bluuebunny/crossref_metadata_2025 huggingface dataset:
Defect formation in GaAs/GaNxAs1-x core/shell nanowires
Authors: Stehr J. E. , Chen S. L. , Jansson M. , Ishikawa F. , Chen W. M. , Buyanova I. A.
Published: November 2016

Photoluminescence and optically detected magnetic resonance (ODMR) spectroscopies are used to investigate the formation and role of defects in GaAs/GaNxAs1-x core/shell nanowires (NWs) grown by molecular beam epitaxy on Si substrates. Gallium vacancies, which act as non-radiative recombination (NRR) centers, are identified by ODMR. It is shown that the defects are formed in bulk regions, i.e., not on the surface, of the GaNAs shell and that their concentration increases with increasing nitrogen content. Temperature dependent photoluminescence experiments reveal, on the other hand, suppressed thermal quenching of the near-band-edge emission with increasing [N]. This leads to the conclusion that the dominant NRR processes in the studied NWs are governed by surface defects, whereas the role of gallium vacancies in the observed thermally activated NRR is minor.
Field-effect transistors of high-mobility few-layer SnSe2
Authors: Guo Chenglei , Tian Zhen , Xiao Yanjun , Mi Qixi , Xue Jiamin
Published: November 2016

We report the transport properties of mechanically exfoliated few-layer SnSe2 flakes, whose mobility is found to be ∼85 cm2 V−1 s−1 at 300 K, higher than those of the majority of few-layer transitional metal dichalcogenides. The mobility increases strongly with decreased temperature, indicating a phonon limited transport. The conductivity of the semiconducting SnSe2 shows a metallic behavior, which is explained by two competing factors involving the different temperature dependence of mobility and carrier density. The Fermi level is found to be 87 meV below the conduction band minima (CBM) at 300 K and 12 meV below the CBM at 78 K, resulting from a heavy n-type doping. Previous studies have found SnSe2 field-effect transistors to be very difficult to turn off. We find the limiting factor to be the flake thickness compared with the maximum depletion width. With fully depleted devices, we are able to achieve a current on-off ratio of ∼105. These results demonstrate the great potential of SnSe2 as a two dimensional (2D) semiconducting material and are helpful for our understanding of other heavily doped 2D materials.
Quasi-optical theory of microwave plasma heating in open magnetic trap
Authors: Shalashov A. G. , Balakin A. A. , Gospodchikov E. D. , Khusainov T. A.
Published: November 2016

Microwave heating of a high-temperature plasma confined in a large-scale open magnetic trap, including all important wave effects like diffraction, absorption, dispersion, and wave beam aberrations, is described for the first time within the first-principle technique based on consistent Maxwell's equations. With this purpose, the quasi-optical approach is generalized over weakly inhomogeneous gyrotrotropic media with resonant absorption and spatial dispersion, and a new form of the integral quasi-optical equation is proposed. An effective numerical technique for this equation's solution is developed and realized in a new code QOOT, which is verified with the simulations of realistic electron cyclotron heating scenarios at the Gas Dynamic Trap at the Budker Institute of Nuclear Physics (Novosibirsk, Russia).
Nonlinear electrostatic solitary pulses in magnetized quantum plasma with relative density effects of spin-up and spin-down electrons
Authors: Ahmad Rashid , Gul Nabi , Adnan Muhammad , Khattak Fida Younus
Published: November 2016

A separated spin evolution quantum hydrodynamics model is employed to study low frequency electrostatic waves in plasmas having inertia-less degenerate electrons with spin-up ne↑ and spin-down ne↓ states and inertial classical ions. A two-dimensional plasma geometry is assumed having a uniform magnetic field, directed along the z-axis, i.e., B=B0ẑ. A Zakharov-Kuznetsov (ZK) type equation is derived for the electrostatic potential via the Reductive Perturbation Technique. The parametric role of the spin density polarization ratio κ in the characteristics of solitary wave structures is investigated. We have observed that both the amplitude and width of the soliton are significantly affected by the spin polarization but the amplitude remains largely un-affected by variation in the magnetic field strength. We have also carried out pulse stability analysis and have found that the pulse soliton solution of the ZK equation is unstable to oblique perturbations. The dependence of the instability growth rate on the density polarization ratio κ along with other significant plasma parameters is traced analytically. We have shown that the first order growth rate of the instability decreases with an increase in the angle between the transverse component of the perturbation and the direction of the magnetic field, in the range (0≤θ<37.8°). We have also observed that the spin polarization affects the growth and increases as we move from the strongly spin-polarized plasma to a zero polarization case.
Enhanced visible photoelectrochemical properties of ZnO/CdS core/shell nanorods and their correlation with improved optical properties
Authors: Yang Xu , Li Hui , Zhang Wu , Sun Mingxuan , Li Lequn , Xu Ning , Wu Jiada , Sun Jian
Published: November 2016

ZnO/CdS core/shell nanorods (NRs) constructed of ZnO NR cores and CdS coating shells were fabricated by hydrothermally growing ZnO NRs and pulsed laser depositing CdS coatings on the grown ZnO NRs. The fabricated ZnO/CdS NRs were characterized by field-emission scanning electron microscopy, transmission electron microscopy, selected-area electron diffraction, X-ray diffraction, and Raman backsattering spectroscopy. The optical and photoelectrochemical properties were evaluated and their correlation was studied. The ZnO cores and CdS shells are both in a hexagonal wurtzite structure with c-axis orientation. Compared with the bare ZnO NRs, the heterostructured ZnO/CdS NRs exhibit improved optical properties including strong visible light absorption and quenched photoluminescence. The former facilitates the generation of electron-hole pairs by visible optical excitation, and the latter reveals the suppressed radiative recombination of photogenerated charges and hence efficient charge transfer and separation. Correlated with the improved optical properties and charge behaviors, the ZnO/CdS NRs show high visible photoelectrochemical activity and excellent photoswitching property, and high visible light harvesting efficiencies can be expected for the ZnO/CdS NRs.
Exchange bias in nano-ferrihydrite
Authors: Balaev D. A. , Krasikov A. A. , Dubrovskiy A. A. , Popkov S. I. , Stolyar S. V. , Iskhakov R. S. , Ladygina V. P. , Yaroslavtsev R. N.
Published: November 2016

We report the results of investigations of the effect of cooling in an external magnetic field starting from the temperature over superparamagnetic blocking temperature TB on the shift of magnetic hysteresis loops in systems of ferrihydrite nanoparticles from ∼2.5 to ∼5 nm in size with different TB values. In virtue of high anisotropy fields of ferrihydrite nanoparticles and open hysteresis loops in the range of experimentally attainable magnetic fields, the shape of hysteresis loops of such objects in the field-cooling mode is influenced by the minor hysteresis loop effect. A technique is proposed for distinguishing the exchange bias effect among the effects related to the minor hysteresis loops caused by high anisotropy fields of ferrihydrite particles. The exchange bias in ferrihydrite is stably observed for particles not less than 3 nm in size or with TB over 40 K, and its characteristic value increases with the particle size.
Off-state current reduction in NbO2-based selector device by using TiO2 tunneling barrier as an oxygen scavenger
Authors: Kang Minkook , Son Junwoo
Published: November 2016

We report a significant off-state current reduction by an order of magnitude in the NbO2-based selector devices by inserting an ultrathin TiO2 (∼2 nm) tunneling barrier. Moreover, the ultrathin TiO2 layer improves the reliability and uniformity of voltage-induced insulator-to-metal transition (IMT) in the NbO2 selector devices by thermodynamically suppressing the formation of a surface Nb2O5 layer. Our study suggests that the suitable combination of tunneling barrier and IMT materials can minimize the “off” current of IMT selector devices and improve their applicability in high-density three dimensional cross point array memory devices.
Osmotic adjustment of young sugar beets (Beta vulgaris) under progressive drought stress and subsequent rewatering assessed by metabolite analysis and infrared thermography
Authors: Wedeking Rita , Mahlein Anne-Katrin , Steiner Ulrike , Oerke Erich-Christian , Goldbach Heiner E. , Wimmer Monika A.
Published: November 2016

The main objective of this work was to provide the chronology of physiological and metabolic alterations occurring under drought and demonstrate how these relate to a phenotypic approach (infrared thermal imaging, IRT). This should provide tools to tailor phenotyping approaches for drought tolerance and underlying metabolic alterations. In the present study, destructive analysis of growth and cell morphology, water status, osmotic adjustment, metabolic changes and membrane damage were combined with non-destructive determination of leaf temperature using infrared thermography (IRT) in 6-week-old sugar beets subjected to progressive drought stress and subsequent rewatering. Different methods were suitable for the characterisation of the dynamic development of distinct stress phases: although IRT allowed detection of initial impairment of transpiration within 1 day of drought stress, destructive methods allowed us to distinguish a phase of metabolic adjustment including redirection of carbon flow into protective mechanisms and a subsequent phase of membrane destabilisation and cellular damage. Only the combination of invasive and non-invasive methods allowed for the differentiation of the complete sequence of physiological changes induced by drought stress. This could be especially beneficial for the selection of phenotypes that are adapted to early drought. During rewatering, sugar beet shoots rapidly re-established water relations, but membrane damage and partial stomatal closure persisted longer, which could have an impact on subsequent stress events. During the onset of secondary growth, taproots required more time to recover the water status and to readjust primary metabolites than shoots.
The eastern grey kangaroo: current management and future directions
Authors: Descovich Kris , Tribe Andrew , McDonald Ian J. , Phillips Clive J. C.
Published: November 2016

The eastern grey kangaroo is a common and iconic species of Australia. Its specialised behaviour and reproduction have evolved as adaptations to the Australian environment, allowing the species to survive and flourish, despite wide climatic and seasonal variations in habitat. Across its range, the eastern grey kangaroo is harvested and subjected to population management for a variety of reasons, including localised over-abundance, livestock competition, crop grazing, native habitat conservation, animal welfare and direct threats to human safety. Population management of kangaroos is most commonly undertaken by shooting, although other methods such as reproductive control, translocation and repellents may also contribute successfully to management. Kangaroo harvesting and population control are controversial and divisive, because the kangaroo is perceived as both a national icon and as a pest species. Although a limited number of surveys have been undertaken on attitudes towards kangaroos and their management, the socio-political aspects affecting these issues are yet to be systematically investigated. Within this review we discuss the relevance of culture and language to species management and conservation, as well as the importance of scrutiny of stakeholder perceptions, motivations and values. Future directions should examine human dimensions that influence kangaroo-management decisions and conservation. The following three key aspects are recommended as research and management priorities: (1) experimental determination of whether gaps exist between actual and perceived impacts of kangaroo populations, (2) empirical investigation of how stakeholder language, culture, identity and values influence perceptions of kangaroos and their management, and (3) where population control is determined to be necessary, an incorporation of stakeholder differences within decision making to ensure best outcomes for both species conservation and population management.
Graft versus self (GvS) against T-cell autoantigens is a mechanism of graft–host interaction
Authors: Mirza Nora , Zierhut Manfred , Korn Andreas , Bornemann Antje , Vogel Wichard , Schmid-Horch Barbara , Bethge Wolfgang A. , Stevanović Stefan , Salih Helmut R. , Kanz Lothar , Rammensee Hans-Georg , Haen Sebastian P.
Published: November 2016

Significance

As the mechanism of graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation (HCT), recognition of the recipient’s body by donor immune cells was previously believed to be based on genetic and immunological differences between donor and recipient. However, evidence in murine models and in autologous HCT has shown that also autoimmunity contributes to GVHD. In this study, we show the development of auto-reactivity after human allogeneic HCT and characterize the specific self-epitopes of T cells that may contribute to mediation of GVHD. Such autoantigens have never been characterized before. These observations contribute to a better understanding of the immune responses that are activated following hematopoietic cell transplantation.
Statistics of natural reverberation enable perceptual separation of sound and space
Authors: Traer James , McDermott Josh H.
Published: November 2016

Significance

Sounds produced in the world reflect off surrounding surfaces on their way to our ears. Known as reverberation, these reflections distort sound but provide information about the world around us. We asked whether reverberation exhibits statistical regularities that listeners use to separate its effects from those of a sound’s source. We conducted a large-scale statistical analysis of real-world acoustics, revealing strong regularities of reverberation in natural scenes. We found that human listeners can estimate the contributions of the source and the environment from reverberant sound, but that they depend critically on whether environmental acoustics conform to the observed statistical regularities. The results suggest a separation process constrained by knowledge of environmental acoustics that is internalized over development or evolution.
Barrierless association of CF
2
and dissociation of C
2
F
4
by variational transition-state theory and system-specific quantum Rice–Ramsperger–Kassel theory
Authors: Bao Junwei Lucas , Zhang Xin , Truhlar Donald G.
Published: November 2016

Significance

Barrierless association reactions and bond dissociation reactions play important roles in combustion and atmospheric chemistry, and calculating their rate constants is challenging for both electronic structure theory and kinetics theory. Here, we validate an exchange–correlation functional against high-level electronic structure theory, and we use the resulting density functional method for direct dynamics calculations of the pressure-dependent rate constants for the C=C bond dissociation of C
2
F
4
by applying multifaceted variable-reaction-coordinate variational transition-state theory with the recently developed system-specific quantum Rice–Ramsperger–Kassel theory. This work presents a prototypical example of the full treatment of the kinetics of barrierless reactions and their reverse reactions, including variational optimization of the transition state, multidimensional tunneling, and pressure effects.
Celso Cittadini e Scipione Maffei studiosi di latino volgare
Authors: Geymonat Francesca Virginia
Published: November 2016

These pages describe how Celso Cittadini in 1601 and Scipione Maffei in 1732 explained the loss of case system and the parallel development of the article in the passage from Latin to Italian.
El tema del represor en El lugar perdido de Norma Huidobro
Authors: Rottenberg Débora
Published: November 2016

The way the theme of the oppressor is inscribed in El lugar perdido by the Argentinian Norma Huidobro is analized based on Angenot´s social discourse theory. It is argued that the social discourse about the oppressor enters El lugar perdido by the discourse of gender. The way in which the discourse of gender is absorbed by the novel and inscribed in it functions as a possible way to humanize the figure of the repressor and, ultimately, as an attempt to understand it in a different way than other social discourses, even aesthetic ones, have done until now.
Morphomic distribution of augments in varieties of Occitan
Authors: Esher Louise
Published: November 2016

This study examines the distribution and function of ‘augments’ within modern Occitan verb paradigms. Most augments in Occitan are
reflexes of the Latin ingressive infix -(Ī/Ē)SC-, as in other Romance languages; but Occitan has also developed novel inflectional
formatives which display similar behaviour. Like the reflexes of -(Ī/Ē)SC-, these formatives serve as inflectional class markers,
and their paradigmatic distribution conforms to existing morphomic templates. The study provides an overview of the diverse
paradigmatic distributions of augments encountered in Occitan; proposes an account of the origin of the novel formatives; and
discusses the apparent correlation between the spread of augments and the neutralisation of conjugational class distinctions in
inflectional desinences.
Neither justice nor charity? Kant on ‘general injustice’
Authors: Moran Kate A.
Published: November 2016

We often make a distinction between what we owe as a matter of repayment, and what we give or offer out of charity. But how shall we describe our obligations to fellow citizens when we are in a position to be charitable because of a past injustice on the part of the state? This essay examines the moral implications of past injustice by considering Immanuel Kant’s remarks on this phenomenon in his lectures and writings. In particular, it discusses the role of the state and the individual in addressing the problem.
Relationships between the expression of hepatocyte nuclear factors and factors essential for lipoprotein production in a human mesenchymal stem cell line, UE7T-13
Authors: Sasaki Akira , Hiwatashi Kazuyuki , Kumagai Masanori , Hata Keishi , Kobayashi Masayuki
Published: November 2016

To clarify the mechanisms regulating lipoprotein production by hepatocyte nuclear factors (HNFs), we generated four kinds of transfectants in human bone marrow mesenchymal stem cells: UE7T-13, stably expressing FOXA2 (also known as HNF3β), HNF4α, HNF1α or co-expressing HNF4α, and HNF1α (HNF4α/HNF1α). In HNF4α/HNF1α transfectants, cellular contents of triglycerides (TG) and cholesterol were markedly higher than in UE7T-13 cells and comparable to those in human hepatoma HepG2 cells. However, TG and cholesterol, which are secreted from cells as components of lipoproteins, were hardly detected in the medium for any of the transfectants. ApoB100 and MTP, which are essential for the formation and secretion of lipoproteins, were undetectable and detected at low levels, respectively, in HNF4α/HNF1α transfectants. We suggest that enforced co-expression of HNF4α and HNF1α is effective for cellular lipid accumulation, while additional factors are probably required for lipoprotein formation and secretion.
Modelling of preconditioning by blasting in block and panel caving
Authors: Catalan Alex , Onederra Italo
Published: November 2016

This paper discusses the results of design and modelling work conducted to estimate the extent of preconditioning from the effect of multiple explosive charges detonated simultaneously within typical block and panel caving layouts. The analysis was conducted to support existing and future implementation strategies of both conventional and higher intensity preconditioning by blasting. The work builds upon research previously published by the authors that concerned the modelling of fracturing, disturbed and interaction zones in confined blasting. In this instance, the Hybrid Stress Blasting Model was used to determine the disturbed and interaction zones for several scenarios involving 3–6 hole layouts. Modelling configurations were divided into two groups: (1) blastholes drilled from the undercut level, and (2) blastholes drilled from both the extraction and undercut levels. The first group considered four design patterns, with the analysis focusing on assessing whether a mining design layout of 32 × 20 m, using inclined holes were able to achieve positive interaction to increase the extent of preconditioning within the volume of interest. The second phase examined two designs where one and two additional holes are drilled from the extraction level in order to maximise the disturbed and interaction zones between blastholes. Variables such as the velocity of detonation; explosive density; intact rock mass strength and in situ the stress field were considered. Results indicated that the pattern that could maximise the extent of the disturbed zone and potential ‘interaction’ between blastholes was a six hole pattern drilled from both the undercut and extraction levels. This design is referred to as ‘ ultra blast preconditioning’. Further work is currently underway to quantify the costs and potential downstream productivity benefits of this particular scenario.
Stress‐related psychological factors for back pain among athletes: Important topic with scarce evidence
Authors: Heidari Jahan , Hasenbring Monika , Kleinert Jens , Kellmann Michael
Published: November 2016

Health issues represent a frequent problem for athletes, as this particular demographic is repeatedly confronted with physically and psychologically stressful situations. Back pain (BP) materialises as comparatively common health problem being regarded as functionally limiting and psychologically straining burden for athletes. According to research conducted on athletes with BP, biomechanical and physiological mechanisms emerge as influential, whereas stress‐related psychological factors appear to be neglected. For athletic injuries, the essential impact of psychological processes on injury occurrence and return from injury has already been corroborated. Hence, the aim of this literature review is to: (1) introduce a conceptual differentiation between injuries and BP; (2) summarise the results obtained regarding stress‐related psychological aspects for injuries; and (3) connect the injury research to the state‐of‐the‐art evidence regarding stress‐related factors for BP among athletes. A distinction between injuries and BP could be established based on previous definitions, despite the fact that a considerable overlap between both concepts prevails. Injuries can be attributed to a physical origin, whereas BP frequently lacks this physical criterion. For BP, our enquiry yielded four studies including psychological measures of stress – with two studies specifically examining the association between BP and psychological stress among athletes longitudinally. Abundant findings from the general population support the importance of considering psychological and specifically stress‐related factors in BP prevention and rehabilitation, but evidence related to the athletic field remains elusive. Further scientific investigations with a wider methodological approach are needed to deepen the knowledge about the crucial relationship between psychological stress, BP, and athletes.
Job Dekker: Hitting the scientific hi-Cs
Authors: O’Donnell Marie Anne
Published: November 2016

Dekker investigates the three-dimensional organization of the genome.
STAT1 regulates marginal zone B cell differentiation in response to inflammation and infection with blood-borne bacteria
Authors: Chen Ting-Ting , Tsai Ming-Hsun , Kung John T. , Lin Kuo-I , Decker Thomas , Lee Chien-Kuo
Published: November 2016

Marginal zone B (MZ B) cells can rapidly produce antibody in response to infection with blood-borne encapsulated pathogens. Although TLR-mediated activation of MZ B is known to trigger humoral immune response, the signal cascade directing this response remains undefined. Here, we demonstrate that STAT1 plays an essential role in TLR-mediated antibody response of MZ B cells. Further, the TLR-induced IgM response is impaired in a type I and type II IFN-independent manner. Although activation, proliferation, and apoptosis are not affected, both differentiation into plasma cells and IgM production are impaired in Stat1−/− MZ B cells. Interestingly, STAT1 directly regulates the expression of Prdm1 (encodes BLIMP-1) by binding to its promoter, and Prdm1 expression is reduced in Stat1−/− MZ B cells. Restoration of BLIMP-1 to cells rescues TLR-induced IgM response. Moreover, Stat1−/− mice are more susceptible to S. pneumoniae infection, which can be rescued by the serum of bacteria-primed WT mice. The increased susceptibility to S. pneumoniae infection in Stat1−/− mice is also intrinsic to STAT1 requirement in MZ B cells. Collectively, these results define a differential regulation of TLR-mediated activation and differentiation of MZ B cells by STAT1 and reveal a STAT1-dependent, but IFN-independent, antibody response during infection and inflammation.
Systemic toxoplasma infection triggers a long-term defect in the generation and function of naive T lymphocytes
Authors: Kugler David G. , Flomerfelt Francis A. , Costa Diego L. , Laky Karen , Kamenyeva Olena , Mittelstadt Paul R. , Gress Ronald E. , Rosshart Stephan P. , Rehermann Barbara , Ashwell Jonathan D. , Sher Alan , Jankovic Dragana
Published: November 2016

Because antigen-stimulated naive T cells either die as effectors or enter the activated/memory pool, continuous egress of new T lymphocytes from thymus is essential for maintenance of peripheral immune homeostasis. Unexpectedly, we found that systemic infection with the protozoanToxoplasma gondiitriggers not only a transient increase in activated CD4+Th1 cells but also a persistent decrease in the size of the naive CD4+T lymphocyte pool. This immune defect is associated with decreased thymic output and parasite-induced destruction of the thymic epithelium, as well as disruption of the overall architecture of that primary lymphoid organ. Importantly, the resulting quantitative and qualitative deficiency in naive CD4+T cells leads to an immunocompromised state that both promotes chronic toxoplasma infection and leads to decreased resistance to challenge with an unrelated pathogen. These findings reveal that systemic infectious agents, such asT. gondii, can induce long-term immune alterations associated with impaired thymic function. When accumulated during the lifetime of the host, such events, even when occurring at low magnitude, could be a contributing factor in immunological senescence.
Euler-Lagrange equation for a minimization problem over monotone transport maps
Authors: Westdickenberg Michael
Published: November 2016

A variational time discretization for the compressible Euler equations has been introduced recently. It involves a minimization problem over the cone of monotone transport maps in each timestep. A matrix-valued measure field appears in the minimization as a Lagrange multiplier for the monotonicity constraint. We show that the absolutely continuous part of this measure field vanishes in the support of the density.
Creep Recovery of Wet Gluten and High‐Molecular‐Weight Glutenin Subunit Composition: Relationship with Viscoelasticity of Dough and Breadmaking Quality of Hard Red Winter Wheat
Authors: Hernández‐Estrada Zorba Josué , Rayas‐Duarte Patricia , Cárdenas Juan de Dios Figueroa
Published: November 2016

Effects of high‐molecular‐weight glutenin subunits on viscoelasticity of wet gluten, and its relationships with mixing, extensibility, and breadmaking parameters, were investigated by creep recovery using the Kelvin–Voigt model on 19 hard red winter wheat flours. Gluten samples with Glu‐A1 1 and 2* showed significant differences in retardation time (λ2), whereas subunit 17+18 in Glu‐B1 showed higher elastic moduli (G0, G1, and G2) and viscosity coefficients (η0, η1, and η2) compared with subunits 7+8 and 7+9. Wheats with Glu‐D1 5+10 had higher values of G0, G1, G2, η0, η1, and η2 compared with Glu‐D1 2+12. Gluten samples were on average 5.5, 3.1, and 1.6 times less stiff than dough when comparing G0, G1, and G2, respectively; these differences suggest that the nongluten components have high influence in the instantaneous and first Kelvin–Voigt elements of the model, and they are manifested more quickly compared with gluten components. Higher explanation of variance of loaf volume was found in parameters η2 and G2 (r = 0.57 and 0.58, respectively, P < 0.0001) compared with η1 and G1 (r = 0.45 and 0.56, P < 0.01 and 0.0001, respectively). These findings indicate that large structures formed primarily by crosslinking and agglomeration of glutenins of long chain sizes (second Kelvin–Voigt element) had major effects on quality compared with short chain sizes (first element).
Physicochemical and Functional Properties of Protein Isolates Obtained from Several Pea Cultivars
Authors: Lam Angie Che Yan , Warkentin Tom D. , Tyler Robert T. , Nickerson Michael T.
Published: November 2016

The goal of this research was to investigate the physicochemical and functional properties of protein isolates obtained from several pea cultivars grown at two locations in Canada. The functionalities of the pea protein isolates (PPIs) were then compared with those of commercial food protein ingredients derived from milk, egg, pea, soy, and wheat. Six pea cultivars (Agassiz, CDC Golden, CDC Dakota, CDC Striker, CDC Tetris, and Cooper) were collected from two years over two locations in Saskatchewan (Canada). Samples were evaluated for composition, surface properties, and functional properties. All PPIs had protein levels of ≈91% (db) and isolate and protein yields of ≈18 and ≈72%, respectively. Cultivars exhibited legumin/vicilin ratios from 0.36 (Agassiz) to 0.79 (CDC Golden). Differences among cultivars as well as significant cultivar × environment interactions were found only for maximum intrinsic fluorescence (195–267 arbitrary units), solubility (63–75%), and foaming capacity (167–244%). No differences owing to either cultivar or environment were observed for surface charge (zeta potential = approximately –24 mV), oil holding capacity (≈3.2 g/g), foam stability (≈75%), or emulsion stability (≈96%). Relative to the commercial isolates, PPIs prepared under laboratory conditions behaved most similarly to soy isolates, with the exception of solubility. Whey and egg were superior in solubility and foaming properties, whereas wheat and the commercial pea protein product were significantly lower in nearly all of the functionality tests. Based on their oil holding properties, the laboratory‐prepared PPIs may serve as good meat extenders. The findings also suggest that pea processors may not need to specify either the cultivar or the environment when acquiring raw material, thus creating advantages in their feedstock sourcing.
Physicochemical and Digestion Characteristics of Starch and Fiber‐Rich Subfractions from Four Pulse Bagasses
Authors: de la Rosa‐Millán Julián , Orona‐Padilla José L. , Flores‐Moreno Victor M. , Serna‐Saldívar Sergio O.
Published: November 2016

The aim of this study was to characterize the physicochemical, functional, and digestion properties of bagasses derived from broad beans, chickpeas, lentils, and white beans, and to isolate the starch and a fiber‐rich fraction that can be used as a food ingredient. The bagasses showed different chemical compositions that were related to their botanical origin. The further processing that involved mechanical separation of starch yielded up to 69.65% with ≥80.12% recovery and high purity (≥94.42%), and a fiber‐rich fraction (total dietary fiber content ≥72.75%) in which the majority was insoluble fiber. The starch digestion fractions of the isolated lentil starch showed the highest amount of slowly digestible starch (30.76%), whereas the white bean contained the highest resistant starch content (15.65%). All starches showed predicted glycemic indexes ≤ 66.90, which classify them as medium glycemic foods. In vitro protein digestion was higher for the bagasse fraction (up to 89.78%), followed by the fiber‐rich fraction (84.36%). This research demonstrates that it is possible to revalorize the use of pulses bagasse, which could contribute to enhance the technological and economic output of the protein isolation process, rendering two potentially functional fractions.
Oomycete Species Associated with Soybean Seedlings in North America—Part II: Diversity and Ecology in Relation to Environmental and Edaphic Factors
Authors: Rojas J. Alejandro , Jacobs Janette L. , Napieralski Stephanie , Karaj Behirda , Bradley Carl A. , Chase Thomas , Esker Paul D , Giesler Loren J , Jardine Doug J , Malvick Dean K , Markell Samuel G , Nelson Berlin D , Robertson Alison E , Rupe John C , Smith Damon L , Sweets Laura E , Tenuta Albert U , Wise Kiersten A , Chilvers Martin I
Published: November 2016

Soybean (Glycine max (L.) Merr.) is produced across a vast swath of North America, with the greatest concentration in the Midwest. Root rot diseases and damping-off are a major concern for production, and the primary causal agents include oomycetes and fungi. In this study, we focused on examination of oomycete species distribution in this soybean production system and how environmental and soil (edaphic) factors correlate with oomycete community composition at early plant growth stages. Using a culture-based approach, 3,418 oomycete isolates were collected from 11 major soybean-producing states and most were identified to genus and species using the internal transcribed spacer region of the ribosomal DNA. Pythium was the predominant genus isolated and investigated in this study. An ecology approach was taken to understand the diversity and distribution of oomycete species across geographical locations of soybean production. Metadata associated with field sample locations were collected using geographical information systems. Operational taxonomic units (OTU) were used in this study to investigate diversity by location, with OTU being defined as isolate sequences with 97% identity to one another. The mean number of OTU ranged from 2.5 to 14 per field at the state level. Most OTU in this study, classified as Pythium clades, were present in each field in every state; however, major differences were observed in the relative abundance of each clade, which resulted in clustering of states in close proximity. Because there was similar community composition (presence or absence) but differences in OTU abundance by state, the ordination analysis did not show strong patterns of aggregation. Incorporation of 37 environmental and edaphic factors using vector-fitting and Mantel tests identified 15 factors that correlate with the community composition in this survey. Further investigation using redundancy analysis identified latitude, longitude, precipitation, and temperature as factors that contribute to the variability observed in community composition. Soil parameters such as clay content and electrical conductivity also affected distribution of oomycete species. The present study suggests that oomycete species composition across geographical locations of soybean production is affected by a combination of environmental and edaphic conditions. This knowledge provides the basis to understand the ecology and distribution of oomycete species, especially those able to cause diseases in soybean, providing cues to develop management strategies.
Characterization of Postharvest Fungicide-Resistant Botrytis cinerea Isolates From Commercially Stored Apple Fruit
Authors: Jurick Wayne M. , Macarisin Otilia , Gaskins Verneta L. , Park Eunhee , Yu Jiujiang , Janisiewicz Wojciech , Peter Kari A.
Published: November 2016

Botrytis cinerea causes gray mold and is an economically important postharvest pathogen of fruit, vegetables, and ornamentals. Fludioxonil-sensitive B. cinerea isolates were collected in 2011 and 2013 from commercial storage in Pennsylvania. Eight isolates had values for effective concentrations for inhibiting 50% of mycelial growth of 0.0004 to 0.0038 μg/ml for fludioxonil and were dual resistant to pyrimethanil and thiabendazole. Resistance was generated in vitro, following exposure to a sublethal dose of fludioxonil, in seven of eight dual-resistant B. cinerea isolates. Three vigorously growing B. cinerea isolates with multiresistance to postharvest fungicides were further characterized and found to be osmosensitive and retained resistance in the absence of selection pressure. A representative multiresistant B. cinerea strain caused decay on apple fruit treated with postharvest fungicides, which confirmed the in vitro results. The R632I mutation in the Mrr1 gene, associated with fludioxonil resistance in B. cinerea, was not detected in multipostharvest fungicide-resistant B. cinerea isolates, suggesting that the fungus may be using additional mechanisms to mediate resistance. Results from this study show for the first time that B. cinerea with dual resistance to pyrimethanil and thiabendazole can also rapidly develop resistance to fludioxonil, which may pose control challenges in the packinghouse environment and during long-term storage.
Millstone: Software for Multiplex Microbial Genome Analysis and Engineering
Authors: Goodman Daniel B. , Kuznetsov Gleb , Lajoie Marc J. , Ahern Brian W. , Napolitano Michael G. , Chen Kevin Y. , Chen Changping , Church George M.
Published: November 2016

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform which automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.
SUPPA2 provides fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
Authors: Trincado Juan L. , Entizne Juan C. , Hysenaj Gerald , Singh Babita , Skalic Miha , Elliott David J. , Eyras Eduardo
Published: November 2016

Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method for differential splicing analysis that addresses these challenges and enables streamlined analysis across multiple conditions taking into account biological variability. Using experimental and simulated data SUPPA2 achieves higher accuracy compared to other methods; especially at low sequencing depth and short read length, with important implications for cost-effective use of RNA-seq for splicing; and was able to identify novel Transformer2-regulated exons. We further analyzed two differentiation series to support the applicability of SUPPA2 beyond binary comparisons. This identified clusters of alternative splicing events enriched in microexons induced during differentiation of bipolar neurons, and a cluster enriched in intron retention events that are present at late stages during erythroblast differentiation. Our data suggest that SUPPA2 is a valuable tool for the robust investigation of the biological complexity of alternative splicing.
Environmental DNA Barcode Sequence Capture: Targeted, PCR-free Sequence Capture for Biodiversity Analysis from Bulk Environmental Samples
Authors: Shokralla Shadi , F. Gibson Joel , King Ian , J. Baird Donald , H. Janzen Daniel , Hallwachs Winnie , Hajibabaei Mehrdad
Published: November 2016

Environmental DNA analysis using PCR amplified marker genes has been a key application of high-throughput sequencing (HTS). However, PCR bias is a major drawback to gain accurate qualitative and quantitative biodiversity data. We developed a PCR-free approach using enrichment baits for species-specific mitochondrial cytochrome c oxidase 1(COI) DNA barcodes. The sequence capture was tested on species-rich bulk terrestrial and aquatic benthic samples. Hybridization capture recovered an average of 6 and 4.7 more arthropod orders than amplicon sequencing for terrestrial and benthic samples, respectively. For the terrestrial sample, the four most abundant arthropod orders comprised 94.0% of the sample biomass. These same four orders comprised 95.5% and 97.5% of the COI sequences recovered by amplification and capture, respectively. Hybridization capture recovered three arthropod orders that were detected by biomass analysis, but not by amplicon sequencing and two other insect orders that were not detected by either biomass or amplicon methods. These results indicate the advantage of using sequence capture for a more accurate analysis of biodiversity in bulk environmental samples. The protocol can be easily customized to other DNA barcode markers or gene regions of interest for a wide range of taxa or for a specific target group.
A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis
Authors: Simonini Sara , Deb Joyita , Moubayidin Laila , Stephenson Pauline , Valluru Manoj , Freire-Rios Alejandra , Sorefan Karim , Weijers Dolf , Friml Jiří , Østergaard Lars
Published: November 2016

Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant's life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormone-sensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants.
Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus
Authors: Gaal Tamas , Bratton Benjamin P. , Sanchez-Vazquez Patricia , Sliwicki Alexander , Sliwicki Kristine , Vegel Andrew , Pannu Rachel , Gourse Richard L.
Published: November 2016

The spatial organization of DNA within the bacterial nucleoid remains unclear. To investigate chromosome organization in Escherichia coli, we examined the relative positions of the ribosomal RNA (rRNA) operons in space. The seven rRNA operons are nearly identical and separated from each other by as much as 180° on the circular genetic map, a distance of ≥2 million base pairs. By inserting binding sites for fluorescent proteins adjacent to the rRNA operons and then examining their positions pairwise in live cells by epifluorescence microscopy, we found that all but rrnC are in close proximity. Colocalization of the rRNA operons required the rrn P1 promoter region but not the rrn P2 promoter or the rRNA structural genes and occurred with and without active transcription. Non-rRNA operon pairs did not colocalize, and the magnitude of their physical separation generally correlated with that of their genetic separation. Our results show that E. coli bacterial chromosome folding in three dimensions is not dictated entirely by genetic position but rather includes functionally related, genetically distant loci that come into close proximity, with rRNA operons forming a structure reminiscent of the eukaryotic nucleolus.
MEF2 transcription factors are key regulators of sprouting angiogenesis
Authors: Sacilotto Natalia , Chouliaras Kira M. , Nikitenko Leonid L. , Lu Yao Wei , Fritzsche Martin , Wallace Marsha D. , Nornes Svanhild , García-Moreno Fernando , Payne Sophie , Bridges Esther , Liu Ke , Biggs Daniel , Ratnayaka Indrika , Herbert Shane P. , Molnár Zoltán , Harris Adrian L. , Davies Benjamin , Bond Gareth L. , Bou-Gharios George , Schwarz John J. , De Val Sarah
Published: November 2016

Angiogenesis, the fundamental process by which new blood vessels form from existing ones, depends on precise spatial and temporal gene expression within specific compartments of the endothelium. However, the molecular links between proangiogenic signals and downstream gene expression remain unclear. During sprouting angiogenesis, the specification of endothelial cells into the tip cells that lead new blood vessel sprouts is coordinated by vascular endothelial growth factor A (VEGFA) and Delta-like ligand 4 (Dll4)/Notch signaling and requires high levels of Notch ligand DLL4. Here, we identify MEF2 transcription factors as crucial regulators of sprouting angiogenesis directly downstream from VEGFA. Through the characterization of a Dll4 enhancer directing expression to endothelial cells at the angiogenic front, we found that MEF2 factors directly transcriptionally activate the expression of Dll4 and many other key genes up-regulated during sprouting angiogenesis in both physiological and tumor vascularization. Unlike ETS-mediated regulation, MEF2-binding motifs are not ubiquitous to all endothelial gene enhancers and promoters but are instead overrepresented around genes associated with sprouting angiogenesis. MEF2 target gene activation is directly linked to VEGFA-induced release of repressive histone deacetylases and concurrent recruitment of the histone acetyltransferase EP300 to MEF2 target gene regulatory elements, thus establishing MEF2 factors as the transcriptional effectors of VEGFA signaling during angiogenesis.
Structural basis for snRNA recognition by the double-WD40 repeat domain of Gemin5
Authors: Jin Wenxing , Wang Yi , Liu Chao-Pei , Yang Na , Jin Mingliang , Cong Yao , Wang Mingzhu , Xu Rui-Ming
Published: November 2016

Assembly of the spliceosomal small nuclear ribonucleoparticle (snRNP) core requires the participation of the multisubunit SMN (survival of motor neuron) complex, which contains SMN and several Gemin proteins. The SMN and Gemin2 subunits directly bind Sm proteins, and Gemin5 is required for snRNP biogenesis and has been implicated in snRNA recognition. The RNA sequence required for snRNP assembly includes the Sm site and an adjacent 3′ stem–loop, but a precise understanding of Gemin5's RNA-binding specificity is lacking. Here we show that the N-terminal half of Gemin5, which is composed of two juxtaposed seven-bladed WD40 repeat domains, recognizes the Sm site. The tandem WD40 repeat domains are rigidly held together to form a contiguous RNA-binding surface. RNA-contacting residues are located mostly on loops between β strands on the apical surface of the WD40 domains. Structural and biochemical analyses show that base-stacking interactions involving four aromatic residues and hydrogen bonding by a pair of arginines are crucial for specific recognition of the Sm sequence. We also show that an adenine immediately 5′ to the Sm site is required for efficient binding and that Gemin5 can bind short RNA oligos in an alternative mode. Our results provide mechanistic understandings of Gemin5's snRNA-binding specificity as well as valuable insights into the molecular mechanism of RNA binding by WD40 repeat proteins in general.