantly displayed or found at atypical levels on cancer cells, glycans can impact essentially all progressive steps, from malignant transformation to metastases formation. Glycans are structural entities that can directly bind promalignant glycan-binding proteins and help elicit optimal receptor–ligand activity of growth factor receptors, integrins, integrin ligands, lectins, and other type-1 transmembrane proteins. Because glycans play an integral role in a cancer cell’s malignant activity and are frequently uniquely expressed, preclinical studies on the suitability of glycans as anticancer therapeutic targets and their promise as biomarkers of disease progression continue to intensify. While sialylation and fucosylation have predominated the focus of cancer-associated glycan modifications, the emergence of blood group I antigens (or I-branched glycans) as key cell surface moieties capable of modulating cancer virulence has reenergized investigations into the role of the glycome in malignant progression. I-branched glycans catalyzed principally by the I-branching enzyme GCNT2 are now indicated in several malignancies. In this Perspective, the putative role of GCNT2/I-branching in cancer progression is discussed, including exciting insights on how I-branches can potentially antagonize the cancer-promoting activity of β-galactose–binding galectins.
Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants
Authors: Chekan Jonathan R. , Ongpipattanakul Chayanid , Wright Terry R. , Zhang Bo , Bollinger J. Martin , Rajakovich Lauren J. , Krebs Carsten , Cicchillo Robert M. , Nair Satish K.
Published: June 2019

The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) is an active ingredient of thousands of commercial herbicides. Multiple species of bacteria degrade 2,4-D via a pathway initiated by the Fe(II) and α-ketoglutarate (Fe/αKG)-dependent aryloxyalkanoate dioxygenases (AADs). Recently, genes encoding 2 AADs have been deployed commercially in herbicide-tolerant crops. Some AADs can also inactivate chiral phenoxypropionate and aryloxyphenoxypropionate (AOPP) herbicides, albeit with varying substrate enantioselectivities. Certain AAD enzymes, such as AAD-1, have expanded utility in weed control systems by enabling the use of diverse modes of action with a single trait. Here, we report 1) the use of a genomic context-based approach to identify 59 additional members of the AAD class, 2) the biochemical characterization of AAD-2 from
Bradyrhizobium diazoefficiens
USDA 110 as a catalyst to degrade (
S
)-stereoisomers of chiral synthetic auxins and AOPP herbicides, 3) spectroscopic data that demonstrate the canonical ferryl complex in the AAD-1 reaction, and 4) crystal structures of representatives of the AAD class. Structures of AAD-1, an (
R
)-enantiomer substrate-specific enzyme, in complexes with a phenoxypropionate synthetic auxin or with AOPP herbicides and of AAD-2, which has the opposite (
S
)-enantiomeric substrate specificity, reveal the structural basis for stereoselectivity and provide insights into a common catalytic mechanism.
Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift
Authors: Rinker David C. , Specian Natalya K. , Zhao Shu , Gibbons John G.
Published: June 2019

Significance

Copy number variation describes the degree to which contiguous genomic regions differ in their number of copies among individuals. Copy number variable regions can drive ecological adaptation, particularly when they contain genes. Here, we compare differences in gene copy numbers among 17 polar bear and 9 brown bear individuals to evaluate the impact of copy number variation on polar bear evolution. Polar bears and brown bears are ideal species for such an analysis as they are closely related, yet ecologically distinct. Our analysis identified variation in copy number for genes linked to dietary and ecological requirements of the bear species. These results suggest that genic copy number variation has played an important role in polar bear adaptation to the Arctic.
Leptin’s hunger-suppressing effects are mediated by the hypothalamic–pituitary–adrenocortical axis in rodents
Authors: Perry Rachel J. , Resch Jon M. , Douglass Amelia M. , Madara Joseph C. , Rabin-Court Aviva , Kucukdereli Hakan , Wu Chen , Song Joongyu D. , Lowell Bradford B. , Shulman Gerald I.
Published: June 2019

Significance

Low levels of leptin, a hormone secreted by adipocytes that signals the body as to the availability of fuel stores, are known to increase food intake. Here, we demonstrate a mechanism by which low leptin stimulates food intake in rodents: Under conditions of hypoleptinemia, stress hormone (glucocorticoid) production is increased, and in turn stimulates AgRP neurons to promote appetite.
Synaptic crosstalk conferred by a zone of differentially regulated Ca
2+
signaling in the dendritic shaft adjoining a potentiated spine
Authors: Dittmer Philip J. , Dell’Acqua Mark L. , Sather William A.
Published: June 2019

Significance

At synaptic contacts between neurons, memory is supported by long-lasting potentiation of synaptic transmission and structural modification of the postsynaptic element, the dendritic spine. Such modification of function and structure occurs in response to strong synaptic stimulation. Here we show that this kind of stimulation also rapidly modifies Ca
2+
signaling in a narrow zone of dendrite centered at the dendrite’s junction with its stimulated spine. This zone is ±10–20 µm in extent along the dendrite, and we show that its length can be increased by activation of neuromodulatory β adrenergic receptors and protein kinase A signaling. β-adrenergic tuning of the length of this zone regulates the range along the dendrite over which crosstalk between stimulated spines can occur.
Shigellapromotes major alteration of gut epithelial physiology and tissue invasion by shutting off host intracellular transport
Authors: Ferrari Mariana L. , Malardé Valérie , Grassart Alexandre , Salavessa Laura , Nigro Giulia , Descorps-Declere Stéphane , Rohde John R. , Schnupf Pamela , Masson Vanessa , Arras Guillaume , Loew Damarys , Sansonetti Philippe J. , Sauvonnet Nathalie
Published: June 2019

Intracellular trafficking pathways in eukaryotic cells are essential to maintain organelle identity and structure, and to regulate cell communication with its environment.Shigella flexneriinvades and subverts the human colonic epithelium by the injection of virulence factors through a type 3 secretion system (T3SS). In this work, we report the multiple effects of twoS. flexnerieffectors, IpaJ and VirA, which target small GTPases of the Arf and Rab families, consequently inhibiting several intracellular trafficking pathways. IpaJ and VirA induce large-scale impairment of host protein secretion and block the recycling of surface receptors. Moreover, these two effectors decrease clathrin-dependent and -independent endocytosis. Therefore,S. flexneriinfection induces a global blockage of host cell intracellular transport, affecting the exchange between cells and their external environment. The combined action of these effectors disorganizes the epithelial cell polarity, disturbs epithelial barrier integrity, promotes multiple invasion events, and enhances the pathogen capacity to penetrate into the colonic tissue in vivo.
Pak2 kinase promotes cellular senescence and organismal aging
Authors: Lee Jong-Sun , Mo Yan , Gan Haiyun , Burgess Rebecca J. , Baker Darren J. , van Deursen Jan M. , Zhang Zhiguo
Published: June 2019

Cellular senescence defines an irreversible cell growth arrest state linked to loss of tissue function and aging in mammals. This transition from proliferation to senescence is typically characterized by increased expression of the cell-cycle inhibitor p16
INK4a
and formation of senescence-associated heterochromatin foci (SAHF). SAHF formation depends on HIRA-mediated nucleosome assembly of histone H3.3, which is regulated by the serine/threonine protein kinase Pak2. However, it is unknown if Pak2 contributes to cellular senescence. Here, we show that depletion of Pak2 delayed oncogene-induced senescence in IMR90 human fibroblasts and oxidative stress–induced senescence of mouse embryonic fibroblasts (MEFs), whereas overexpression of Pak2 accelerated senescence of IMR90 cells. Importantly, depletion of Pak2 in BubR1 progeroid mice attenuated the onset of aging-associated phenotypes and extended life span. Pak2 is required for expression of genes involved in cellular senescence and regulated the deposition of newly synthesized H3.3 onto chromatin in senescent cells. Together, our results demonstrate that Pak2 is an important regulator of cellular senescence and organismal aging, in part through the regulation of gene expression and H3.3 nucleosome assembly.
Borrelia burgdorferipeptidoglycan is a persistent antigen in patients with Lyme arthritis
Authors: Jutras Brandon L. , Lochhead Robert B. , Kloos Zachary A. , Biboy Jacob , Strle Klemen , Booth Carmen J. , Govers Sander K. , Gray Joe , Schumann Peter , Vollmer Waldemar , Bockenstedt Linda K. , Steere Allen C. , Jacobs-Wagner Christine
Published: June 2019

Significance

Lyme disease, caused by the spirocheteBorrelia burgdorferi, is the most common vector-borne disease in North America. If early infection is untreated, it can result in late-stage manifestations, including arthritis. Although antibiotics are generally effective at all stages of the disease, arthritis may persist in some patients for months to several years despite oral and intravenous antibiotic treatment. Excessive, dysregulated host immune responses are thought to play an important role in this outcome, but the underlying mechanisms are not completely understood. This study identifies theB. burgdorferipeptidoglycan, a major component of the cell wall, as an immunogen likely to contribute to inflammation during infection and in cases of postinfectious Lyme arthritis.
Pattern of dopamine signaling during aversive events predicts active avoidance learning
Authors: Stelly Claire E. , Haug Graham C. , Fonzi Kaitlyn M. , Garcia Miriam A. , Tritley Sean C. , Magnon Alexa P. , Ramos Maria Alicia P. , Wanat Matthew J.
Published: June 2019

Significance

Exposure to aversive stimuli can elicit a range of responses across a population, with some readily learning to avoid the aversive outcome whereas others do not. The neurotransmitter dopamine is thought to regulate behavioral responses to aversive stimuli. However, it is unclear whether intrinsic differences in dopamine signaling can account for the diversity of actions exhibited in response to an aversive event. We performed voltammetry recordings of dopamine transmission in the ventral striatum of rodents exposed to inescapable and escapable aversive stimuli. These experiments 1) identified the characteristics of the dopamine response during an aversive event that are predictive of learning to avoid aversive outcomes and 2) demonstrated that dopamine encodes a safety prediction error signal.
The constrained architecture of mammalian
Hox
gene clusters
Authors: Darbellay Fabrice , Bochaton Célia , Lopez-Delisle Lucille , Mascrez Bénédicte , Tschopp Patrick , Delpretti Saskia , Zakany Jozsef , Duboule Denis
Published: June 2019

In many animal species with a bilateral symmetry,
Hox
genes are clustered either at one or at several genomic loci. This organization has a functional relevance, as the transcriptional control applied to each gene depends upon its relative position within the gene cluster. It was previously noted that vertebrate
Hox
clusters display a much higher level of genomic organization than their invertebrate counterparts. The former are always more compact than the latter, they are generally devoid of repeats and of interspersed genes, and all genes are transcribed by the same DNA strand, suggesting that particular factors constrained these clusters toward a tighter structure during the evolution of the vertebrate lineage. Here, we investigate the importance of uniform transcriptional orientation by engineering several alleles within the
HoxD
cluster, such as to invert one or several transcription units, with or without a neighboring CTCF site. We observe that the association between the tight structure of mammalian
Hox
clusters and their regulation makes inversions likely detrimental to the proper implementation of this complex genetic system. We propose that the consolidation of
Hox
clusters in vertebrates, including transcriptional polarity, evolved in conjunction with the emergence of global gene regulation via the flanking regulatory landscapes, to optimize a coordinated response of selected subsets of target genes in
cis
.
Solar thermal desalination as a nonlinear optical process
Authors: Dongare Pratiksha D. , Alabastri Alessandro , Neumann Oara , Nordlander Peter , Halas Naomi J.
Published: June 2019

Significance

One critical challenge of solar thermal distillation is the need to collect and focus sunlight, since purified water output increases with increasing solar intensity. Here we show substantial increases in the efficiency of solar thermal distillation by redistributing direct sunlight intensity with small focusing elements rather than by increasing overall intensity with large solar concentrators. This is because solar thermal distillation depends upon the saturation vapor pressure of water, which has an exponential temperature dependence, making purified water output exponentially dependent upon light intensity. This observation should redirect design efforts to focus on exploiting this nonlinearity, rather than increasing solar collector size, for higher-performance solar water purification systems within a small footprint, suitable for portability and use in remote locations.
The network organization of rat intrathalamic macroconnections and a comparison with other forebrain divisions
Authors: Swanson Larry W. , Sporns Olaf , Hahn Joel D.
Published: June 2019

The thalamus is 1 of 4 major divisions of the forebrain and is usually subdivided into epithalamus, dorsal thalamus, and ventral thalamus. The 39 gray matter regions comprising the large dorsal thalamus project topographically to the cerebral cortex, whereas the much smaller epithalamus (2 regions) and ventral thalamus (5 regions) characteristically project subcortically. Before analyzing extrinsic inputs and outputs of the thalamus, here, the intrinsic connections among all 46 gray matter regions of the rat thalamus on each side of the brain were expertly collated and subjected to network analysis. Experimental axonal pathway-tracing evidence was found in the neuroanatomical literature for the presence or absence of 99% of 2,070 possible ipsilateral connections and 97% of 2,116 possible contralateral connections; the connection density of ipsilateral connections was 17%, and that of contralateral connections 5%. One hub, the reticular thalamic nucleus (of the ventral thalamus), was found in this network, whereas no high-degree rich club or clear small-world features were detected. The reticular thalamic nucleus was found to be primarily responsible for conferring the property of complete connectedness to the intrathalamic network in the sense that there is, at least, one path of finite length between any 2 regions or nodes in the network. Direct comparison with previous investigations using the same methodology shows that each division of the forebrain (cerebral cortex, cerebral nuclei, thalamus, hypothalamus) has distinct intrinsic network topological organization. A future goal is to analyze the network organization of connections within and among these 4 divisions of the forebrain.