bluuebunny/crossref_metadata_2025 huggingface dataset:
Growth modes and epitaxy of FeAl thin films on a-cut sapphire prepared by pulsed laser and ion beam assisted deposition
Authors: Yao Xiang , Wiedwald Ulf , Trautvetter Moritz , Ziemann Paul
Published: January 2014

FeAl films around equiatomic composition are grown on a-cut (112¯0) sapphire substrates by ion beam assisted deposition (IBAD) and pulsed laser deposition (PLD) at ambient temperature. Subsequent successive annealing is used to establish chemical order and crystallographic orientation of the films with respect to the substrate. We find a strongly [110]-textured growth for both deposition techniques. Pole figures prove the successful preparation of high quality epitaxial films by PLD with a single in-plane orientation. IBAD-grown films, however, exhibit three in-plane orientations, all of them with broad angular distributions. The difference of the two growth modes is attributed to the existence of a metastable intermediate crystalline orientation as concluded from nonassisted sputter depositions at different substrate temperatures. The formation of the chemically ordered crystalline B2 phase is accompanied by the expected transition from ferromagnetic to paramagnetic behavior of the films. In accordance with the different thermally induced structural recovery, we find a step-like magnetic transition to paramagnetic behavior after annealing for 1 h at TA = 300 °C for IBAD deposition, while PLD-grown films show a gradual decrease of ferromagnetic signals with rising annealing temperatures.
Investigation on the electrical transport properties of highly (00l)-textured Sb2Te3 films deposited by molecular beam epitaxy
Authors: Zhang Xiangpeng , Zeng Zhigang , Shen Chao , Zhang Ziqiang , Wang Zhichong , Lin Cong , Hu Zhiyu
Published: January 2014

Highly (00l)-textured antimony telluride films were fabricated using molecular beam epitaxy (MBE) on Si (111) substrate at 280 °C. X-ray diffraction analysis implying the samples have good crystalline quality, simultaneously, the grain sizes coarsening with increasing thickness. The results of Hall coefficient measurement demonstrated that the carrier concentration and mobility are strongly affected by grain boundaries and microcrystalline internal defects. It was found that the grain boundaries play a primary factor influencing the carrier concentration in thinner film. At room temperature, the results in a maximum mobility value of 305 cm2/Vs for 121-nm-thick film, and the electrical conductivity increased from 425.7 S/cm to 1036 S/cm as the thickness varied from 28 nm to 121 nm. In the range of room temperature to 150 °C, the resistivity almost linearly increased with increasing temperature. This may be explained by low concentration of impurities or defects and shallow impurity band. For difference thickness films, temperature coefficients of resistivity are substantially equal, and the values are about 3 ∼ 4 μΩ⋅cm/K.
Interstitial Fe in MgO
Authors: Mølholt T. E. , Mantovan R. , Gunnlaugsson H. P. , Svane A. , Masenda H. , Naidoo D. , Bharuth-Ram K. , Fanciulli M. , Gislason H. P. , Johnston K. , Langouche G. , Ólafsson S. , Sielemann R. , Weyer G. ,   ISOLDE collaboration
Published: January 2014

Isolated 57Fe atoms were studied in MgO single-crystals by emission Mössbauer spectroscopy following implantation of 57Mn decaying to 57Fe. Four Mössbauer spectral components were found corresponding to different Fe lattice positions and/or charge states. Two components represent Fe atoms substituting Mg as Fe2+ and Fe3+, respectively; a third component is due to Fe in a strongly implantation-induced disturbed region. The fourth component, which is the focus of this paper, can be assigned to Fe at an interstitial site. Comparison of its measured isomer shift with ab initio calculations suggests that the interstitial Fe is located on, or close to, the face of the rock-salt MgO structure. To harmonize such an assignment with the measured near-zero quadrupole interaction a local motion process (cage motion) of the Fe has to be stipulated. The relation of such a local motion as a starting point for long range diffusion is discussed.
Amorphous silicon oxide window layers for high-efficiency silicon heterojunction solar cells
Authors: Peter Seif Johannes , Descoeudres Antoine , Filipič Miha , Smole Franc , Topič Marko , Charles Holman Zachary , De Wolf Stefaan , Ballif Christophe
Published: January 2014

In amorphous/crystalline silicon heterojunction solar cells, optical losses can be mitigated by replacing the amorphous silicon films by wider bandgap amorphous silicon oxide layers. In this article, we use stacks of intrinsic amorphous silicon and amorphous silicon oxide as front intrinsic buffer layers and show that this increases the short-circuit current density by up to 0.43 mA/cm2 due to less reflection and a higher transparency at short wavelengths. Additionally, high open-circuit voltages can be maintained, thanks to good interface passivation. However, we find that the gain in current is more than offset by losses in fill factor. Aided by device simulations, we link these losses to impeded carrier collection fundamentally caused by the increased valence band offset at the amorphous/crystalline interface. Despite this, carrier extraction can be improved by raising the temperature; we find that cells with amorphous silicon oxide window layers show an even lower temperature coefficient than reference heterojunction solar cells (−0.1%/°C relative drop in efficiency, compared to −0.3%/°C). Hence, even though cells with oxide layers do not outperform cells with the standard design at room temperature, at higher temperatures—which are closer to the real working conditions encountered in the field—they show superior performance in both experiment and simulation.
Phononic crystal strip based anchors for reducing anchor loss of micromechanical resonators
Authors: Feng Duan , Xu Dehui , Wu Guoqiang , Xiong Bin , Wang Yuelin
Published: January 2014

Micromechanical resonators must be clamped to the substrate via anchors to support the suspended microstructure. However, these anchors will introduce anchor loss, and decrease quality factors (Qs) of the micromechanical resonators. To reduce the anchor loss, one dimensional phononic crystal based strips are employed as anchors of the microresonators in this paper. The dispersion relations and eigenmodes of the phononic crystal strips are presented. Flexural mode ring resonator and Lamé mode square plate resonator are designed to verify the effect of phononic crystal strips. The calculated results and finite-element simulations indicate that the leaky energy could be effectively reduced by the phononic crystal strip anchor design. Resonators with different anchor designs are also fabricated and characterized. The measured Qs of the microresonators show that the phononic crystal strips could reduce the energy dissipated through anchors, and with increasing the number of phononic strip periods, Qs of the resonators could be further enhanced. Furthermore, the experimental result also shows that compared with the Lamé mode square plate resonator, the flexural mode ring resonator is more susceptible to the anchor loss.
Electric field control of magnetism in FePd/PMN-PT heterostructure for magnetoelectric memory devices
Authors: Yang Y. T. , Song Y. Q. , Wang D. H. , Gao J. L. , Lv L. Y. , Cao Q. Q. , Du Y. W.
Published: January 2014

We report a strain-mediated magnetoelectric random access memory in FePd/PMN-PT heterostructure. Due to the strong converse magnetoelectric effect, the effective anisotropy of the FePd film is controlled by the applied electric field and used to switch the magnetization from one state to the other. Taking the advantage of the large electric-field modulation of magnetic properties, the electric-write/magnetic-read memory is obtained in such heterostructure. This magnetoelectric memory provides a promising approach to the development of a practical magnetoelectric device at room temperature.
Rectifying performance and negative differential behavior in graphite—chain—carbon nanotube junctions
Authors: Qiu Ming , Li Jiangfan , Liew K. M. , Yuan Chris
Published: January 2014

In this paper, the (5, 5) capped carbon nanotubes (CNTs) in contact with different lengths of sp monoatomic chains grown on the surface of graphite substrate are fabricated and its electronic transport properties sandwiched between CNT and graphite electrodes are investigated. The first-principles calculations based on nonequilibrium Green's function in combination with density-functional theory show that their rectifying performance and negative differential resistance behavior are observed under very low biases and obviously are enhanced when the length increases. From our analysis, the charge transfer, transmission spectra, projected density of states and evolutions of molecular orbitals are responsible for these phenomena.
Ballistic transport in graphene grown by chemical vapor deposition
Authors: Calado V. E. , Zhu Shou-En , Goswami S. , Xu Q. , Watanabe K. , Taniguchi T. , Janssen G. C. A. M. , Vandersypen L. M. K.
Published: January 2014

In this letter, we report the observation of ballistic transport on micron length scales in graphene synthesised by chemical vapour deposition (CVD). Transport measurements were done on Hall bar geometries in a liquid He cryostat. Using non-local measurements, we show that electrons can be ballistically directed by a magnetic field (transverse magnetic focussing) over length scales of ∼1 μm. Comparison with atomic force microscope measurements suggests a correlation between the absence of wrinkles and the presence of ballistic transport in CVD graphene.
Mode stability in photonic-crystal surface-emitting lasers with large κ1DL
Authors: Liang Yong , Okino Tsuyoshi , Kitamura Kyoko , Peng Chao , Ishizaki Kenji , Noda Susumu
Published: January 2014

We study mode stability in photonic-crystal surface-emitting lasers (PCSELs) with large coupling-coefficient-length product κ1DL(>6). We observe that mode competition occurs at high current levels above threshold. Our combined experimental and theoretical study provides the first evidence of the mode competition originating from the high-order band-edge modes. The decreased threshold margin between these competing high-order modes and the main lasing mode with increasing cavity length as well as the spatial hole burning effect may deteriorate the single-mode stability. Our finding is essential for designing single-mode high-power PCSELs for which the strategy to suppress the high-order modes must be considered.
Electrically controlled spin polarization and selection in a topological insulator sandwiched between ferromagnetic electrodes
Authors: Guo Junji , Liao Wenhu , Zhao Heping , Zhou Guanghui
Published: January 2014

We theoretically investigate the electrically controllable spin polarization and selective efficiency of the edge state Dirac electron in a two-dimensional topological insulator (TI) sandwiched between ferromagnetic (FM) electrodes by using the method of Keldysh nonequilibrium Green's function. A nearly full spin polarization of the topological edge state with giant inversion of ∼80% is observed, which is much higher than the value previously reported. Moreover, the selective efficiency for spin-up electrons under the modulation of the parallel configuration of FM electrodes has been demonstrated to be larger than 95% for the first time, while that for spin-down electrons in the antiparallel case is higher than 90% in a wide energy range, owing to the inter-edge spin tunneling induced backscattering and spin dephasing effect. The obtained results may provide a deeper understanding of the TI edge states and a valuable guidance to design spin switch and filter with high on-off speed and selective efficiency based on TIs.
Ferrite-filled cavities for compact planar resonators
Authors: Keatley P. S. , Durrant C. J. , Berry S. J. , Sirotkin E. , Hibbins A. P. , Hicken R. J.
Published: January 2014

Sub-wavelength metallic planar cavities, closed at one end, have been constructed by wrapping aluminium foil around teflon or ferrite slabs. Finite cavity width perturbs the fundamental cavity mode frequency of ferrite-filled cavities due to different permeability inside and outside of the cavity, in contrast to teflon-filled cavities, while the cavity length required to achieve a specific resonance frequency is significantly reduced for a ferrite-filled cavity. Ferrite-filled cavities may be excited by an in-plane alternating magnetic field and may be advantageous for high-frequency (HF) and ultra HF tagging and radio frequency identification of metallic objects within security, manufacturing, and shipping environments.
Experimental and theoretical study of the dynamics of self-sustained oscillations in a standing wave thermoacoustic engine
Authors: Guedra M. , Penelet G. , Lotton P.
Published: January 2014

A model for the description of the transient regime leading to steady-state sound in a quarter-wavelength thermoacoustic prime mover is proposed, which is based on the description of the unsteady heat transfer in the system, coupled with an ordinary differential equation describing wave amplitude growth/attenuation. The equations are derived by considering a cross-sectional averaged temperature distribution along the resonator, and by assuming that both the characteristic time associated with heat diffusion through the stack and that associated with the thermoacoustic amplification are much larger than the acoustic period. Attention is here focused on the only mechanism of saturation due to heat transport by sound within the stack. The numerical solving of the governing equations leads to the prediction of the transient regime, which is compared with experimental results for several values of the heat power supplied to the system and for several positions of the stack in the resonator. The model reproduces the experiments quite well, notably showing that a small diminution of the temperature in the vicinity of the hot end of the stack is associated to an overshoot of wave amplitude growth, while heat diffusion through the whole stack impacts the subsequent evolution of wave amplitude leading to steady state. Additional experimental results exhibiting complicated regimes of wave amplitude evolution are provided, which are not reproduced by the present model.
An integrative assay to quantify the nutritional quality of the selected diet of two Mediterranean free-living deer by faecal-FT-NIRS
Authors: Tellado S. , Azorit C.
Published: January 2014

Integrating the interaction between cell wall components through a lignin and neutral detergent fibre ratio as a cell wall digestibility (CWD) index may provide a suitable method for diet quality and fibre digestibility estimation. Predictive faecal-Fourier-transform (FT)-near infrared reflectance spectroscopy (NIRS) equations useful for CWD determination were developed as an integrative assessment of the digestibility and quality of the diet selected by red (Cervus elaphus hispanicus) and fallow (Dama dama) deer in southern Spain. A chemometric regression was used from spectra of faeces and wet chemical rumen contents analysis as reference data coupled with partial least-squares. The accuracy and feasibility of the equations obtained for red and fallow deer samples separately were evaluated, as well as after pooling all samples for both species. The predictive equations had a high linearity with correlation coefficients (r) ranging between 0.89 and 0.99, as well as a reliable accuracy considering the errors of prediction (RMSEP 0.57–0.87), calibration (RMS 0.04–0.45) and cross-calibration (RMSECV 0.80–1.12) in relation to the range of values for which the NIRS calibration was set for each parameter, giving very good RER (residual error value) indices (7.44–13.23). The ability of the calibration equations to predict new samples from the same deer populations was also assessed through an external validation. Equations obtained for the red deer data were successfully applied not only to red deer but also to fallow deer, and vice versa. Feasible CWD simultaneous determination in red and fallow deer was also obtained by using the broad-based equations. There was variation of the CWD index throughout the year and differences between the two deer species. A lower CWD of the forage was recorded in red deer, while a lower CWD ratio was detected at the end of winter coinciding with the highest browsing levels in both species. This technique has potential to enable closer examination of the non-grass variables and distinguish between browse and herbage feeding behaviour. The faecal-NIRS method of CWD ratio determination is a useful, non-invasive tool for monitoring variations in the diet quality of Mediterranean deer in their natural environment.
Ranking and combining multiple predictors without labeled data
Authors: Parisi Fabio , Strino Francesco , Nadler Boaz , Kluger Yuval
Published: January 2014

Significance

A key challenge in a broad range of decision-making and classification problems is how to rank and combine the possibly conflicting suggestions of several advisers of unknown reliability. We provide mathematical insights of striking conceptual simplicity that explain mutual relationships between independent advisers. These insights enable the design of efficient, robust, and reliable methods to rank the advisers’ performances and construct improved predictions in the absence of ground truth. Furthermore, these methods are robust to the presence of small subgroups of malicious advisers (cartels) attempting to veer the combined decisions to their interest.
Oncogenes induce a vimentin filament collapse mediated by HDAC6 that is linked to cell stiffness
Authors: Rathje Li-Sophie Z. , Nordgren Niklas , Pettersson Torbjörn , Rönnlund Daniel , Widengren Jerker , Aspenström Pontus , Gad Annica K. B.
Published: January 2014

Significance

Oncogenes deregulate fundamental cellular functions, which can lead to the development of tumors and metastases. We show that oncogenes change the spatial organization of the vimentin fibers of the intracellular cytoskeleton, induce cell stiffness, and promote the invasive capacity of cells. We further show that this vimentin reorganization and increased cell stiffness requires histone deacetylase 6 (HDAC6). Taken together, these data support the concept that oncogenes can induce cellular stiffness via HDAC6-dependent reorganization of the vimentin filament network. These findings—that key molecules in oncogenic cell transformation, such as oncogenes and HDAC6, can modulate cell stiffness—highlight the importance of the need for further investigation of the mechanical properties of cells to better understand the mechanisms behind tumor and metastasis formation.
Structure of an HIV-1–neutralizing antibody target, the lipid-bound gp41 envelope membrane proximal region trimer
Authors: Reardon Patrick N. , Sage Harvey , Dennison S. Moses , Martin Jeffrey W. , Donald Bruce R. , Alam S. Munir , Haynes Barton F. , Spicer Leonard D.
Published: January 2014

Significance

A major roadblock in the development of an HIV vaccine is the need to develop vaccine regimens that will induce antibodies that bind to conserved regions of the HIV envelope and neutralize many different virus quasispecies. One such envelope target is at the region closest to the membrane, the glycoprotein (gp) 41 membrane proximal external region (MPER). Previous work has demonstrated that antibodies that target this region bind both to the gp41 polypeptide and to the adjacent viral membrane. However, what has been missing is a view of what the MPER-neutralizing epitopes may look like in the context of a trimeric orientation with lipids. We have constructed an MPER trimer associated with lipids and solved the trimer structure by NMR spectroscopy.
Self-poisoning of
Mycobacterium tuberculosis
by interrupting siderophore recycling
Authors: Jones Christopher M. , Wells Ryan M. , Madduri Ashoka V. R. , Renfrow Matthew B. , Ratledge Colin , Moody D. Branch , Niederweis Michael
Published: January 2014

Significance

Many bacteria acquire iron from the environment by secreting small iron-binding molecules called siderophores.
Mycobacterium tuberculosis
, the causative agent of tuberculosis, produces the siderophores mycobactin and carboxymycobactin. Here, we demonstrate that
M. tuberculosis
recycles its siderophores to enable efficient iron use. Disrupting this process causes the intracellular accumulation of deferrated siderophores, which poisons
M. tuberculosis.
Both externally available and internally synthesized siderophores are toxic for the recycling-deficient mutant, despite its ability to use heme as an iron source. These findings suggest that targeting siderophore recycling may lead to the development of much-needed drugs to combat one of the world’s most deadly bacterial pathogens.
Notch signaling regulates cardiomyocyte proliferation during zebrafish heart regeneration
Authors: Zhao Long , Borikova Asya L. , Ben-Yair Raz , Guner-Ataman Burcu , MacRae Calum A. , Lee Richard T. , Burns C. Geoffrey , Burns Caroline E.
Published: January 2014

Significance

Heart failure is a term used to describe the heart’s inability to pump sufficient oxygen-rich blood throughout the body. This condition is commonly caused by the loss of heart muscle cells termed cardiomyocytes that results from a heart attack. As one of the least regenerative organs in the human body, the heart fails to regenerate damaged cardiomyocytes, forms a noncontractile scar instead, and progressively fails. Unlike mammals, adult zebrafish robustly regenerate their hearts following injury through division of uninjured cardiomyocytes, thus providing an opportunity to dissect innate cardiac regenerative mechanisms. Here, we provide evidence that Notch signaling is required for cardiomyocyte division and heart regeneration in zebrafish and, therefore, highlight a genetic determinant of natural heart renewal.
Deletion of conserved protein phosphatases reverses defects associated with mitochondrial DNA damage inSaccharomyces cerevisiae
Authors: Garipler Görkem , Mutlu Nebibe , Lack Nathan A. , Dunn Cory D.
Published: January 2014

Significance

The mitochondrion harbors a genome inherited from its prokaryotic ancestor. Damage to mtDNA causes severe consequences for the cell. Disease-causing mtDNA mutations can be inherited, or harmful changes in the mitochondrial genome can accumulate during treatment with anticancer or antiviral agents. Furthermore, mutation of mtDNA correlates with and may have a causal role in aging. We have used a single-celled organism in which many studies of mitochondrial function have been performed to investigate how pathways that sense the nutritional status of the cell determine the consequences of mtDNA damage. We found that the deletion of two protein phosphatases conserved across many eukaryotes has greatly beneficial effects on cells lacking a mitochondrial genome, suggesting a potential therapeutic approach for mitochondrial disease.
Carlactone is an endogenous biosynthetic precursor for strigolactones
Authors: Seto Yoshiya , Sado Aika , Asami Kei , Hanada Atsushi , Umehara Mikihisa , Akiyama Kohki , Yamaguchi Shinjiro
Published: January 2014

Significance

Strigolactones (SLs) were initially characterized as root-derived signals for parasitic and symbiotic interactions with root parasitic plants and arbuscular mycorrhizal fungi, respectively. SLs were later shown to act as endogenous hormones that regulate shoot branching. Carlactone (CL) was identified as a product of three SL biosynthetic enzymes in vitro, and therefore a putative biosynthetic precursor for SLs. However, it was neither detected from plant tissues, nor was the conversion of CL to SL demonstrated in vivo. In this paper, we show that13C-labeled CL is converted to SLs in vivo, and that endogenous CL is successfully identified from rice andArabidopsis. These results demonstrate that CL is a true biosynthetic precursor for SLs.
Evolution of microbial markets
Authors: Werner Gijsbert D. A. , Strassmann Joan E. , Ivens Aniek B. F. , Engelmoer Daniel J. P. , Verbruggen Erik , Queller David C. , Noë Ronald , Johnson Nancy Collins , Hammerstein Peter , Kiers E. Toby
Published: January 2014

Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions.
C3 opsonization regulates endocytic handling of apoptotic cells resulting in enhanced T-cell responses to cargo-derived antigens
Authors: Baudino Lucie , Sardini Alessandro , Ruseva Marieta M. , Fossati-Jimack Liliane , Cook H. Terence , Scott Diane , Simpson Elizabeth , Botto Marina
Published: January 2014

Significance

Activation of the complement system, a network of circulating and surface-bound molecules, is known to enhance humoral immunity. However, paradoxically, the lack of some complement components (mainly C1q and C4), but not C3, is associated with the development of autoimmunity. Prior studies have suggested that this association could be explained by the role of complement in the disposal of dying cells that are a potential source of autoantigens. This study demonstrates that C3 bound to dying cells can direct the intracellular route of the cargo and modulate the subsequent T-cell response to antigens displayed on dying cells. These results uncover a new role of C3 and have important implications for our understanding of the role of complement in health and disease.
Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes
Authors: Horton Brent M. , Hudson William H. , Ortlund Eric A. , Shirk Sandra , Thomas James W. , Young Emily R. , Zinzow-Kramer Wendy M. , Maney Donna L.
Published: January 2014

Significance

In this series of studies, we provide a rare illustration of how a chromosomal polymorphism has affected overt social behavior in a vertebrate. White-throated sparrows occur in two alternative phenotypes, or morphs, distinguished by a chromosomal rearrangement. That the morphs differ in territorial and parental behavior has been known for decades, but how the rearrangement affects behavior is not understood. Here we show that genetic differentiation between the morphs affects the transcription of a gene well known to be involved in social behavior. We then show that in a free-living population, the neural expression of this gene predicts both territorial and parental behavior. We hypothesize that this mechanism has played a causal role in the evolution of alternative life-history strategies.
Crystal structure of the essential transcription antiterminator M2-1 protein of human respiratory syncytial virus and implications of its phosphorylation
Authors: Tanner Sian J. , Ariza Antonio , Richard Charles-Adrien , Kyle Hannah F. , Dods Rachel L. , Blondot Marie-Lise , Wu Weining , Trincão José , Trinh Chi H. , Hiscox Julian A. , Carroll Miles W. , Silman Nigel J. , Eléouët Jean-François , Edwards Thomas A. , Barr John N.
Published: January 2014

Significance

Human respiratory syncytial virus (HRSV) is the leading cause of lower respiratory tract illness in young children; however, no vaccine exists and current immunoprophylaxis regimes are both expensive and incompletely protective. We report the crystal structure of the HRSV M2-1 transcription factor that is essential for virus gene expression and thus growth. This structure reveals how M2-1 forms an extremely stable tetramer and has allowed us to pinpoint the location of critical regions that regulate M2-1 activity, providing insight into its function. This structure may represent a potent target for new antiviral compounds.
Human and
Helicobacter pylori
coevolution shapes the risk of gastric disease
Authors: Kodaman Nuri , Pazos Alvaro , Schneider Barbara G. , Piazuelo M. Blanca , Mera Robertino , Sobota Rafal S. , Sicinschi Liviu A. , Shaffer Carrie L. , Romero-Gallo Judith , de Sablet Thibaut , Harder Reed H. , Bravo Luis E. , Peek Richard M. , Wilson Keith T. , Cover Timothy L. , Williams Scott M. , Correa Pelayo
Published: January 2014

Significance

Theory predicts that chronic pathogens with vertical or familial transmission should become less virulent over time because of coevolution. Although transmitted in this way,
Helicobacter pylori
is the major causative agent of gastric cancer. In two distinct Colombian populations with similar levels of
H. pylori
infection but different incidences of gastric cancer, we examined human and pathogen ancestry in matched samples to assess whether their genomic variation affects the severity of premalignant lesions. Interaction between human Amerindian ancestry and
H. pylori
African ancestry accounted for the geographic disparity in clinical presentation. We conclude that coevolutionary relationships are important determinants of gastric disease risk and that the historical colonization of the Americas continues to influence health in modern American populations.
Drosha-independent DGCR8/Pasha pathway regulates neuronal morphogenesis
Authors: Luhur Arthur , Chawla Geetanjali , Wu Yen-Chi , Li Jing , Sokol Nicholas S.
Published: January 2014

Significance

Understanding the neuronal functions of diverse RNA pathways will lead to treatments of human neurological diseases that are caused by perturbations in RNA metabolism. Two proteins, Drosha and Pasha/DGCR8, play important roles in neurons, where they are responsible for the biogenesis of many microRNAs. Here, we show that Pasha/DGCR8 also promotes the morphogenesis of neurons in developing fruit flies independently of Drosha and therefore of most microRNA production. These studies therefore illuminate a novel function of Pasha that is medically relevant, because loss of the human ortholog of Pasha may contribute to cognitive and behavioral disorders associated with DiGeorge syndrome.
Circadian rhythms synchronize mitosis in
Neurospora crassa
Authors: Hong Christian I. , Zámborszky Judit , Baek Mokryun , Labiscsak Laszlo , Ju Kyungsu , Lee Hyeyeong , Larrondo Luis F. , Goity Alejandra , Chong Hin Siong , Belden William J. , Csikász-Nagy Attila
Published: January 2014

Significance

Circadian rhythms provide temporal information to other cellular processes, such as metabolism. We investigate the coupling between the cell cycle and the circadian clock using mathematical modeling and experimentally validate model-driven predictions with a model filamentous fungus,
Neurospora crassa
. We demonstrate a conserved coupling mechanism between the cell cycle and the circadian clock in Neurospora as in mammals, which results in circadian clock-gated mitotic cycles. Furthermore, we observe circadian clock-dependent phase shifts of G1 and G2 cyclins, which may alter the timing of divisions. Our work has large implications for the general understanding of the connection between the cell cycle and the circadian clock.
Neural representation of expected value in the adolescent brain
Authors: Barkley-Levenson Emily , Galván Adriana
Published: January 2014

Significance

The brain undergoes significant maturation during adolescence that influences reward sensitivity and risk-taking behavior. However, it is unknown if the adolescent brain truly values rewards in a way that is unique from the mature brain or if confounding factors contribute to this developmental difference. Here we show that adolescents place greater value on rewards than do adults through exaggerated activation of the ventral striatum and that this valuation increases gambling behavior. This developmental effect remains even when controlling for income and task performance. We also find that heightened reward sensitivity leads to more advantageous risk-taking in adolescents versus adults. These data provide behavioral and neural evidence for ontogenetic differences in how value computation is used to bias reward-related behavior during adolescence.
Thymocyte apoptosis drives the intrathymic generation of regulatory T cells
Authors: Konkel Joanne E. , Jin Wenwen , Abbatiello Brittany , Grainger John R. , Chen WanJun
Published: January 2014

Significance

Thymus-derived regulatory T cells (tTregs) are vital to maintaining immune homeostasis, and as such the signals driving their development have been extensively studied. Despite this, a cohesive model describing tTreg generation and aligning all conflicting data has been elusive. Here we outline a comprehensive model controlling the generation of tTregs and show that tTreg generation is tied to thymic apoptosis. We show that the presence of apoptotic cells in the thymus drives the production of TGFβ intrathymically and that this cytokine then acts to specify the tTreg fate. Thus, our results reveal an apoptosis–TGFβ–Foxp3 axis that mediates the development of tTregs.
Near-infrared–actuated devices for remotely controlled drug delivery
Authors: Timko Brian P. , Arruebo Manuel , Shankarappa Sahadev A. , McAlvin J. Brian , Okonkwo Obiajulu S. , Mizrahi Boaz , Stefanescu Cristina F. , Gomez Leyre , Zhu Jia , Zhu Angela , Santamaria Jesus , Langer Robert , Kohane Daniel S.
Published: January 2014

Significance

Devices that release a drug in response to a remote trigger would enable on-demand control of the timing and dose of drug released. They would allow the patient or physician to adjust therapy precisely to a target effect, thus improving treatment and reducing toxicity. We have developed implantable reservoirs that release a drug when irradiated with near-infrared laser light. The release rate was correlated to laser intensity, with negligible leakage between doses. Devices containing aspart, a fast-acting analog of insulin, were implanted in diabetic rats and were able to achieve glycemic control upon irradiation. Such devices can be loaded with a wide range of drugs to treat a variety of clinical indications.
Ndfip1 mediates peripheral tolerance to self and exogenous antigen by inducing cell cycle exit in responding CD4+T cells
Authors: Altin John A. , Daley Stephen R. , Howitt Jason , Rickards Helen J. , Batkin Alison K. , Horikawa Keisuke , Prasad Simon J. , Nelms Keats A. , Kumar Sharad , Wu Lawren C. , Tan Seong-Seng , Cook Matthew C. , Goodnow Christopher C.
Published: January 2014

Significance

Advances in organ transplantation and treatment of allergy and autoimmune disease hinge upon harnessing a physiological switch that allows T cells to decide between proliferating extensively or actively becoming tolerant. The experiments presented here illuminate a critical element of this natural switch, Ndfip1 (neural precursor cell expressed, developmentally down-regulated protein 4 family-interacting protein 1), a partner protein of ubiquitin ligases induced during the first several divisions after T cells encounter antigen. They define the cellular action of Ndfip1 in vivo, acting within dividing helper T cells that have responded to innocuous foreign or self-antigen that should normally be tolerated, to force their exit from cell cycle before they have divided so many times that they acquire tissue-damaging effector functions.
O-GlcNAcylation regulates EZH2 protein stability and function
Authors: Chu Chi-Shuen , Lo Pei-Wen , Yeh Yi-Hsien , Hsu Pang-Hung , Peng Shih-Huan , Teng Yu-Ching , Kang Ming-Lun , Wong Chi-Huey , Juan Li-Jung
Published: January 2014

Significance

The present study identifies a cross-talk of two important posttranslational modifications, revealing that enhancer of zeste homolog 2 (EZH2) O-GlcNAcylation (GlcNac,
N
-acetylglucosamine) at serine 75 is required for EZH2 protein stability and therefore facilitates the histone H3 trimethylation at K27 to form H3K27me3. The finding is significant because both O-linked GlcNAc transferase-mediated O-GlcNAcylation and EZH2-mediated H3K27me3 formation play a pivotal role in development, and their up-regulation is believed to participate in tumor malignancy. The identification of O-linked GlcNAc transferase association with the polycomb repressive complex 2 (PRC2) further provides a new approach to regulate PRC2 function.
Sub-10-nm intracellular bioelectronic probes from nanowire–nanotube heterostructures
Authors: Fu Tian-Ming , Duan Xiaojie , Jiang Zhe , Dai Xiaochuan , Xie Ping , Cheng Zengguang , Lieber Charles M.
Published: January 2014

Significance

The miniaturization of bioelectronic probes to enable interrogation of small subcellular structures could impact significantly biology and medicine. This paper describes the design, fabrication, and demonstration of the sub-10-nm bioelectronic devices by exploiting a unique three-dimension nanowire–nanotube structure, where a nanowire detector is synthetically integrated with a nanotube probe. Devices with nanotube probe dimensions as small as 5 nm, which approach the size of a single ion channel, have been realized. Experimental measurements and numerical simulations show that these devices have sufficient time resolution to record the fastest electrical signals in neurons and other cells. Measurement of the cell transmembrane resting potential with these ultrasmall bioelectronic devices further demonstrates their capability for intracellular electrophysiology studies.
Transcriptional occlusion caused by overlapping promoters
Authors: Zafar M. Ammar , Carabetta Valerie J. , Mandel Mark J. , Silhavy Thomas J.
Published: January 2014

Significance

Under nitrogen-limiting conditions, the master regulator RpoS protects against stress, but slowed growth is the price cells pay for this protection. Under these conditions, transcription of the gene for the RpoS activator Crl increases. Strikingly, we show that this increase in transcription actually decreases Crl protein levels, thus decreasing RpoS activity and increasing growth rate. This unique regulatory mechanism has as its basis two overlapping promoters. Transcription from the promoter used under nitrogen-limitation prevents transcription of the functional
crl
mRNA producing instead a long noncoding RNA that has no function. Under conditions where protein synthesis is compromised, this simple, but economical mechanism causes a near-instantaneous reduction in Crl levels and RpoS activity without the need to synthesize a regulatory molecule.
Two contrasting Australian Curriculum responses to globalisation: what students should learn or become
Authors: Lingard Bob , McGregor Glenda
Published: January 2014

This paper compares two contrasting educational policy responses to globalisation in Australia: the ‘New Basics’ experiment that occurred in the State of Queensland (2000–2003) and the Australian Curriculum, which is currently being implemented across the nation from preschool to Year 10 in English, history, mathematics and science. These initiatives illustrate the tensions that have continued to mount during the last decade over answers to the question of ‘what counts’ as the most valuable knowledge and/or skills needed to negotiate the complexities of a rapidly globalising world. Illustrating one international trend of favouring the development of competencies and dispositions, the New Basics project abandoned traditional school subjects for futures oriented, ‘real‐world’ learning. The Australian Curriculum demonstrates a strong return to ‘the disciplines’, partly as a local backlash against experiments like the New Basics and Outcomes Based Education, but also motivated by the desire to improve the nation%s performance on international tests; however, via its framework of ‘cross‐curriculum priorities’ and ‘general capabilities’, the Australian Curriculum also pays heed to the rhetoric of shaping the individual as the kind of person with the skills and dispositions required by the global millennium citizen and worker.
Pragmatising the curriculum: bringing knowledge back into the curriculum conversation, but via pragmatism
Authors: Biesta Gert
Published: January 2014

In this paper, I explore the role of knowledge in the curriculum through a discussion of John Dewey%s transactional theory of knowing. I do so against the background of recent calls to bring knowledge back into the discussion about the curriculum in which pragmatism has been depicted as a problematic form of relativism that should have no place in contemporary curriculum theory and practice. I show that rather than being a form of relativism, pragmatism actually moves beyond the modern opposition of objectivism versus relativism. Dewey%s transactional theory of knowing moves the question of knowledge from the domain of certainty to the domain of possibility. I show in this paper how Dewey develops this argument and give reasons why this is an important contribution to the ongoing discussion about knowledge and the curriculum.
Gata3 drives development of RORγt+ group 3 innate lymphoid cells
Authors: Serafini Nicolas , Klein Wolterink Roel G.J. , Satoh-Takayama Naoko , Xu Wei , Vosshenrich Christian A.J. , Hendriks Rudi W. , Di Santo James P.
Published: January 2014

Group 3 innate lymphoid cells (ILC3) include IL-22–producing NKp46+ cells and IL-17A/IL-22–producing CD4+ lymphoid tissue inducerlike cells that express RORγt and are implicated in protective immunity at mucosal surfaces. Whereas the transcription factor Gata3 is essential for T cell and ILC2 development from hematopoietic stem cells (HSCs) and for IL-5 and IL-13 production by T cells and ILC2, the role for Gata3 in the generation or function of other ILC subsets is not known. We found that abundant GATA-3 protein is expressed in mucosa-associated ILC3 subsets with levels intermediate between mature B cells and ILC2. Chimeric mice generated with Gata3-deficient fetal liver hematopoietic precursors lack all intestinal RORγt+ ILC3 subsets, and these mice show defective production of IL-22 early after infection with the intestinal pathogen Citrobacter rodentium, leading to impaired survival. Further analyses demonstrated that ILC3 development requires cell-intrinsic Gata3 expression in fetal liver hematopoietic precursors. Our results demonstrate that Gata3 plays a generalized role in ILC lineage determination and is critical for the development of gut RORγt+ ILC3 subsets that maintain mucosal barrier homeostasis. These results further extend the paradigm of Gata3-dependent regulation of diversified innate ILC and adaptive T cell subsets.
Calcium-dependent stoichiometries of the KCa2.2 (SK) intracellular domain/calmodulin complex in solution
Authors: Halling D. Brent , Kenrick Sophia A. , Riggs Austen F. , Aldrich Richard W.
Published: January 2014

Ca2+ activates SK Ca2+-activated K+ channels through the protein Ca2+ sensor, calmodulin (CaM). To understand how SK channels operate, it is necessary to determine how Ca2+ regulates CaM binding to its target on SK. Tagless, recombinant SK peptide (SKp), was purified for binding studies with CaM at low and high Ca2+ concentrations. Composition gradient multi-angle light scattering accurately measures the molar mass, stoichiometry, and affinity of protein complexes. In 2 mM Ca2+, SKp and CaM bind with three different stoichiometries that depend on the molar ratio of SKp:CaM in solution. These complexes include 28 kD 1SKp/1CaM, 39 kD 2SKp/1CaM, and 44 kD 1SKp/2CaM. A 2SKp/2CaM complex, observed in prior crystallographic studies, is absent. At <5 nM Ca2+, 1SKp/1CaM and 2SKp/1CaM were observed; however, 1SKp/2CaM was absent. Analytical ultracentrifugation was used to characterize the physical properties of the three SKp/CaM stoichiometries. In high Ca2+, the sedimentation coefficient is smaller for a 1SKp:1CaM solution than it is for either 2SKp:1CaM or 1SKp:2CaM. At low Ca2+ and at >100 µM protein concentrations, a molar excess of SKp over CaM causes aggregation. Aggregation is not observed in Ca2+ or with CaM in molar excess. In low Ca2+ both 1SKp:1CaM and 1SKp:2CaM solutions have similar sedimentation coefficients, which is consistent with the absence of a 1SKp/2CaM complex in low Ca2+. These results suggest that complexes with stoichiometries other than 2SKp/2CaM are important in gating.
Impacts of Kafirin Allelic Diversity, Starch Content, and Protein Digestibility on Ethanol Conversion Efficiency in Grain Sorghum
Authors: Cremer Julia E. , Liu Liman , Bean Scott R. , Ohm Jae‐Bom , Tilley Michael , Wilson Jeff D. , Kaufman Rhett C. , Vu Thanh H. , Gilding Edward K. , Godwin Ian D. , Wang Donghai
Published: January 2014

Seed protein and starch composition determine the efficiency of the fermentation process in the production of grain‐based ethanol. Sorghum, a highly water‐ and nutrient‐efficient plant, provides an alternative to fuel crops with greater irrigation and fertilizer requirements, such as maize. However, sorghum grain is generally less digestible because of extensive disulfide cross‐linking among sulfur‐rich storage proteins in the protein– starch matrix. Thus, the fine structure and composition of the seed endosperm directly impact grain end use, including fermentation performance. To test the hypothesis that kafirin (prolamin) seed storage proteins specifically influence the efficiency of ethanol production from sorghum, 10 diverse genetic lines with allelic variation in the β‐, γ‐, and (δ‐kafirins, including three β‐kafirin null mutants, were tested for ethanol yield and fermentation efficiency. Our selected lines showed wide variation in grain biochemical features, including total protein (9.96–16.47%), starch (65.52–74.29%), and free amino nitrogen (FAN) (32.84–73.51 mg/L). Total ethanol yield (ranging from 384 to 426 L/metric ton), was positively correlated to starch content (R2 = 0.74), and there was a slight positive correlation between protein digestibility and ethanol yield (R2 = 0.52). Increases in FAN content enhanced fermentation efficiency (R2 = 0.65). The highest ethanol producer was elite staygreen breeding line B923296, and the line with the highest fermentation efficiency at the 72 h time point was inbred BT×623. A large‐seeded genotype, KS115, carrying a novel γ‐kafirin allele, was rich in FAN and exhibited excellent short‐term fermentation efficiency at 85.68% at the 20 h time point. However, the overall ethanol yield from this line was comparatively low at 384 L/metric ton, because of insufficient starch, low digestibility, and high crude protein. Multivariate analysis indicated an association between the β‐kafirin allele and variation in grain digestibility (P = 0.042) and FAN (P = 0.036), with subsequent effects on ethanol yield. Reversed‐phase HPLC profiling of the alcohol‐soluble kafirin protein fraction revealed diversity in protein content and composition across the lines, with similarities in peak distribution profiles among β‐kafirin null mutants compared with normal lines.