bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Transglutaminase, Citrate Buffer, and Temperature on a Soft Wheat Flour Dough System
Authors: Bagagli Marcela P. , Jazaeri Sahar , Bock Jayne E. , Seetharaman Koushik , Sato Helia H.
Published: June 2014

Transglutaminase (TGase) can improve the functional characteristics of proteins by introducing covalent bonds inter‐ or intrachains. Temperature and pH interfere with the protein structure and the catalytic activity of enzymes. Because these three factors can act synergistically, TGase, citrate buffer, and temperature were evaluated for their effects on the rheological and chemical changes in low‐protein wheat flour dough. Dough strength, measured by microextension test, significantly increased with increasing levels of TGase (8 U/g of protein), with changes in pH of the citrate buffer (pH 6.5), and by the effect of interaction between these factors. The same trend was observed in the size‐exclusion HPLC measurements, indicating that these two parameters have the effect of increasing gluten protein aggregation. Temperature had a significant effect on dough extension, measured by microextension test. The changes in secondary structure of gluten protein were investigated by FTIR second‐derivative spectra (amide I region, 1,600–1,700 cm−1) and showed an increase in β‐sheet structures initiated by TGase, citrate buffer pH, and their interaction.
Targeted Gene Disruption of OsCERK1 Reveals Its Indispensable Role in Chitin Perception and Involvement in the Peptidoglycan Response and Immunity in Rice
Authors: Kouzai Yusuke , Mochizuki Susumu , Nakajima Keisuke , Desaki Yoshitake , Hayafune Masahiro , Miyazaki Hideo , Yokotani Naoki , Ozawa Kenjirou , Minami Eiichi , Kaku Hanae , Shibuya Naoto , Nishizawa Yoko
Published: June 2014

OsCERK1 is a rice receptor-like kinase that mediates the signal of a fungal cell wall component, chitin, by coordinating with a lysin motif (LysM)-containing protein CEBiP. To further elucidate the function of OsCERK1 in the defense response, we disrupted OsCERK1 using an Agrobacterium-mediated gene targeting system based on homologous recombination. In OsCERK1-disrupted lines, the generation of hydrogen peroxide and the alteration of gene expression in response to a chitin oligomer were completely abolished. The OsCERK1-disrupted lines also showed lowered responsiveness to a bacterial cell wall component, peptidoglycan. Yeast two-hybrid analysis indicated that OsCERK1 interacts with the LysM-containing proteins LYP4 and LYP6, which are known to participate in the peptidoglycan response in rice. Observation of the infection behavior of rice blast fungus (Magnaporthe oryzae) revealed that disruption of OsCERK1 led to increased hyphal growth in leaf sheath cells. Green fluorescent protein-tagged OsCERK1 was localized around the primary infection hyphae. These results demonstrate that OsCERK1 is indispensable for chitin perception and participates in innate immunity in rice, and also mediates the peptidoglycan response. It is also suggested that OsCERK1 mediates the signaling pathways of both fungal and bacterial molecular patterns by interacting with different LysM-containing receptor-like proteins.
Virus-Induced Gene Silencing Suggests (1,3;1,4)-β-glucanaseIs a Susceptibility Factor in the Compatible Russian Wheat Aphid–Wheat Interaction
Authors: Anderson Victoria A. , Haley Scott D. , Peairs Frank B. , van Eck Leon , Leach Jan E. , Lapitan Nora L. V.
Published: June 2014

The Russian wheat aphid (RWA), Diuraphis noxia (Kurdjumov), is a significant insect pest of wheat (Triticum aestivum L.) and has a major economic impact worldwide, especially on winter wheat in the western United States. The continuing emergence of new RWA biotypes virulent to existing resistance genes reinforces the need for more durable resistance. Studies have indicated that resistance in previously susceptible plants can be produced by knock-down of susceptibility genes or other genes involved in host plant susceptibility. Therefore, investigation into genes involved in compatible RWA–wheat interactions could be a feasible approach to achieving durable RWA resistance. The objective of this study was to test whether silencing (1,3;1,4)-β-glucanase, previously observed to be highly induced in susceptible compared with resistant wheat during aphid infestation, would confer resistance to a susceptible wheat genotype. Barley stripe mosaic virus–mediated virus-induced gene silencing was employed to test whether (1,3;1,4)-β-glucanase is involved in the susceptible reaction of ‘Gamtoos-S' (GS). Controlled infestation with U.S. biotype RWA2 was done to assess aphid reproduction and host symptom development. Aphids on (1,3;1,4)-β-glucanase-silenced plants reproduced less per day and had longer prenymphipositional periods than those on control GS plants. Furthermore, the (1,3;1,4)-β-glucanase-silenced plants exhibited less chlorosis and greater dry weight compared with GS. Aphid reproduction and host plant symptom development showed linear relationships with (1,3;1,4)-β-glucanase transcript levels. Our results suggest that (1,3;1,4)-β-glucanase is required for successful infestation by the RWA and may be a susceptibility factor that could be exploited as a potential target for RWA resistance breeding.
Initial Inoculum and Spatial Dispersal of Colletotrichum gloeosporioides, the Causal Agent of Strawberry Anthracnose Crown Rot
Authors: Rahman Mahfuzur , Ojiambo Peter , Louws Frank
Published: June 2014

Anthracnose crown rot (ACR), caused by Colletotrichum gloeosporioides, is a serious disease of strawberry (Fragaria × ananassa) in nurseries and fruiting fields in the southeastern United States. This study was conducted to determine the potential of alternative hosts for initial inoculum source and spread that causes ACR in strawberry nurseries. Results indicated that Parthenocissus quinquefolia is a noncultivated host of C. gloeosporioides in North Carolina and may serve as an initial inoculum source for planting material. Sources of inoculum data were complemented with a 2-year study of disease incidence and spread in simulated nursery production experiments. Sixty days after inoculation of the mother plants in the nursery, three different inoculation levels showed a significant positive correlation (r = 0.78, P < 0.004) with the quiescent infection (QI) incidence on the runner or daughter plants at the end of the nursery production cycle. Runner plant counts from different proportion of mother plants' inoculation treatments indicated that runner plant production was negatively and significantly (P < 0.001) affected by C. gloeosporioides. Infected tips used to produce transplants destined for fruit production resulted in 29.3 and 16.8% mortality in plug trays in 2007 and 2008, respectively. Tracking foliar QI incidence that resulted from dispersal of inoculum from an introduced point source in the nursery showed a sharp decline at 1 m and beyond from the inoculation focus. Although the exponential model (R2 = 0.92 to 0.94) had slightly higher coefficients of determination than the modified power law (R2 = 0.89 to 0.90), residual plots indicated that the modified power law model fit the disease gradient data better than the exponential model in both years. Results from our dispersal study indicated that rogueing of infected plants within a 4-m radius of infection foci would reduce the risk of transferring infected runner plants from the nursery to the fruiting field.
Coupling Spore Traps and Quantitative PCR Assays for Detection of the Downy Mildew Pathogens of Spinach (Peronospora effusa) and Beet (P. schachtii)
Authors: Klosterman Steven J. , Anchieta Amy , McRoberts Neil , Koike Steven T. , Subbarao Krishna V. , Voglmayr Hermann , Choi Young-Joon , Thines Marco , Martin Frank N.
Published: June 2014

Downy mildew of spinach (Spinacia oleracea), caused by Peronospora effusa, is a production constraint on production worldwide, including in California, where the majority of U.S. spinach is grown. The aim of this study was to develop a real-time quantitative polymerase chain reaction (qPCR) assay for detection of airborne inoculum of P. effusa in California. Among oomycete ribosomal DNA (rDNA) sequences examined for assay development, the highest nucleotide sequence identity was observed between rDNA sequences of P. effusa and P. schachtii, the cause of downy mildew on sugar beet and Swiss chard in the leaf beet group (Beta vulgaris subsp. vulgaris). Single-nucleotide polymorphisms were detected between P. effusa and P. schachtii in the 18S rDNA regions for design of P. effusa- and P. schachtii-specific TaqMan probes and reverse primers. An allele-specific probe and primer amplification method was applied to determine the frequency of both P. effusa and P. schachtii rDNA target sequences in pooled DNA samples, enabling quantification of rDNA of P. effusa from impaction spore trap samples collected from spinach production fields. The rDNA copy numbers of P. effusa were, on average, ≈3,300-fold higher from trap samples collected near an infected field compared with those levels recorded at a site without a nearby spinach field. In combination with disease-conducive weather forecasting, application of the assays may be helpful to time fungicide applications for disease management.
Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses
Authors: Dobrzyński Maciej , Nguyen Lan K. , Birtwistle Marc R. , von Kriegsheim Alexander , Blanco Fernández Alfonso , Cheong Alex , Kolch Walter , Kholodenko Boris N.
Published: June 2014

We show theoretically and experimentally a mechanism behind the emergence of wide or bimodal protein distributions in biochemical networks with nonlinear input–output characteristics (the dose–response curve) and variability in protein abundance. Large cell-to-cell variation in the nonlinear dose–response characteristics can be beneficial to facilitate two distinct groups of response levels as opposed to a graded response. Under the circumstances that we quantify mathematically, the two distinct responses can coexist within a cellular population, leading to the emergence of a bimodal protein distribution. Using flow cytometry, we demonstrate the appearance of wide distributions in the hypoxia-inducible factor-mediated response network in HCT116 cells. With help of our theoretical framework, we perform a novel calculation of the magnitude of cell-to-cell heterogeneity in the dose–response obtained experimentally.
A dynamic broadband reflector built from microscopic silica spheres in the ‘disco’ clam
Ctenoides ales
Authors: Dougherty Lindsey F. , Johnsen Sönke , Caldwell Roy L. , Marshall N. Justin
Published: June 2014

The ‘disco’ or ‘electric’ clam
Ctenoides ales
(Limidae) is the only species of bivalve known to have a behaviourally mediated photic display. This display is so vivid that it has been repeatedly confused for bioluminescence, but it is actually the result of scattered light. The flashing occurs on the mantle lip, where electron microscopy revealed two distinct tissue sides: one highly scattering side that contains dense aggregations of spheres composed of silica, and one highly absorbing side that does not. High-speed video confirmed that the two sides act in concert to alternate between vivid broadband reflectance and strong absorption in the blue region of the spectrum. Optical modelling suggests that the diameter of the spheres is nearly optimal for scattering visible light, especially at shorter wavelengths which predominate in their environment. This simple mechanism produces a striking optical effect that may function as a signal.
The contagious nature of imprisonment: an agent-based model to explain racial disparities in incarceration rates
Authors: Lum Kristian , Swarup Samarth , Eubank Stephen , Hawdon James
Published: June 2014

We build an agent-based model of incarceration based on the susceptible–infected–suspectible (SIS) model of infectious disease propagation. Our central hypothesis is that the observed racial disparities in incarceration rates between Black and White Americans can be explained as the result of differential sentencing between the two demographic groups. We demonstrate that if incarceration can be spread through a social influence network, then even relatively small differences in sentencing can result in large disparities in incarceration rates. Controlling for effects of transmissibility, susceptibility and influence network structure, our model reproduces the observed large disparities in incarceration rates given the differences in sentence lengths for White and Black drug offenders in the USA without extensive parameter tuning. We further establish the suitability of the SIS model as applied to incarceration by demonstrating that the observed structural patterns of recidivism are an emergent property of the model. In fact, our model shows a remarkably close correspondence with California incarceration data. This work advances efforts to combine the theories and methods of epidemiology and criminology.
Pressurized honeycombs as soft-actuators: a theoretical study
Authors: Guiducci Lorenzo , Fratzl Peter , Bréchet Yves J. M. , Dunlop John W. C.
Published: June 2014

The seed capsule of
Delosperma nakurense
is a remarkable example of a natural hygromorph, which unfolds its protecting valves upon wetting to expose its seeds. The beautiful mechanism responsible for this motion is generated by a specialized organ based on an anisotropic cellular tissue filled with a highly swelling material. Inspired by this system, we study the mechanics of a diamond honeycomb internally pressurized by a fluid phase. Numerical homogenization by means of iterative finite-element (FE) simulations is adapted to the case of cellular materials filled with a variable pressure fluid phase. Like its biological counterpart, it is shown that the material architecture controls and guides the otherwise unspecific isotropic expansion of the fluid. Deformations up to twice the original dimensions can be achieved by simply setting the value of input pressure. In turn, these deformations cause a marked change of the honeycomb geometry and hence promote a stiffening of the material along the weak direction. To understand the mechanism further, we also developed a micromechanical model based on the Born model for crystal elasticity to find an explicit relation between honeycomb geometry, swelling eigenstrains and elastic properties. The micromechanical model is in good qualitative agreement with the FE simulations. Moreover, we also provide the force-stroke characteristics of a soft actuator based on the pressurized anisotropic honeycomb and show how the internal pressure has a nonlinear effect which can result in negative values of the in-plane Poisson's ratio. As nature shows in the case of the
D. nakurense
seed capsule, cellular materials can be used not only as low-weight structural materials, but also as simple but convenient actuating materials.
Quantifying the correlation between spatially defined oxygen gradients and cell fate in an engineered three-dimensional culture model
Authors: Ardakani Amir G. , Cheema Umber , Brown Robert A. , Shipley Rebecca J.
Published: June 2014

A challenge in three-dimensional tissue culture remains the lack of quantitative information linking nutrient delivery and cellular distribution. Both
in vivo
and
in vitro
, oxygen is delivered by diffusion from its source (blood vessel or the construct margins). The oxygen level at a defined distance from its source depends critically on the balance of diffusion and cellular metabolism. Cells may respond to this oxygen environment through proliferation, death and chemotaxis, resulting in spatially resolved gradients in cellular density. This study extracts novel spatially resolved and simultaneous data on tissue oxygenation, cellular proliferation, viability and chemotaxis in three-dimensional spiralled, cellular collagen constructs. Oxygen concentration gradients drove preferential cellular proliferation rates and viability in the higher oxygen zones and induced chemotaxis along the spiral of the collagen construct; an oxygen gradient of 1.03 mmHg mm
−1
in the spiral direction induced a mean migratory speed of 1015 μm day
−1
. Although this movement was modest, it was effective in balancing the system to a stable cell density distribution, and provided insights into the natural cell mechanism for adapting cell number and activity to a prevailing oxygen regime.
Free and constrained inflation of a pre-stretched cylindrical membrane
Authors: Patil Amit , Nordmark Arne , Eriksson Anders
Published: June 2014

This paper presents the free and constrained inflation of a pre-stretched hyperelastic cylindrical membrane and a subsequent constrained deflation. The membrane material is assumed as a homogeneous and isotropic Mooney–Rivlin solid. The constraining soft cylindrical substrate is assumed to be a distributed linear stiffness normal to the undeformed surface. Both frictionless and adhesive contact are modelled during the inflation as an interaction between the dry surfaces of the membrane and the substrate. An adhesive contact is modelled during deflation. The free and constrained inflation yields governing equations and boundary conditions, which are solved by a finite difference method in combination with a fictitious time integration method. Continuity in the principal stretches and stresses at the contact boundary is dependent on the contact conditions and inflation–deflation phase. The pre-stretch has a counterintuitive softening effect on free and constrained inflation. The variation of limit point pressures with pre-stretch and the occurrence of a cusp point is shown. Interesting trends are observed in the stretch and stress distributions after the interaction of the membrane with soft substrate, which underlines the effect of material parameters, pre-stretch and constraining properties.
Cultural selection drives the evolution of human communication systems
Authors: Tamariz Monica , Ellison T. Mark , Barr Dale J. , Fay Nicolas
Published: June 2014

Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems.
Phylogenomics provides strong evidence for relationships of butterflies and moths
Authors: Kawahara Akito Y. , Breinholt Jesse W.
Published: June 2014

Butterflies and moths constitute some of the most popular and charismatic insects. Lepidoptera include approximately 160 000 described species, many of which are important model organisms. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. We generated a molecular dataset with 46 taxa, combining 33 new transcriptomes with 13 available genomes, transcriptomes and expressed sequence tags (ESTs). Using HaMStR with a Lepidoptera-specific core-orthologue set of single copy loci, we identified 2696 genes for inclusion into the phylogenomic analysis. Nucleotides and amino acids of the all-gene, all-taxon dataset yielded nearly identical, well-supported trees. Monophyly of butterflies (Papilionoidea) was strongly supported, and the group included skippers (Hesperiidae) and the enigmatic butterfly–moths (Hedylidae). Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with greater than or equal to 87% bootstrap support. Establishing confident relationships among the four most diverse macroheteroceran superfamilies was previously challenging, but we recovered 100% bootstrap support for the following relationships: ((Geometroidea, Noctuoidea), (Bombycoidea, Lasiocampoidea)). We present the first robust, transcriptome-based tree of Lepidoptera that strongly contradicts historical placement of butterflies, and provide an evolutionary framework for genomic, developmental and ecological studies on this diverse insect order.
Gracilibacillus alcaliphilus sp. nov., a facultative alkaliphile isolated from indigo fermentation liquor for dyeing
Authors: Hirota Kikue , Hanaoka Yoshiko , Nodasaka Yoshinobu , Yumoto Isao
Published: June 2014

A facultatively alkaliphilic, lactic-acid-producing and halophilic strain, designated SG103T, was isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample for dyeing prepared in a laboratory. 16S rRNA gene sequence phylogeny suggested that SG103T is a member of the genus

Gracilibacillus

with the closest relatives being ‘Gracilibacillus
xinjiangensis’ J2 (similarity: 97.06 %),

Gracilibacillus thailandensis

TP2-8T (97.06 %) and

Gracilibacillus halotolerans

NNT (96.87 %). Cells of the isolate stained Gram-positive and were facultatively anaerobic straight rods that were motile by peritrichous flagella. The strain grew at temperatures between 13 and 48 °C with the optimum at 39 °C. It grew in the range pH 7–10 with the optimum at pH 9. The isoprenoid quinone detected was menaquinone-7 (MK-7) and the DNA G+C content was 41.3 mol%. The whole-cell fatty acid profile mainly (>10 %) consisted of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Unlike other reported species of the genus

Gracilibacillus

, the strain lacked diphosphatidylglycerol as a major polar lipid. DNA–DNA hybridization experiments with strains exhibiting greater than 96.87 % 16S rRNA gene sequence similarity, ‘G. xinjiangensis’ J2,

G. thailandensis

TP2-8T and

G. halotolerans

NNT, revealed 2±4 %, 4±9 % and 3±2 % relatedness, respectively. On the basis of the differences in phenotypic and chemotaxonomic characteristics, and the results of phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data from reported species of the genus

Gracilibacillus

, strain SG103T merits classification as a members of a novel species, for which the name Gracilibacillus
alcaliphilus sp. nov. is proposed. The type strain is SG103T ( = JCM 17253T = NCIMB 14683T).
Salmonella methylglyoxal detoxification by STM3117-encoded lactoylglutathione lyase affects virulence in coordination with Salmonella pathogenicity island 2 and phagosomal acidification
Authors: Chakraborty Sangeeta , Chaudhuri Debalina , Balakrishnan Arjun , Chakravortty Dipshikha
Published: June 2014

Intracellular pathogens such asSalmonella entericaserovar Typhimurium (S. Typhimurium) manipulate their host cells through the interplay of various virulence factors. A multitude of such virulence factors are encoded on the genome ofS. Typhimurium and are usually organized in pathogenicity islands. The virulence-associated genomic stretch ofSTM3117–3120has structural features of pathogenicity islands and is present exclusively in non-typhoidal serovars ofSalmonella. It encodes metabolic enzymes predicted to be involved in methylglyoxal metabolism.STM3117-encoded lactoylglutathione lyase significantly impacts the proliferation of intracellularSalmonella. The deletion mutant ofSTM3117(Δlgl) fails to grow in epithelial cells but hyper-replicates in macrophages. This difference in proliferation outcome was the consequence of failure to detoxify methylglyoxal by Δlgl, which was also reflected in the form of oxidative DNA damage and upregulation ofkefBin the mutant. Within macrophages, the toxicity of methylglyoxal adducts elicits the potassium efflux channel (KefB) in the mutant which subsequently modulates the acidification of mutant-containing vacuoles (MCVs). The perturbation in the pH of the MCV milieu and bacterial cytosol enhances theSalmonellapathogenicity island 2 translocation in Δlgl, increasing its net growth within macrophages. In epithelial cells, however, the maturation of Δlgl-containing vacuoles were affected as these non-phagocytic cells maintain less acidic vacuoles compared to those in macrophages. Remarkably, ectopic expression of Toll-like receptors 2 and 4 on epithelial cells partially restored the survival of Δlgl. This study identified a novel metabolic enzyme inS. Typhimurium whose activity during intracellular infection within a given host cell type differentially affected the virulence of the bacteria.
It takes two to tango: two TatA paralogues and two redox enzyme-specific chaperones are involved in the localization of twin-arginine translocase substrates in Campylobacter jejuni
Authors: Liu Yang-Wei , Hitchcock Andrew , Salmon Robert C. , Kelly David J.
Published: June 2014

The food-borne zoonotic pathogen Campylobacter jejuni has complex electron transport chains required for growth in the host, many of which contain cofactored periplasmic enzymes localized by the twin-arginine translocase (TAT). We report here the identification of two paralogues of the TatA translocase component in C. jejuni strain NCTC 11168, encoded by cj1176c (tatA1) and cj0786 (tatA2). Deletion mutants constructed in either or both of the tatA1 and tatA2 genes displayed distinct growth and enzyme activity phenotypes. For sulphite oxidase (SorAB), the multi-copper oxidase (CueO) and alkaline phosphatase (PhoX), complete dependency on TatA1 for correct periplasmic activity was observed. However, the activities of nitrate reductase (NapA), formate dehydrogenase (FdhA) and trimethylamine N-oxide reductase (TorA) were significantly reduced in the tatA2 mutant. In contrast, the specific rate of fumarate reduction catalysed by the flavoprotein subunit of the methyl menaquinone fumarate reductase (MfrA) was similar in periplasmic fractions of both the tatA1 and the tatA2 mutants and only the deletion of both genes abolished activity. Nevertheless, unprocessed MfrA accumulated in the periplasm of the tatA1 (but not tatA2) mutant, indicating aberrant signal peptide cleavage. Surprisingly, TatA2 lacks two conserved residues (Gln8 and Phe39) known to be essential in Escherichia coli TatA and we suggest it is unable to function correctly in the absence of TatA1. Finally, only two TAT chaperones (FdhM and NapD) are encoded in strain NCTC 11168, which mutant studies confirmed are highly specific for formate dehydrogenase and nitrate reductase assembly, respectively. Thus, other TAT substrates must use general chaperones in their biogenesis.
Preparation of Synaptosomes from Postmortem Human Prefrontal Cortex
Authors: Smalheiser Neil R. , Lugli Giovanni
Published: June 2014

Synaptosomes are a popular type of isolated synaptic fraction intensively used in neuroscience and cell biology. They are prepared by layering on density gradients and thought to consist largely of axonal endings with attached postsynaptic structures (Morgan, 1976), in contrast to synaptoneurosomes (Hollingsworth et al, 1985) which are prepared by filtration and are thought to consist largely of pinched-off dendritic spines with attached presynaptic structures. Although most studies of synaptosomes have utilized rodent or primate tissue, a score of studies have employed human samples derived from surgical specimens or postmortem brain. We recently described the isolation of synaptosomes from human postmortem prefrontal cortex to study the expression of synaptic microRNAs and other small RNAs in depression, schizophrenia and bipolar disorder (Smalheiser et al, 2014). This protocol alluded to methods and modifications that are scattered among several publications, and did not explain the reasons for the procedures chosen. Because our protocol differs from other published human synaptosome protocols in a variety of respects, we present here a detailed description of synaptosome preparation that should facilitate the use of this standardized synaptic fraction by other workers.
Inducible Repression of Nuclear-Encoded Subunits of the Cytochrome b6f Complex in Tobacco Reveals an Extraordinarily Long Lifetime of the Complex
Authors: Hojka Marta , Thiele Wolfram , Tóth Szilvia Z. , Lein Wolfgang , Bock Ralph , Schöttler Mark Aurel
Published: June 2014

The biogenesis of the cytochrome b6f complex in tobacco (Nicotiana tabacum) seems to be restricted to young leaves, suggesting a high lifetime of the complex. To directly determine its lifetime, we employed an ethanol-inducible RNA interference (RNAi) approach targeted against the essential nuclear-encoded Rieske protein (PetC) and the small M subunit (PetM), whose function in higher plants is unknown. Young expanding leaves of both PetM and PetC  RNAi transformants bleached rapidly and developed necroses, while mature leaves, whose photosynthetic apparatus was fully assembled before RNAi induction, stayed green. In line with these phenotypes, cytochrome b6f complex accumulation and linear electron transport capacity were strongly repressed in young leaves of both RNAi transformants, showing that the M subunit is as essential for cytochrome b6f complex accumulation as the Rieske protein. In mature leaves, all photosynthetic parameters were indistinguishable from the wild type even after 14 d of induction. As RNAi repression of PetM and PetC was highly efficient in both young and mature leaves, these data indicate a lifetime of the cytochrome b6f complex of at least 1 week. The switch-off of cytochrome b6f complex biogenesis in mature leaves may represent part of the first dedicated step of the leaf senescence program.
(N-Phenylthiourea-κS)bis(triphenylphosphane-κP)silver(I) nitrate
Authors: Mekarat Sofia , Pakawatchai Chaveng , Saithong Saowanit
Published: June 2014

In the title salt, [Ag(C7H8N2S)(C18H15P)2]NO3, the coordination geometry about the AgIatom is shallow trigonal pyramidal, with the metal atom displaced by 0.372 (1) Å from the plane of the P and S atoms. In the crystal, the cations are linked to the anions by N—H...O hydrogen bonds, generating tetramers (two cations and two anions), which featureR22(8) andR44(8) loops. The cations are linked by weak C—H...π interactions, generating a three-dimensional network.
Diafenthiuron: 1-tert-butyl-3-(2,6-diisopropyl-4-phenoxyphenyl)thiourea
Authors: Jeon Youngeun , Kang Gihaeng , Cho Seonghwa , Kim Tae Ho
Published: June 2014

The title compound, C23H32N2OS, is a thiourea-based insecticide. The dihedral angle between the phenyl ring and the diisopropyl benzene ring plane is 73.18 (6)°, while that between the plane of the thiourea group and the diisopropyl benzene ring is 86.00 (5)°. Disorder was modelled for the S atom and the two methyl C atoms of the isopropyl group over two sets of sites with an occupancy ratio of 0.742 (4):0.258 (4). In the crystal, N—H...S hydrogen bonds link adjacent molecules, formingR22(8) inversion dimers that pack into chains along theb-axis direction.
N1-[(1H-Imidazol-2-yl)methylidene]-N4-phenylbenzene-1,4-diamine
Authors: Faizi Md. Serajul Haque , Mashrai Ashraf , Shahid M. , Ahmad Musheer
Published: June 2014

The title compound, C16H14N4, is non-planar with dihedral angles between the planes of the imidazole and phenylenediamine rings of 30.66 (4)° and between the planes of the phenylenediamine andN-phenyl rings of 56.63 (7)°. In the crystal, molecules are connected by N—H...N hydrogen bonds, generating a chain extending along theb-axis direction. The crystal structure is also stabilized by C—H...π interactions betweenN-phenyl and imidazole rings and slipped π–π stacking interactions between imidazole rings [centroid–centroid distance = 3.516 (4) Å] giving an overall two-dimensional layered structure lying parallel to (010).
[4-(Allyloxy)phenyl](phenyl)methanone
Authors: D'Vries Richard F. , Grande Carlos D. , Chaur Manuel N. , Ellena Javier A. , Advincula Rigoberto C.
Published: June 2014

The structure of the title compound, C16H14O2, features a dihedral angle of 54.4 (3)° between the aromatic rings. The allyl group is rotated by 37.4 (4)° relative to the adjacent benzene ring. The crystal packing is characterized by numerous C—H...O and C—H...π interactions. Most of these interactions occur in layers along (011). The layers are linked by C—H...π interactions along [100], forming a three-dimensional network.
2,6-Diamino-4-(4-chlorophenyl)-1-methyl-1,4-dihydropyridine-3,5-dicarbonitrile
Authors: Purushothaman Michael , Thanigaimani Kaliyaperumal , Arshad Suhana , Silambarasan Sekar , Razak Ibrahim Abdul , Ali Kather Mohideen Sithick
Published: June 2014

In the title compound, C14H12ClN5, the dihydropyridine ring adopts a shallow boat conformation. The dihedral angle between the plane of this ring and that of the chlorobenzene ring is 69.15 (15)°. In the crystal, molecules are linked by N—H...N and N—H...Cl hydrogen bonds, generating (001) sheets.
5-Amino-5′-bromo-6-(4-methylbenzoyl)-8-nitro-2,3-dihydro-1H-spiro[imidazo[1,2-a]pyridine-7,3′-indolin]-2′-one including an unknown solvate
Authors: Nagalakshmi R. A. , Suresh J. , Sivakumar S. , Kumar R. Ranjith , Lakshman P. L. Nilantha
Published: June 2014

In the title compound, C22H18BrN5O4, the central six-membered ring, derived from 1,4-dihydropyridine, adopts a distorted boat conformation with a puckering amplitude of 0.197 (3) Å, the imidazole ring adopts a twisted conformation with a puckering amplitude of 0.113 (3) Å, and the oxindole moiety is planar with an r.m.s. deviation of 0.0125 Å. Two intramolecular N—H...O hydrogen bonds are formed, each closing anS(6) loop. In the crystal, strong N—H...O hydrogen bonds lead to the formation of zigzag chains along thecaxis. These are consolidated in the three-dimensional crystal packing by weak N—H...O hydrogen bonding, as well as by C—H...O, C—H...Br and C—H...π interactions. A small region of electron density well removed from the main molecule was removed with the SQUEEZE procedure inPLATON[Spek (2009).Acta Cryst. D65, 148–155] following unsuccessful attempts to model it as a plausible solvent molecule. The unit-cell characteristics do not take into account this feature of the structure.
Bis[trans-difluoridotetrakis(pyridine-κN)chromium(III)] sodium tetrachloridozincate perchlorate from synchrotron data
Authors: Moon Dohyun , Ryoo Keon Sang , Choi Jong-Ha
Published: June 2014

The title salt, Na[CrF2(C5H5N)4]2[ZnCl4]ClO4, consists of two cationic CrIIIcomplexes, an Na+cation, one [ZnCl4]2−anion and one ClO4−anion. The CrIIIatoms are coordinated by four pyridine (py) N atoms and two F atoms in atransarrangement, displaying a distorted octahedral geometry. The mean Cr—N(py) and Cr—F bond lengths are 2.086 (8) and 1.864 (14) Å, respectively. The [ZnCl4]2−anion has a distorted tetrahedral geometry. The most notable feature of the crystal packing is the formation of weak pyridine–perchlorate C—H...O hydrogen bonds, resulting in supramolecular chains along theb-axis direction. The perchlorate anion was disordered over two sets of sites in a 0.868 (3):0.132 (3) ratio.
3-Cyano-N-methylpyridinium perchlorate
Authors: McCormick Cameron A. , Nguyen Vu D. , Koplitz Lynn V. , Mague Joel T.
Published: June 2014

In the crystal of the title molecular salt, C7H7N2+·ClO4−, the components are linked by C—H...O and C—H...N interactions, generating zigzag chains running parallel to [100].
2-Bromo-5-tert-butyl-N-methyl-N-[2-(methylamino)phenyl]-3-(1-methyl-1H-benzimidazol-2-yl)benzamide
Authors: Prasad Poonam Rajesh , Das Shikha , Singh Harkesh B. , Butcher Ray J.
Published: June 2014

In the title compound, C27H29BrN4O, benzimidazole ring system and the amide moiety are planar [r.m.s. deviations = 0.016 (2) and 0.017 (1) Å, respectively]. The molecule adopts a conformation in which the amide linkage is almost perpendicular to the central ring [dihedral angle = 85.79 (8)°], while the benzimidazole ring system makes a dihedral angle of 70.26 (11)° with the central ring. In the crystal, the molecules form dimers through N—H...O hydrogen bonds and C—H...O interactions. These dimers are further linked into zigzag ribbons along [201] by weak C—H...Br interactions. As a result of the bulky nature of the molecule, as evidenced by the large dihedral angles between rings, there is little evidence for any π–π interactions.
5-Bromo-3-ethylsulfinyl-2-(4-methylphenyl)-1-benzofuran
Authors: Choi Hong Dae , Seo Pil Ja , Lee Uk
Published: June 2014

In the title compound, C17H15BrO2S, the dihedral angle between the plane of the benzofuran ring system [r.m.s. deviation = 0.004 (3) Å] and that of the 4-methylphenyl ring is 0.9 (2)°. In the crystal, molecules are linked by C—H...O, C—H...π and Br...π [3.636 (2) Å] interactions, and by π–π interactions between the 4-methylphenyl and furan rings of neighbouring molecules [centroid–centroid distance = 3.650 (2) Å], forming a three-dimensional network.
1-[(Cyclohexylidene)amino]-3-(prop-2-en-1-yl)thiourea
Authors: Mohamed Shaaban K. , Mague Joel T. , Akkurt Mehmet , Hassan Alaa A. , Albayati Mustafa R.
Published: June 2014

The asymmetric unit of the title compound, C10H17N3S, consists of three symmetry-independent molecules with distinctly different conformations, as indicated for example by the C—N—C—C torsion angles of −155.9 (3), 89.9 (3) and 81.1 (4)° along the bond between thiourea and allyl units. In the crystal, molecules are connectedviaN—H...N and N—H...S hydrogen bonds into chains extending along [110] that are further associated through C—H...N interactions into layers parallel to (001). The allyl group in one of the independent molecules is disordered over two sets of sites with an occupancy ratio of 0.853 (6):0.147 (6).
Genetic structure of a hybrid zone between two violets, Viola rossii Hemsl. and V. bissetii Maxim.: dominance of F1 individuals in a narrow contact range
Authors: Nagano Yusuke , Hirao Akira S. , Itino Takao
Published: June 2014

The genetic composition of a hybrid zone can provide insight into the evolution of diversification in plants. We carried out morphological and amplified fragment length polymorphism analyses to investigate the genetic composition of a hybrid zone between two violets, Viola bissetii Hemsl. and Viola rossii Maxim. Our aim was to clarify the formation and maintenance of hybrids between these Viola species. We found that most hybrid individuals (V. bissetii × V. rossii) were of the F1 generation, with a few of the F2 generation. We found no backcrosses. The scarcity of post‐F1 hybrids indicates that a species barrier is established between the parental species. The F1‐dominated hybrid zone occupied only a narrow, intermediate ecotone between the parental habitats, suggesting that selection by environmental factors against hybrids may help to maintain the current conditions in this hybrid zone.
Natural Additives in Wheat‐Based Pasta and Noodle Products: Opportunities for Enhanced Nutritional and Functional Properties
Authors: Li Man , Zhu Ke‐Xue , Guo Xiao‐Na , Brijs Kristof , Zhou Hui‐Ming
Published: June 2014

Pasta products and noodles have been staple foods since ancient times in many countries all over the world. These cereal products are still increasingly popular worldwide for their convenience, nutritional properties, special flavor, and taste. Pasta and noodles are essentially the same type of food but differ in their raw materials and shaping process, as well as the people and regions in the world consuming them. Many additives have been developed and are being used today in pasta and noodle products for various purposes. However, due to lack of knowledge about specific uses for some additives, they are sometimes misused by manufacturers. This can lead to opposite technological effects instead and may even cause damage to human health. Due to consumer demands, interest now focuses on natural “green” food additives with broad‐spectrum functions, high effectiveness, and low toxicity. In order to provide detailed references for noodle and pasta production, as well as to provide ideas for developing new types of these products, here we summarize the types of natural additives that are being incorporated in pasta and noodle products, mainly for quality improvement and food preservation.
Zinc: The Metal of Life
Authors: Kaur Kuljeet , Gupta Rajiv , Saraf Shubhini A. , Saraf Shailendra K.
Published: June 2014

The importance of zinc was 1st reported for Aspergillus niger. It took over 75 y to realize that zinc is also an essential trace element for rats, and an additional 30 y went by before it was recognized that this was also true for humans. The adult body contains about 2 to 3 g of zinc. Zinc is found in organs, tissues, bones, fluids, and cells. It is essential for many physiological functions and plays a significant role in a number of enzyme actions in the living systems. Bioinformatics estimates report that 10% of the human proteome contains zinc‐binding sites. Based on its role in such a plethora of cellular components, zinc has diverse biological functions from enzymatic catalysis to playing a crucial role in cellular neuronal systems. Thus, based on the various published studies and reports, it is pertinent to state that zinc is one of the most important essential trace metals in human nutrition and lifestyle. Its deficiency may severely affect the homeostasis of a biological system. This review compiles the role of zinc in prophylaxis/therapeutics and provides current information about its effect on living beings.
Structure, Physicochemical Properties, Modifications, and Uses of Sorghum Starch
Authors: Zhu Fan
Published: June 2014

Sorghum has great drought resistance and can be cultivated on marginal lands with minimal input costs. Thus, the supply of sorghum starch, the major component of the seeds, can be cheap and sustainable. This review summarizes the present knowledge of extraction, composition, granular and molecular structures, physicochemical properties, modifications, and uses of sorghum starch, and provides suggestions for needed research to improve our understanding and utilization of this starch.
Molecular Methods in Food Safety Microbiology: Interpretation and Implications of Nucleic Acid Detection
Authors: Ceuppens Siele , Li Dan , Uyttendaele Mieke , Renault Pierre , Ross Paul , Ranst Marc Van , Cocolin Luca , Donaghy John
Published: June 2014

Because of increasing demand for rapid results, molecular techniques are now applied for the detection of microorganisms in foodstuffs. However, interpretation problems can arise for the results generated by molecular methods in relation to the associated public health risk. Discrepancies between results obtained by molecular and conventional culture methods stem from the difference in target, namely nucleic acids instead of actively growing microorganisms. Nucleic acids constitute 5% to 15% of the dry weight of all living cells and are relatively stable, even after cell death, so they may be present in a food matrix after the foodborne microorganisms have been inactivated. Therefore, interpretation of the public health significance of positive results generated by nucleic acid detection methods warrants some additional consideration. This review discusses the stability of nucleic acids in general and highlights the persistence of microbial nucleic acids after diverse food‐processing techniques based on data from the scientific literature. Considerable amounts of DNA and RNA (intact or fragmented) persist after inactivation of bacteria and viruses by most of the commonly applied treatments in the food industry. An overview of the existing adaptations for molecular assays to cope with these problems is provided, including large fragment amplification, flotation, (enzymatic) pretreatment, and various binding assays. Finally, the negligible risks of ingesting free microbial nucleic acids are discussed and this review ends with the future perspectives of molecular methods such as next‐generation sequencing in diagnostic and source attribution food microbiology.
Methods to Evaluate Uptake of Engineered Nanomaterials by the Alimentary Tract
Authors: Alger Heather , Momcilovic Dragan , Carlander David , Duncan Timothy V.
Published: June 2014

This article is one of a series of 4 that report on a task of the NanoRelease Food Additive project of the International Life Science Institute Center for Risk Science Innovation and Application to identify, evaluate, and develop methods that are needed to confidently detect, characterize, and quantify intentionally produced engineered nanomaterials (ENMs) released from food along the alimentary tract. This particular article focuses on the problem of detecting and characterizing ENMs in the various compartments of the alimentary tract after they have been ingested from dietary sources. An in depth analysis of the literature related to oral toxicity of ENMs is presented, paying particular attention to analytical methodology and sample preparation. The review includes a discussion of model systems that can be used to study oral uptake of ENMs in the absence of human toxicological data or other live‐animal studies. The strengths and weaknesses of various analytical and sample preparation techniques are discussed. The article concludes with a summary of findings and a discussion of potential knowledge gaps and targets for method development in this area.
Measurement Methods for the Oral Uptake of Engineered Nanomaterials from Human Dietary Sources: Summary and Outlook
Authors: Szakal Christopher , Tsytsikova Lyubov , Carlander David , Duncan Timothy V.
Published: June 2014

This article is one of a series of 4 that report on a task of the NanoRelease Food Additive (NRFA) project of the International. Life Science Institute Center for Risk Science Innovation and Application. The project aims are to identify, evaluate, and develop methods that are needed to confidently detect, characterize, and quantify intentionally produced engineered nanomaterials (ENMs) released from food along the alimentary tract. This particular article offers an overview of the NRFA project, describing the project scope and goals, as well as the strategy by which the task group sought to achieve these goals. A condensed description of the general challenge of detecting ENMs in foods and a brief review of available and emerging methods for ENM detection is provided here, paying particular attention to the kind of information that might be desired from an analysis and the strengths and weaknesses of the various approaches that might be used to attain this information. The article concludes with an executive summary of the task group's broad findings related to the 3 topic areas, which are covered in more detail in 3 subsequent articles in this series. The end result is a thorough evaluation of the state of ENM measurement science specifically as it applies to oral uptake of ENMs from human dietary sources.