bluuebunny/crossref_metadata_2025 huggingface dataset:
Tree-ansatz percolation of hard spheres
Authors: Grimaldi Claudio
Published: August 2017

Suspensions of hard core spherical particles of diameter D with inter-core connectivity range δ can be described in terms of random geometric graphs, where nodes represent the sphere centers and edges are assigned to any two particles separated by a distance smaller than δ. By exploiting the property that closed loops of connected spheres become increasingly rare as the connectivity range diminishes, we study continuum percolation of hard spheres by treating the network of connected particles as having a tree-like structure for small δ/D. We derive an analytic expression of the percolation threshold which becomes increasingly accurate as δ/D diminishes and whose validity can be extended to a broader range of connectivity distances by a simple rescaling.
Infinite S-expansion with ideal subtraction and some applications
Authors: Peñafiel D. M. , Ravera L.
Published: August 2017

According to the literature, the S-expansion procedure involving a finite semigroup is valid no matter what the structure of the original Lie (super)algebra is; however, when something about the structure of the starting (super)algebra is known and when certain particular conditions are met, the S-expansion method (with its features of resonance and reduction) is able not only to lead to several kinds of expanded (super)algebras but also to reproduce the effects of the standard as well as the generalized Inönü-Wigner contraction. In the present paper, we propose a new prescription for S-expansion, involving an infinite abelian semigroup S(∞) and the subtraction of an infinite ideal subalgebra. We show that the subtraction of the infinite ideal subalgebra corresponds to a reduction. Our approach is a generalization of the finite S-expansion procedure presented in the literature, and it offers an alternative view of the generalized Inönü-Wigner contraction. We then show how to write the invariant tensors of the target (super)algebras in terms of those of the starting ones in the infinite S-expansion context presented in this work. We also give some interesting examples of application on algebras and superalgebras.
Intense fluorescence of Au20
Authors: Yu Chongqi , Harbich Wolfgang , Sementa Luca , Ghiringhelli Luca , Aprá Edoardo , Stener Mauro , Fortunelli Alessandro , Brune Harald
Published: August 2017

Ligand-protected Au clusters are non-bleaching fluorescence markers in bio- and medical applications. Here we show that their fluorescence can be an intrinsic property of the Au cluster itself. We find a very intense and sharp fluorescence peak located at λ=739.2 nm (1.68 eV) for Au20 clusters in a Ne matrix held at 6 K. The fluorescence reflects the Highest Occupied Molecular Orbital-Lowest Unoccupied Molecular Orbital (HOMO-LUMO) diabatic bandgap of the cluster. Au20 shows a very rich absorption fine structure reminiscent of well defined molecule-like quantum levels. These levels are resolved since Au20 has only one stable isomer (tetrahedral); therefore our sample is mono-disperse in cluster size and conformation. Density-functional theory (DFT) and time-dependent DFT calculations clarify the nature of optical absorption and predict both main absorption peaks and intrinsic fluorescence in fair agreement with experiment.
Terahertz spectroscopy of an electron-hole bilayer system in AlN/GaN/AlN quantum wells
Authors: Condori Quispe H. , Islam S. M. , Bader S. , Chanana A. , Lee K. , Chaudhuri R. , Nahata A. , Xing H. G. , Jena D. , Sensale-Rodriguez B.
Published: August 2017

We report studies on the nanoscale transport dynamics of carriers in strained AlN/GaN/AlN quantum wells: an electron-hole bilayer charge system with a large difference in transport properties between charge layers. From electronic band diagram analysis, the presence of spatially separated two-dimensional electron and hole charge layers is predicted at opposite interfaces. Since these charge layers exhibit distinct spectral signatures at terahertz frequencies, a combination of terahertz and far-infrared spectroscopy enables us to extract (a) individual contributions to the total conductivity and (b) effective scattering rates for charge-carriers in each layer. Furthermore, by comparing direct-current and THz-extracted conductivity levels, we are able to determine the extent to which structural defects affect charge transport. Our results evidence that (i) a non-unity Hall-factor and (ii) the considerable contribution of holes to the overall conductivity lead to a lower apparent mobility in Hall-effect measurements. Overall, our work demonstrates that terahertz spectroscopy is a suitable technique for studying bilayer charge systems with large differences in transport properties between layers such as quantum wells in III-nitride semiconductors.
Measurement of surface acoustic wave resonances in ferroelectric domains by microwave microscopy
Authors: Johnston Scott R. , Yang Yongliang , Cui Yong-Tao , Ma Eric Yue , Kämpfe Thomas , Eng Lukas M. , Zhou Jian , Chen Yan-Feng , Lu Minghui , Shen Zhi-Xun
Published: August 2017

Surface Acoustic Wave (SAW) resonances were imaged within a closed domain in the ferroelectric LiTaO3 via scanning Microwave Impedance Microscopy (MIM). The MIM probe is used for both SAW generation and measurement, allowing the contact-less measurement within a mesoscopic structure. Measurements taken over a range of microwave frequencies are consistent with a constant acoustic velocity, demonstrating the acoustic nature of the measurement.
Periodic modeling of zeolite Ti-LTA
Authors: Hernandez-Tamargo Carlos E. , Roldan Alberto , Ngoepe Phuti E. , de Leeuw Nora H.
Published: August 2017

We have proposed a combination of density functional theory calculations and interatomic potential-based simulations to study the structural, electronic, and mechanical properties of pure-silica zeolite Linde Type A (LTA), as well as two titanium-doped compositions. The energetics of the titanium distribution within the zeolite framework suggest that the inclusion of a second titanium atom with configurations Ti–(Si)0–Ti, Ti–(Si)1–Ti, and Ti–(Si)2–Ti is more energetically favorable than the mono-substitution. Infra-red spectra have been simulated for the pure-silica LTA, the single titanium substitution, and the configurations Ti–(Si)0–Ti and Ti–(Si)2–Ti, comparing against experimental benchmarks where available. The energetics of the direct dissociation of water on these Lewis acid sites indicate that this process is only favored when two titanium atoms form a two-membered ring (2MR) sharing two hydroxy groups, Ti–(OH)2–Ti, which suggests that the presence of water may tune the distribution of titanium atoms within the framework of zeolite LTA. The electronic analysis indicates charge transfer from H2O to the Lewis acid site and hybridization of their electronic states.
High-bandwidth and flexible tracking control for precision motion with application to a piezo nanopositioner
Authors: Feng Zhao , Ling Jie , Ming Min , Xiao Xiao-Hui
Published: August 2017

For precision motion, high-bandwidth and flexible tracking are the two important issues for significant performance improvement. Iterative learning control (ILC) is an effective feedforward control method only for systems that operate strictly repetitively. Although projection ILC can track varying references, the performance is still limited by the fixed-bandwidth Q-filter, especially for triangular waves tracking commonly used in a piezo nanopositioner. In this paper, a wavelet transform-based linear time-varying (LTV) Q-filter design for projection ILC is proposed to compensate high-frequency errors and improve the ability to tracking varying references simultaneously. The LVT Q-filter is designed based on the modulus maximum of wavelet detail coefficients calculated by wavelet transform to determine the high-frequency locations of each iteration with the advantages of avoiding cross-terms and segmenting manually. The proposed approach was verified on a piezo nanopositioner. Experimental results indicate that the proposed approach can locate the high-frequency regions accurately and achieve the best performance under varying references compared with traditional frequency-domain and projection ILC with a fixed-bandwidth Q-filter, which validates that through implementing the LTV filter on projection ILC, high-bandwidth and flexible tracking can be achieved simultaneously by the proposed approach.
Beyond Born-Oppenheimer theory for ab initio constructed diabatic potential energy surfaces of singlet H3+ to study reaction dynamics using coupled 3D time-dependent wave-packet approach
Authors: Ghosh Sandip , Mukherjee Saikat , Mukherjee Bijit , Mandal Souvik , Sharma Rahul , Chaudhury Pinaki , Adhikari Satrajit
Published: August 2017

The workability of beyond Born-Oppenheimer theory to construct diabatic potential energy surfaces (PESs) of a charge transfer atom-diatom collision process has been explored by performing scattering calculations to extract accurate integral cross sections (ICSs) and rate constants for comparison with most recent experimental quantities. We calculate non-adiabatic coupling terms among the lowest three singlet states of H3+ system (11A′, 21A′, and 31A′) using MRCI level of calculation and solve the adiabatic-diabatic transformation equation to formulate the diabatic Hamiltonian matrix of the same process [S. Mukherjee et al., J. Chem. Phys. 141, 204306 (2014)] for the entire region of nuclear configuration space. The nonadiabatic effects in the D+ + H2 reaction has been studied by implementing the coupled 3D time-dependent wave packet formalism in hyperspherical coordinates [S. Adhikari and A. J. C. Varandas, Comput. Phys. Commun. 184, 270 (2013)] with zero and non-zero total angular momentum (J) on such newly constructed accurate (ab initio) diabatic PESs of H3+. We have depicted the convergence profiles of reaction probabilities for the reactive non-charge transfer, non-reactive charge transfer, and reactive charge transfer processes for different collisional energies with respect to the helicity (K) and total angular momentum (J) quantum numbers. Finally, total and state-to-state ICSs are calculated as a function of collision energy for the initial rovibrational state (v = 0, j = 0) of the H2 molecule, and consequently, those quantities are compared with previous theoretical and experimental results.
Frequency graded 1D metamaterials: A study on the attenuation bands
Authors: Banerjee Arnab , Das Raj , Calius Emilio P.
Published: August 2017

Depending on the frequency, waves can either propagate (transmission band) or be attenuated (attenuation band) while travelling through a one-dimensional spring-mass chain with internal resonators. The literature on wave propagation through a 1D mass-in-mass chain is vast and continues to proliferate because of its versatile applicability in condensed matter physics, optics, chemistry, acoustics, and mechanics. However, in all these areas, a uniformly periodic arrangement of identical linear resonating units is normally used which limits the attenuation band to a narrow frequency range. To counter this limitation of linear uniformly periodic metamaterials, the attenuation bandwidth in a one-dimensional finite chain with frequency graded linear internal resonators are investigated in this paper. The result shows that a properly tuned frequency graded arrangement of resonating units can extend the upper part of the attenuation band of 1D metamaterial theoretically up to infinity and also increases the lower part of the attenuation bandwidth by around 40% of an equivalent uniformly periodic metamaterial without increasing the mass. Therefore, the frequency graded metamaterials can be a potential solution towards low frequency and wideband acoustic or vibration insulation. In addition, this paper provides analytical expressions for the attenuation and transmission frequency limits for a periodic mass-in-mass metamaterial and demonstrates the attenuation band is generated by the high absolute value of the effective mass not only due to the negative effective mass.
Magnetization reversal mechanism and coercivity enhancement in three-dimensional granular Nd-Fe-B magnets studied by micromagnetic simulations
Authors: Lee Jae-Hyeok , Choe Jinhyeok , Hwang Shinwon , Kim Sang-Koog
Published: August 2017

We studied the mechanism of magnetization reversals and coercivity enhancements in three-dimensional (3D) granular Nd-Fe-B permanent magnets using finite-element micromagnetic simulations. The magnetization reversals in the hard magnets consisting of hard-phase grains separated by relatively soft-phase grain boundaries were analyzed with reference to the simulation results for the magnetic field-dependent distributions of the local magnetizations. The saturation magnetization of the grain-boundary phase plays a crucial role in the transition between nucleation- and domain-wall-propagation-controlled reversal processes. The smaller the saturation magnetization of the grain-boundary phase is, the more preferable is the nucleation-controlled process, which results in a larger coercivity. The exchange stiffness of the grain-boundary phase determines the preferred paths of domain-wall propagations, whether inward into grains or along the grain boundaries for relatively small and large exchange stiffness, respectively. However, the exchange stiffness of the grain-boundary phase alone does not significantly contribute to coercivity enhancement in cases where the size of hard-phase grains is much greater than the exchange length. This work paves the way for the design of high-performance hard magnets of large coercivity and maximum-energy-product values.
Insights into fighting against blackleg disease of Brassica napus in Canada
Authors: Zhang Xuehua , Fernando W. G. Dilantha
Published: August 2017

Blackleg disease, caused by the ascomycete fungal pathogen Leptosphaeria maculans, is a devastating disease of canola (Brassica napus) in Australia, Canada and Europe. Although cultural strategies such as crop rotation, fungicide application, and tillage are adopted to control the disease, the most promising disease control strategy is the utilisation of resistant canola varieties. However, field populations of L. maculans display a high evolutionary potential and are able to overcome major resistance genes within a few years, making disease control relying on resistant varieties challenging. In the early 1990s, blackleg resistance gene Rlm3 was introduced into Canadian canola varieties and provided good resistance against the fungal populations until the early 2000s, when moderate to severe blackleg outbreaks were observed in some areas across western Canada. However, the breakdown of Rlm3 resistance was not reported until recently, based on studies on R genes present in Canadian canola varieties and the avirulence allele frequency in L. maculans populations in western Canada. The fact that Rlm3 was overcome by the evolution of fungal populations demands canola breeding programs in Canada to be prepared to develop canola varieties with diversified and efficient R genes. In addition, frequent monitoring of fungal populations can provide up-to-date guidance for proper resistance genes deployment. This literature review provides insights into the outbreaks and management of blackleg disease in Canada.
Preliminary observations of dingo responses to assumed aversive stimuli
Authors: Appleby Rob , Smith Bradley , Mackie Jess , Bernede Lilia , Jones Darryl
Published: August 2017

Occasionally, interactions between dingoes (Canis dingo) and people on Fraser Island result in serious injury, and, in one case, death. The risk to human safety from such interactions may be mitigated if people could carry a suitably defensive repellent, similar in principle to bear (Ursus spp.) repellent spray advocated in North America. In the first step towards searching for suitable stimuli that might be used as repellents with dingoes, we observed the responses of nine dingoes to three stimuli during interactions with a researcher on Fraser Island. Two treatment stimuli were assumed to be potentially aversive (an air horn blast and a water jet from a motorised water pistol), and one was considered unlikely to be aversive and therefore suitable as a control (a whistle being blown). Responses to the stimuli varied. All nine dingoes were initially presented with the whistle; however, only one adult male responded as if the whistle was aversive. Seven of the nine dingoes were later presented with a whistle and treatment stimuli together. None of the seven dingoes were repelled during any air horn treatment trials; however, six of seven dingoes (all juveniles) were repelled by the water pistol stimulus. Although a water pistol was effective at repelling young dingoes on many occasions, responses between individuals were inconsistent. Results from this pilot study suggest that a water pistol stimulus may offer some protection as a repellent to close approaches by young dingoes, particularly if enhanced with a mild irritant.
Mathematical model reveals role of nucleotide signaling in airway surface liquid homeostasis and its dysregulation in cystic fibrosis
Authors: Sandefur Conner I. , Boucher Richard C. , Elston Timothy C.
Published: August 2017

Significance

The intrapulmonary airways conduct air to the alveoli and are defended from inhaled pathogens by a highly regulated protective system of mucus, cilia, and liquid. In healthy lungs, a well-hydrated mucus layer is cleared by cilia from airway surfaces. In cystic fibrosis (CF), airway surfaces are dehydrated, leading to a failure of cilia-mediated mucus clearance and accumulation of pathogen-infected mucus. In this study, we created a mathematical model of airway surface liquid regulation in normal and CF cells and used the model to investigate a potential therapy to rehydrate CF airways and restore proper mucus clearance.
Feedback amplification loop drives malignant growth in epithelial tissues
Authors: Muzzopappa Mariana , Murcia Lada , Milán Marco
Published: August 2017

Significance

Progression of epithelial tumors and successful colonization of target tissues rely in many cases on the presence of the tumor microenvironment (TME), which acts as a niche to provide secreted signaling molecules and growth factors to tumor cells. Here we used
Drosophila
to show that the TME is not an absolute requirement for the growth of epithelial tumors caused by chromosomal instability (CIN) or compromised cell polarity. Instead, tumor growth is driven by a feedback amplification loop between two well-defined—but not necessarily genetically different—tumor cell populations. As CIN or impaired cell polarity are frequently observed in human tumors of epithelial origin, our results will provide insight to the mechanistic understanding of their unlimited growth potential.
BDNF-TrkB controls cocaine-induced dendritic spines in rodent nucleus accumbens dissociated from increases in addictive behaviors
Authors: Anderson Ethan M. , Wissman Anne Marie , Chemplanikal Joyce , Buzin Nicole , Guzman Daniel , Larson Erin B. , Neve Rachael L. , Nestler Eric J. , Cowan Christopher W. , Self David W.
Published: August 2017

Significance

Chronic cocaine use leads to both increased motivation for the drug and long-lasting morphological changes in the form of increased dendritic spine density in medium spiny neurons of the nucleus accumbens. Here we show that the cocaine-induced morphological changes are mediated by local brain-derived neurotrophic factor (BDNF)-tyrosine kinase B (TrkB) signaling, similar to activity-dependent dendritic spine increases in other brain regions. However, the same BDNF-TrkB signaling pathway can reverse these spine increases after their formation, suggesting BDNF-TrkB mediates a form of “cataplasticity” that resets accumbens neurons to their preaddiction morphological state. Importantly, however, the changes in spine density are dissociated from BDNF-TrkB effects on motivation for cocaine, demonstrating that the increased dendritic spine density is likely not a causal factor in maintaining cocaine addiction.
Voltage-gated calcium flux mediates
Escherichia coli
mechanosensation
Authors: Bruni Giancarlo N. , Weekley R. Andrew , Dodd Benjamin J. T. , Kralj Joel M.
Published: August 2017

Significance

Bacteria cope with changing external environments and must therefore sense and respond to their local conditions. In addition to sensing numerous chemical cues, in this paper we show that
Escherichia coli
can sense the local mechanical environment through voltage-induced calcium flux. This mechanism is similar to sensory neurons in vertebrates, suggesting an ancient process of voltage-regulated mechanotransduction. Mechanical contact drives pathogenicity in several species of bacteria and we now propose a potential mechanism for this sensation.
Fission yeast myosin Myo2 is down-regulated in actin affinity by light chain phosphorylation
Authors: Pollard Luther W. , Bookwalter Carol S. , Tang Qing , Krementsova Elena B. , Trybus Kathleen M. , Lowey Susan
Published: August 2017

Significance

The separation of daughter cells during cell division, or cytokinesis, is a process that requires contractile rings which develop tension using actin and myosin. Current models of contractile ring dynamics are based on quantitative data from two decades of research using the tractable fission yeast system. However, it is unknown how fission yeast’s essential myosin, Myo2, is regulated in the contractile ring. Here, we find that Myo2 does not assemble into minifilaments, consistent with its role in ring precursor nodes. Unphosphorylated Myo2 exhibits robust enzymatic and motor activity whereas phosphorylation of Myo2’s regulatory light chain reduces its affinity for actin. This reduction likely weakens the tension in the contractile ring, potentially to delay cytokinesis until segregation of chromosomes is complete.
Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria
Authors: Choi Philip H. , Vu Thu Minh Ngoc , Pham Huong Thi , Woodward Joshua J. , Turner Mark S. , Tong Liang
Published: August 2017

Significance

Cyclic di-3′,5′-adenosine monophosphate (c-di-AMP) is a broadly conserved bacterial second messenger that has been implicated in a wide range of cellular processes. We report here structural, biochemical, and functional studies on the inhibition of
Lactococcus lactis
pyruvate carboxylase (LlPC) by c-di-AMP. The compound has a distinct binding mode in LlPC compared with that in
Listeria monocytogenes
PC. Mutations of residues in the binding site can abolish c-di-AMP inhibition. LlPC is required for efficient milk acidification through its essential role in aspartate biosynthesis. The aspartate pool in
L. lactis
is negatively regulated by c-di-AMP, and high aspartate levels can be restored by a c-di-AMP–insensitive LlPC. LlPC has high intrinsic catalytic activity and is insensitive to acetyl-CoA activation, in contrast to other PCs.
Two transmembrane dimers of the bovine papillomavirus E5 oncoprotein clamp the PDGF β receptor in an active dimeric conformation
Authors: Karabadzhak Alexander G. , Petti Lisa M. , Barrera Francisco N. , Edwards Anne P. B. , Moya-Rodríguez Andrés , Polikanov Yury S. , Freites J. Alfredo , Tobias Douglas J. , Engelman Donald M. , DiMaio Daniel
Published: August 2017

Significance

Highly specific protein–protein interactions between transmembrane domains play crucial roles in many biological processes, but are difficult to study because they occur within membranes. The E5 protein of bovine papillomavirus is a 44-residue transmembrane protein that transforms cells by binding the transmembrane domain of the PDGF receptor, resulting in receptor activation. By combining computational modeling, genetic analysis, and biochemical studies, we propose a quaternary structure of the complex between the E5 protein and the PDGF receptor, in which two dimers of the E5 protein clamp two molecules of the receptor transmembrane domain into an active dimeric conformation. These studies reveal the molecular mechanism of action of an unusual oncogene and provide a pathway to study biologically interesting transmembrane complexes.
Separate mesocortical and mesolimbic pathways encode effort and reward learning signals
Authors: Hauser Tobias U. , Eldar Eran , Dolan Raymond J.
Published: August 2017

Significance

Learning about multiple features of a choice option is crucial for optimal decision making. How such multiattribute learning is realized remains unclear. Using functional MRI, we show that the brain exploits separate mesolimbic and mesocortical networks to simultaneously learn about reward and effort attributes. We show a double dissociation, evident in the expression of effort learning signals in dorsomedial prefrontal and reward learning in ventral striatal areas, with this dissociation being spatially mirrored in dopaminergic midbrain. At the time of choice, these segregated signals are integrated in ventral striatum. These findings highlight how the brain parses parallel learning demands.
Oxytocin-enforced norm compliance reduces xenophobic outgroup rejection
Authors: Marsh Nina , Scheele Dirk , Feinstein Justin S. , Gerhardt Holger , Strang Sabrina , Maier Wolfgang , Hurlemann René
Published: August 2017

Significance

In the midst of rapid globalization, the peaceful coexistence of cultures requires a deeper understanding of the forces that compel prosocial behavior and thwart xenophobia. Yet, the conditions promoting such outgroup-directed altruism have not been determined. Here we report the results of a double-blind, placebo-controlled experiment showing that enhanced activity of the oxytocin system paired with charitable social cues can help counter the effects of xenophobia by fostering altruism toward refugees. These findings suggest that the combination of oxytocin and peer-derived altruistic norms reduces outgroup rejection even in the most selfish and xenophobic individuals, and thereby would be expected to increase the ease by which people adapt to rapidly changing social ecosystems.
Disaggregating sorghum yield reductions under warming scenarios exposes narrow genetic diversity in US breeding programs
Authors: Tack Jesse , Lingenfelser Jane , Jagadish S. V. Krishna
Published: August 2017

Significance

Sorghum’s ability to withstand harsh environmental conditions has placed it in the forefront of discussions regarding potential adaptation paths under climate change. While sorghum may indeed be a good candidate to substitute for other major row crops as warming materializes in areas where it has not traditionally been grown, an equally important consideration is whether its production can be sustained in the warmer areas where it has traditionally been grown. Our findings suggest limited potential for climate change adaption using currently available cultivars but do not preclude the overall role of genetic innovation and enhanced decision making in adapting to climate change. Successful adaptation could perhaps best be facilitated by expanding the scope of genetic stock within sorghum breeding programs.
Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on Vγ9Vδ2 T cell activation
Authors: Gu Siyi , Sachleben Joseph R. , Boughter Christopher T. , Nawrocka Wioletta I. , Borowska Marta T. , Tarrasch Jeffrey T. , Skiniotis Georgios , Roux Benoît , Adams Erin J.
Published: August 2017

Significance

Gamma delta T cells, a group of immune cells that exhibit features from both innate and adaptive immunity, possess significant potential in clinical applications such as treatment of microbial infections and cancer immunotherapy. To fully understand their biology and harness them in the clinic it is imperative to dissect the molecular mechanisms involved in their recognition of infected and tumor cells. In this paper we focus on Vγ9Vδ2 T cells, a major subset of human gamma delta T cells in blood and investigate the phosphoantigen-induced, MHC-independent molecular mechanisms governing their activation.
Signaling from the plasma-membrane localized plant immune receptor RPM1 requires self-association of the full-length protein
Authors: El Kasmi Farid , Chung Eui-Hwan , Anderson Ryan G. , Li Jinyue , Wan Li , Eitas Timothy K. , Gao Zhiyong , Dangl Jeffery L.
Published: August 2017

Significance

Pathogen recognition first occurs at the plasma membrane, where receptor-like kinases perceive pathogen-derived molecules and initiate immune responses. To abrogate this immune response, pathogens evolved effector proteins that act as virulence factors, often following delivery to the host cell. Plants evolved intracellular receptors, known as NOD-like receptors (NLRs), to detect effectors, thereby ensuring activation of effector-triggered immunity. However, despite their importance in immunity, the molecular mechanisms underlying effector recognition and subsequent immune activation by membrane-localized NLRs remain to be fully elucidated. Our analyses reveal the importance of and need for self-association and the coordinated interplay of specific domains and conserved residues for NLR activity. This could provide strategies for crop improvement, contributing to effective, environmentally friendly, and sustainable solutions for future agriculture.
Antitumor effect of
Batf2
through IL-12 p40 up-regulation in tumor-associated macrophages
Authors: Kanemaru Hisashi , Yamane Fumihiro , Fukushima Kiyoharu , Matsuki Takanori , Kawasaki Takahiro , Ebina Isao , Kuniyoshi Kanako , Tanaka Hiroki , Maruyama Kenta , Maeda Kazuhiko , Satoh Takashi , Akira Shizuo
Published: August 2017

Significance

The therapeutic activity of checkpoint blockers and toll-like receptor (TLR) agonists, which show some efficacy against malignancies, appears to at least partially result from the secretion of type-I IFNs. Thus, we hypothesized that type-I IFN-inducible transcription factors, such as
basic leucine zipper transcription factor ATF-like 2
(
Batf2
), might play a role in tumor immunity. Here, we investigated the role of
Batf2
, especially its positive transcriptional activities, and evaluated its antitumor effect. This study shows that
Batf2
has an antitumor effect through the up-regulation of IL-12 p40 in tumor-associated macrophages, which eventually induces the activation of CD8
+
T cells and their accumulation within the tumor.
Batf2
may be an important target in anticancer treatment with immune checkpoint blockers and TLR agonists.
De novo mutations in inhibitors of Wnt, BMP, and Ras/ERK signaling pathways in non-syndromic midline craniosynostosis
Authors: Timberlake Andrew T. , Furey Charuta G. , Choi Jungmin , Nelson-Williams Carol ,   Yale Center for Genome Analysis, Loring Erin , Galm Amy , Kahle Kristopher T. , Steinbacher Derek M. , Larysz Dawid , Persing John A. , Lifton Richard P. , Bilguvar Kaya , Mane Shrikant , Tikhonova Irina , Castaldi Christopher , Knight James
Published: August 2017

Significance

Craniosynostosis is a common congenital malformation resulting from premature fusion of the bones that comprise the cranial vault, requiring surgery in infancy to prevent adverse neurologic outcomes. Eighty-five percent of cases are non-syndromic and of unknown cause. By exome sequencing of families with non-syndromic midline craniosynostosis, we show that 5% of cases have de novo damaging mutations in negative regulators of the Wnt, bone morphogenetic protein (BMP), and Ras/ERK signaling pathways, developmental cascades that converge on common nuclear targets to promote bone formation. Another 5% have transmitted mutations in these pathways. Common variants nearBMP2show genetic interaction with these rare mutations. The results provide insight into pathophysiology and have immediate implications for the diagnosis and genetic counseling of families with craniosynostosis.
KCNE1 and KCNE3 modulate KCNQ1 channels by affecting different gating transitions
Authors: Barro-Soria Rene , Ramentol Rosamary , Liin Sara I. , Perez Marta E. , Kass Robert S. , Larsson H. Peter
Published: August 2017

Significance

Regulatory β-subunits associate with voltage-gated K
+
channels to modulate their biophysical properties and physiological roles. KCNE1 and KCNE3 β-subunits turn voltage-dependent KCNQ1 channels into delayed activating KCNQ1/KCNE1 channels and apparent voltage-independent KCNQ1/KCNE3 channels, respectively, which are important for cardiac action potentials and transport of water and salts across epithelial cells. Mutations in KCNQ1/KCNE1 and KCNQ1/KCNE3 channels are associated with diseases, such as cardiac arrhythmias, congenital deafness, secretory diarrhea, and tinnitus. Therefore, KCNQ1, KCNE1, and KCNE3 are potential drug targets. We here propose a model for how KCNE1 and KCNE3 differentially modulate KCNQ1 that will allow for a better understanding of how mutations in KCNQ1, KCNE1, and KCNE3 cause diseases and how to design drugs to treat these diseases.
The transcriptional program, functional heterogeneity, and clinical targeting of mast cells
Authors: Cildir Gökhan , Pant Harshita , Lopez Angel F. , Tergaonkar Vinay
Published: August 2017

Mast cells are unique tissue-resident immune cells that express an array of receptors that can be activated by several extracellular cues, including antigen–immunoglobulin E (IgE) complexes, bacteria, viruses, cytokines, hormones, peptides, and drugs. Mast cells constitute a small population in tissues, but their extraordinary ability to respond rapidly by releasing granule-stored and newly made mediators underpins their importance in health and disease. In this review, we document the biology of mast cells and introduce new concepts and opinions regarding their role in human diseases beyond IgE-mediated allergic responses and antiparasitic functions. We bring to light recent discoveries and developments in mast cell research, including regulation of mast cell functions, differentiation, survival, and novel mouse models. Finally, we highlight the current and future opportunities for therapeutic intervention of mast cell functions in inflammatory diseases.
Vertical distribution of snow crab (Chionoecetes opilio) pelagic stages in the Gulf of St. Lawrence (Canada) and effect of temperature on development and survival
Authors: Ouellet Patrick , Sainte-Marie Bernard
Published: August 2017

Knowledge of the vertical distribution, thermal habitat, and growth of the larvae of the cold stenothermic snow crab (Chionoecetes opilio) is incomplete and inconsistent. This study explored aspects of the vertical distribution and development rate of larvae from eastern Canada. In the Gulf of St. Lawrence (GSL), during 2002, the mean vertical positions of the snow crab zoeae I and II larvae were recorded within and above the permanent thermocline and in close association with the depth of strong density discontinuities in the stratified water column. No statistically significant differences were detected between nighttime and daytime vertical positions. The water temperatures at the centre of the larvae distributions were 2–3 °C in late May in the colder northern GSL and 7–8 °C in June in the warmer southern GSL. Data from the literature and from a rearing experiment in 2014 were used to develop functions linking development and survival to water temperature. Assuming the snow crab larvae remain in the upper mixed layer until final metamorphosis, development may last 2.2–4 months depending on hatch time and location. Development would be prolonged by several weeks if premolt megalopae move into and reside in the deeper, colder waters as appears to be the case. A relative survival index suggests that optimum temperature for development is around 10.8 °C, 9.5 °C, and 8.7 °C for snow crab zoea I, zoea II, and megalopa, respectively. These results should contribute to modelling efforts that aim to evaluate the extent of larval drift and location of potential settlement areas, as well as the potential impact of climate change on snow crab in the North Atlantic.
Minimally Clinically Important Change in the Activity Measure for Post-Acute Care (AM-PAC), a Generic Patient-Reported Outcome Tool, in People With Low Back Pain
Authors: Lee Natalie , Thompson Nicolas R. , Passek Sandra , Stilphen Mary , Katzan Irene L.
Published: August 2017

Background

The Activity Measure for Post-Acute Care (AM-PAC) is a generic metric of patient-reported functional status. The minimal clinically important difference (MCID) in the AM-PAC score has not been determined.

Objective

The study objective was to determine the MCID for AM-PAC in people with low back pain.

Design

This was a retrospective cohort study.

Methods

Anchor-based and distribution-based methods were used to estimate the MCID. The Modified Low Back Pain Disability Questionnaire was used as the anchor. Adults who had a primary ICD-9 code for low back pain in at least 1 outpatient physical therapist visit during an episode of care and who completed both the AM-PAC and the Modified Low Back Pain Disability Questionnaire in at least 2 visits during the care episode were included. The MCID was calculated for the AM-PAC basic mobility version as well its adapted version, which the Cleveland Clinic uses for patients 65 years old or older.

Results

A total of 1,271 participants were eligible for study. For the AM-PAC basic mobility version, anchor-based methods yielded MCID estimates of between 3.4 and 5.1, whereas distribution-based methods yielded estimates of 1.7 to 4.2. The minimal detectable change (MDC) for the AM-PAC basic mobility version was 3.3. For the adapted AM-PAC basic mobility version, the MCID was estimated to be between 2.9 and 4.0 via anchor-based methods and between 1.2 to 3.5 via distribution-based methods. The MDC for the adapted AM-PAC basic mobility version was 3.5.

Limitations

The estimated MCID was designed for people with low back pain only.

Conclusions

The MCID ranged from 3.3 to 5.1 for the AM-PAC basic mobility version and 3.5 to 4 for the adapted version, with the MDC as the lower limit. Changes in the AM-PAC for people with low back pain may be interpreted using the estimated MCID. Future studies are needed to determine the AM-PAC MCID for populations other than those with low back pain.
Photoprotection through ultrafast charge recombination in photochemical reaction centres under oxidizing conditions
Authors: Ma Fei , Swainsbury David J. K. , Jones Michael R. , van Grondelle Rienk
Published: August 2017

Engineering natural photosynthesis to address predicted shortfalls in food and energy supply requires a detailed understanding of its molecular basis and the intrinsic photoprotective mechanisms that operate under fluctuating environmental conditions. Long-lived triplet or singlet excited electronic states have the potential to cause photodamage, particularly in the presence of oxygen, and so a variety of mechanisms exist to prevent formation of such states or safely dissipate their energy. Here, we report a dramatic difference in spectral evolution in fully reduced and partially oxidized
Rhodobacter sphaeroides
reaction centres (RCs) following excitation of the monomeric bacteriochlorophyll (BChl) cofactors at 805 nm. Three types of preparation were studied, including RCs purified as protein/lipid nanodiscs using the copolymer styrene maleic acid. In fully reduced RCs such excitation produces membrane-spanning charge separation. In preparations of partially oxidized RCs the spectroscopic signature of this charge separation is replaced by that of an energy dissipation process, including in the majority sub-population of reduced RCs. This process, which appears to take place on both cofactor branches, involves formation of a BChl
+
/bacteriopheophytin
−
radical pair that dissipates energy via recombination to a vibrationally hot ground state. The possible physiological role of this dissipative process under mildly oxidizing conditions is considered.

This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
Overexpression of plastid terminal oxidase in
Synechocystis
sp. PCC 6803 alters cellular redox state
Authors: Feilke Kathleen , Ajlani Ghada , Krieger-Liszkay Anja
Published: August 2017

Cyanobacteria are the most ancient organisms performing oxygenic photosynthesis, and they are the ancestors of plant plastids. All plastids contain the plastid terminal oxidase (PTOX), while only certain cyanobacteria contain PTOX. Many putative functions have been discussed for PTOX in higher plants including a photoprotective role during abiotic stresses like high light, salinity and extreme temperatures. Since PTOX oxidizes PQH
2
and reduces oxygen to water, it is thought to protect against photo-oxidative damage by removing excess electrons from the plastoquinone (PQ) pool. To investigate the role of PTOX we overexpressed rice PTOX fused to the maltose-binding protein (MBP-OsPTOX) in
Synechocystis
sp. PCC 6803, a model cyanobacterium that does not encode PTOX. The fusion was highly expressed and OsPTOX was active, as shown by chlorophyll fluorescence and P
700
absorption measurements. The presence of PTOX led to a highly oxidized state of the NAD(P)H/NAD(P)
+
pool, as detected by NAD(P)H fluorescence. Moreover, in the PTOX overexpressor the electron transport capacity of PSI relative to PSII was higher, indicating an alteration of the photosystem I (PSI) to photosystem II (PSII) stoichiometry. We suggest that PTOX controls the expression of responsive genes of the photosynthetic apparatus in a different way from the PQ/PQH
2
ratio.

This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
Increased SBPase activity improves photosynthesis and grain yield in wheat grown in greenhouse conditions
Authors: Driever Steven M. , Simkin Andrew J. , Alotaibi Saqer , Fisk Stuart J. , Madgwick Pippa J. , Sparks Caroline A. , Jones Huw D. , Lawson Tracy , Parry Martin A. J. , Raines Christine A.
Published: August 2017

To meet the growing demand for food, substantial improvements in yields are needed. This is particularly the case for wheat, where global yield has stagnated in recent years. Increasing photosynthesis has been identified as a primary target to achieve yield improvements. To increase leaf photosynthesis in wheat, the level of the Calvin–Benson cycle enzyme sedoheptulose-1,7-biphosphatase (SBPase) has been increased through transformation and expression of aBrachypodium distachyonSBPase gene construct. Transgenic lines with increased SBPase protein levels and activity were grown under greenhouse conditions and showed enhanced leaf photosynthesis and increased total biomass and dry seed yield. This showed the potential of improving yield potential by increasing leaf photosynthesis in a crop species such as wheat. The results are discussed with regard to future strategies for further improvement of photosynthesis in wheat.

This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
Recruitment of pre-existing networks during the evolution of C
4
photosynthesis
Authors: Reyna-Llorens Ivan , Hibberd Julian M.
Published: August 2017

During C
4
photosynthesis, CO
2
is concentrated around the enzyme RuBisCO. The net effect is to reduce photorespiration while increasing water and nitrogen use efficiencies. Species that use C
4
photosynthesis have evolved independently from their C
3
ancestors on more than 60 occasions. Along with mimicry and the camera-like eye, the C
4
pathway therefore represents a remarkable example of the repeated evolution of a highly complex trait. In this review, we provide evidence that the polyphyletic evolution of C
4
photosynthesis is built upon pre-existing metabolic and genetic networks. For example, cells around veins of C
3
species show similarities to those of the C
4
bundle sheath in terms of C
4
acid decarboxylase activity and also the photosynthetic electron transport chain. Enzymes of C
4
photosynthesis function together in gluconeogenesis during early seedling growth of C
3
Arabidopsis thaliana
. Furthermore, multiple C
4
genes appear to be under control of both light and chloroplast signals in the ancestral C
3
state. We, therefore, hypothesize that relatively minor rewiring of pre-existing genetic and metabolic networks has facilitated the recurrent evolution of this trait. Understanding how these changes are likely to have occurred could inform attempts to install C
4
traits into C
3
crops.

This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
A bioarchitectonic approach to the modular engineering of metabolism
Authors: Kerfeld Cheryl A.
Published: August 2017

Dissociating the complexity of metabolic processes into modules is a shift in focus from the single gene/gene product to functional and evolutionary units spanning the scale of biological organization. When viewing the levels of biological organization through this conceptual lens, modules are found across the continuum: domains within proteins, co-regulated groups of functionally associated genes, operons, metabolic pathways and (sub)cellular compartments. Combining modules as components or subsystems of a larger system typically leads to increased complexity and the emergence of new functions. By virtue of their potential for ‘plug and play’ into new contexts, modules can be viewed as units of both evolution and engineering. Through consideration of lessons learned from recent efforts to install new metabolic modules into cells and the emerging understanding of the structure, function and assembly of protein-based organelles, bacterial microcompartments, a structural bioengineering approach is described: one that builds from an architectural vocabulary of protein domains. This bioarchitectonic approach to engineering cellular metabolism can be applied to microbial cell factories, used in the programming of members of synthetic microbial communities or used to attain additional levels of metabolic organization in eukaryotic cells for increasing primary productivity and as the foundation of a green economy.

This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
Interaction between photosynthetic electron transport and chloroplast sinks triggers protection and signalling important for plant productivity
Authors: Gollan Peter J. , Lima-Melo Yugo , Tiwari Arjun , Tikkanen Mikko , Aro Eva-Mari
Published: August 2017

The photosynthetic light reactions provide energy that is consumed and stored in electron sinks, the products of photosynthesis. A balance between light reactions and electron consumption in the chloroplast is vital for plants, and is protected by several photosynthetic regulation mechanisms. Photosystem I (PSI) is particularly susceptible to photoinhibition when these factors become unbalanced, which can occur in low temperatures or in high light. In this study we used the
pgr5 Arabidopsis
mutant that lacks ΔpH-dependent regulation of photosynthetic electron transport as a model to study the consequences of PSI photoinhibition under high light. We found that PSI damage severely inhibits carbon fixation and starch accumulation, and attenuates enzymatic oxylipin synthesis and chloroplast regulation of nuclear gene expression after high light stress. This work shows that modifications to regulation of photosynthetic light reactions, which may be designed to improve yield in crop plants, can negatively impact metabolism and signalling, and thereby threaten plant growth and stress tolerance.

This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.