bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemical warfare and survival strategies in bacterial range expansions
Authors: Weber Markus F. , Poxleitner Gabriele , Hebisch Elke , Frey Erwin , Opitz Madeleine
Published: May 2014

Dispersal of species is a fundamental ecological process in the evolution and maintenance of biodiversity. Limited control over ecological parameters has hindered progress in understanding of what enables species to colonize new areas, as well as the importance of interspecies interactions. Such control is necessary to construct reliable mathematical models of ecosystems. In our work, we studied dispersal in the context of bacterial range expansions and identified the major determinants of species coexistence for a bacterial model system of three
Escherichia coli
strains (toxin-producing, sensitive and resistant). Genetic engineering allowed us to tune strain growth rates and to design different ecological scenarios (cyclic and hierarchical). We found that coexistence of all strains depended on three strongly interdependent factors: composition of inoculum, relative strain growth rates and effective toxin range. Robust agreement between our experiments and a thoroughly calibrated computational model enabled us to extrapolate these intricate interdependencies in terms of phenomenological biodiversity laws. Our mathematical analysis also suggested that cyclic dominance between strains is not a prerequisite for coexistence in competitive range expansions. Instead, robust three-strain coexistence required a balance between growth rates and either a reduced initial ratio of the toxin-producing strain, or a sufficiently short toxin range.
Through the eyes of a bird: modelling visually guided obstacle flight
Authors: Lin Huai-Ti , Ros Ivo G. , Biewener Andrew A.
Published: May 2014

Various flight navigation strategies for birds have been identified at the large spatial scales of migratory and homing behaviours. However, relatively little is known about close-range obstacle negotiation through cluttered environments. To examine obstacle flight guidance, we tracked pigeons (Columba livia) flying through an artificial forest of vertical poles. Interestingly, pigeons adjusted their flight path only approximately 1.5 m from the forest entry, suggesting a reactive mode of path planning. Combining flight trajectories with obstacle pole positions, we reconstructed the visual experience of the pigeons throughout obstacle flights. Assuming proportional–derivative control with a constant delay, we searched the relevant parameter space of steering gains and visuomotor delays that best explained the observed steering. We found that a pigeon's steering resembles proportional control driven by the error angle between the flight direction and the desired opening, or gap, between obstacles. Using this pigeon steering controller, we simulated obstacle flights and showed that pigeons do not simply steer to the nearest opening in the direction of flight or destination. Pigeons bias their flight direction towards larger visual gaps when making fast steering decisions. The proposed behavioural modelling method converts the obstacle avoidance behaviour into a (piecewise) target-aiming behaviour, which is better defined and understood. This study demonstrates how such an approach decomposes open-loop free-flight behaviours into components that can be independently evaluated.
Reconciling the concurrent fast and slow cycling of proteins on gene promoters
Authors: Wang Yaolai , Liu Feng , Li Jun , Wang Wei
Published: May 2014

During gene transcription, proteins appear to cycle on and off some gene promoters with both long (tens of minutes) and short periods (no more than several minutes). The essence of these phenomena still remains unclear. Here, we propose a stochastic model for the state evolution of promoters in terms of DNA–protein interactions. The model associates the characteristics of microscopic molecular interactions with macroscopic measurable quantities. Through theoretical derivation, we reconcile the contradictory viewpoints on the concurrent fast and slow cycling; both the cycling phenomena are further reproduced by fitting simulation results to the experimental data on the
pS2
gene. Our results suggest that the fast cycling dictates how the proteins behave on the promoter and that stable binding hardly occurs. Different kinds of proteins rapidly bind/unbind the promoter at distinct transcriptional stages fulfilling specific functions; this feature is essentially manifested as the slow cycling of proteins when detected by chromatin immunoprecipitation assays. Thus, the slow cycling represents neither stable binding of proteins nor external modulation of the fast cycling. This work also reveals the relationship between the essence and measurement of transcriptional dynamics.
Hierarchical multiscale structure–property relationships of the red-bellied woodpecker (Melanerpes carolinus) beak
Authors: Lee Nayeon , Horstemeyer M. F. , Rhee Hongjoo , Nabors Ben , Liao Jun , Williams Lakiesha N.
Published: May 2014

We experimentally studied beaks of the red-bellied woodpecker to elucidate the hierarchical multiscale structure–property relationships. At the macroscale, the beak comprises three structural layers: an outer rhamphotheca layer (keratin sheath), a middle foam layer and an inner bony layer. The area fraction of each layer changes along the length of the beak giving rise to a varying constitutive behaviour similar to functionally graded materials. At the microscale, the rhamphotheca comprises keratin scales that are placed in an overlapping pattern; the middle foam layer has a porous structure; and the bony layer has a big centre cavity. At the nanoscale, a wavy gap between the keratin scales similar to a suture line was evidenced in the rhamphotheca; the middle foam layer joins two dissimilar materials; and mineralized collagen fibres were revealed in the inner bony layer. The nano- and micro-indentation tests revealed that the hardness (associated with the strength, modulus and stiffness) of the rhamphotheca layer (approx. 470 MPa for nano and approx. 320 MPa for micro) was two to three times less than that of the bony layer (approx. 1200 MPa for nano and approx. 630 MPa for micro). When compared to other birds (chicken, finch and toucan), the woodpecker's beak has more elongated keratin scales that can slide over each other thus admitting dissipation via shearing; has much less porosity in the bony layer thus strengthening the beak and focusing the stress wave; and has a wavy suture that admits local shearing at the nanoscale. The analysis of the woodpeckers' beaks provides some understanding of biological structural materials' mechanisms for energy absorption.
Synchrotron imaging reveals bone healing and remodelling strategies in extinct and extant vertebrates
Authors: Anné Jennifer , Edwards Nicholas P. , Wogelius Roy A. , Tumarkin-Deratzian Allison R. , Sellers William I. , van Veelen Arjen , Bergmann Uwe , Sokaras Dimosthenis , Alonso-Mori Roberto , Ignatyev Konstantin , Egerton Victoria M. , Manning Phillip L.
Published: May 2014

Current understanding of bone healing and remodelling strategies in vertebrates has traditionally relied on morphological observations through the histological analysis of thin sections. However, chemical analysis may also be used in such interpretations, as different elements are known to be absorbed and used by bone for different physiological purposes such as growth and healing. These chemical signatures are beyond the detection limit of most laboratory-based analytical techniques (e.g. scanning electron microscopy). However, synchrotron rapid scanning–X-ray fluorescence (SRS–XRF) is an elemental mapping technique that uniquely combines high sensitivity (ppm), excellent sample resolution (20–100 µm) and the ability to scan large specimens (decimetre scale) approximately 3000 times faster than other mapping techniques. Here, we use SRS–XRF combined with microfocus elemental mapping (2–20 µm) to determine the distribution and concentration of trace elements within pathological and normal bone of both extant and extinct archosaurs (Cathartes auraandAllosaurus fragilis). Results reveal discrete chemical inventories within different bone tissue types and preservation modes. Chemical inventories also revealed detail of histological features not observable in thin section, including fine structures within the interface between pathological and normal bone as well as woven texture within pathological tissue.
The scholar as craftsman: Derek de Solla Price and the reconstruction of a medieval instrument
Authors: Falk Seb
Published: May 2014

The Royal Society Conversaziones were biannual social evenings at which distinguished guests could learn about the latest scientific developments. The Conversazione in May 1952 featured an object that came to be called King Arthur's Table. It was a planetary equatorium, made in Cambridge's Cavendish Laboratory at the behest of Sir Lawrence Bragg. Conceived by the historian of science Derek de Solla Price as a huge, tangible realization of Chaucerian astronomy, it was displayed at the new Whipple Museum of the History of Science, discarded, stored incognito, catalogued with that whimsical name, and finally re-identified in 2012. This article examines the biography of that object and, through it, the early, inchoate years of the discipline of history of science in Cambridge. The process of disciplinary establishment involved a range of actors beyond well-known figures such as Herbert Butterfield and Joseph Needham; the roles of Price and Bragg are highlighted here. Study of these individuals, and of the collaboration that brought about the reconstruction, reveals much about the establishment of a discipline, as well as changing scholarly and curatorial attitudes towards replicas.
Identification of 2R-ohnologue gene families displaying the same mutation-load skew in multiple cancers
Authors: Tinti Michele , Dissanayake Kumara , Synowsky Silvia , Albergante Luca , MacKintosh Carol
Published: May 2014

The complexity of signalling pathways was boosted at the origin of the vertebrates, when two rounds of whole genome duplication (2R-WGD) occurred. Those genes and proteins that have survived from the 2R-WGD—termed 2R-ohnologues—belong to families of two to four members, and are enriched in signalling components relevant to cancer. Here, we find that while only approximately 30% of human transcript-coding genes are 2R-ohnologues, they carry 42–60% of the gene mutations in 30 different cancer types. Across a subset of cancer datasets, including melanoma, breast, lung adenocarcinoma, liver and medulloblastoma, we identified 673 2R-ohnologue families in which one gene carries mutations at multiple positions, while sister genes in the same family are relatively mutation free. Strikingly, in 315 of the 322 2R-ohnologue families displaying such a skew in multiple cancers, the same gene carries the heaviest mutation load in each cancer, and usually the second-ranked gene is also the same in each cancer. Our findings inspire the hypothesis that in certain cancers, heterogeneous combinations of genetic changes impair parts of the 2R-WGD signalling networks and force information flow through a limited set of oncogenic pathways in which specific non-mutated 2R-ohnologues serve as effectors. The non-mutated 2R-ohnologues are therefore potential therapeutic targets. These include proteins linked to growth factor signalling, neurotransmission and ion channels.
PINK1 deficiency in β-cells increases basal insulin secretion and improves glucose tolerance in mice
Authors: Deas Emma , Piipari Kaisa , Machhada Asif , Li Abi , Gutierrez-del-Arroyo Ana , Withers Dominic J. , Wood Nicholas W. , Abramov Andrey Y.
Published: May 2014

The Parkinson's disease (PD) gene,
PARK6
, encodes the PTEN-induced putative kinase 1 (PINK1) mitochondrial kinase, which provides protection against oxidative stress-induced apoptosis. Given the link between glucose metabolism, mitochondrial function and insulin secretion in β-cells, and the reported association of PD with type 2 diabetes, we investigated the response of PINK1-deficient β-cells to glucose stimuli to determine whether loss of PINK1 affected their function. We find that loss of PINK1 significantly impairs the ability of mouse pancreatic β-cells (MIN6 cells) and primary intact islets to take up glucose. This was accompanied by higher basal levels of intracellular calcium leading to increased basal levels of insulin secretion under low glucose conditions. Finally, we investigated the effect of PINK1 deficiency
in vivo
and find that PINK1 knockout mice have improved glucose tolerance. For the first time, these combined results demonstrate that loss of PINK1 function appears to disrupt glucose-sensing leading to enhanced insulin release, which is uncoupled from glucose uptake, and suggest a key role for PINK1 in β-cell function.
Optimally designing games for behavioural research
Authors: Rafferty Anna N. , Zaharia Matei , Griffiths Thomas L.
Published: May 2014

Computer games can be motivating and engaging experiences that facilitate learning, leading to their increasing use in education and behavioural experiments. For these applications, it is often important to make inferences about the knowledge and cognitive processes of players based on their behaviour. However, designing games that provide useful behavioural data are a difficult task that typically requires significant trial and error. We address this issue by creating a new formal framework that extends optimal experiment design, used in statistics, to apply to game design. In this framework, we use Markov decision processes to model players' actions within a game, and then make inferences about the parameters of a cognitive model from these actions. Using a variety of concept learning games, we show that in practice, this method can predict which games will result in better estimates of the parameters of interest. The best games require only half as many players to attain the same level of precision.
Deformation near a liquid contact line on an elastic substrate
Authors: Hui Chung-Yuen , Jagota Anand
Published: May 2014

The equilibrium configuration of a liquid drop on a solid is determined by local energy balance. For a very stiff substrate, energy balance is represented by Young's equation. The equilibrium configuration near a line separating three fluids, in contrast, is determined by a balance of forces—their surface tensions—which is represented graphically by Neumann's triangle. We argue that these two are limiting cases of the more general situation of a drop on an elastic substrate in which both configurational energy balance and force balance must be satisfied independently. By analysing deformation close to the contact line of a liquid drop on an elastic substrate, we show that the transition from the surface tension-dominated regime to the elasticity-dominated regime is controlled by a dimensionless parameter: the ratio of an elasto-capillary length to the characteristic length scale over which surface tension acts. Because of the influence of substrate elasticity, the contact angle is not necessarily given by Young's equation. For compliant solids, we show that the local deformation and stress fields near the contact line are governed by surface tensions. However, if surface tension happens to be different from surface energy, configurational energy balance may not be consistent with force balance.
Assessing host extinction risk following exposure to
Batrachochytrium dendrobatidis
Authors: Louca Stilianos , Lampo Margarita , Doebeli Michael
Published: May 2014

Wildlife diseases are increasingly recognized as a major threat to biodiversity. Chytridiomycosis is an emerging infectious disease of amphibians caused by the fungus
Batrachochytrium dendrobatidis
(
Bd
). Using a mathematical model and simulations, we study its effects on a generic riparian host population with a tadpole and adult life stage. An analytical expression for the basic reproduction quotient,
Q
o
, of the pathogen is derived. By sampling the entire relevant parameter space, we perform a statistical assessment of the importance of all considered parameters in determining the risk of host extinction, upon exposure to
Bd
. We find that
Q
o
not only gives a condition for the initial invasion of the fungus, but is in fact the best predictor for host extinction. We also show that the role of tadpoles, which in some species tolerate infections, is ambivalent. While tolerant tadpoles may provide a reservoir for the fungus, thus facilitating its persistence or even amplifying its outbreaks, they can also act as a
rescue buffer
for a stressed host population. Our results have important implications for amphibian conservation efforts.
The oxidative environment: a mediator of interspecies communication that drives symbiosis evolution
Authors: Moné Yves , Monnin David , Kremer Natacha
Published: May 2014

Symbiotic interactions are ubiquitous in nature and play a major role in driving the evolution of life. Interactions between partners are often mediated by shared signalling pathways, which strongly influence both partners' biology and the evolution of the association in various environments. As an example of ‘common language’, the regulation of the oxidative environment plays an important role in driving the evolution of symbiotic associations. Such processes have been occurring for billions of years, including the increase in Earth's atmospheric oxygen and the subsequent evolution of mitochondria. The effect of reactive oxygen species and reactive nitrogen species (RONS) has been characterized functionally, but the molecular dialogue between partners has not been integrated within a broader evolutionary context yet. Given the pleiotropic role of RONS in cell–cell communication, development and immunity, but also their associated physiological costs, we discuss here how their regulation can influence the establishment, the maintenance and the breakdown of various symbiotic associations. By synthesizing recent developments in redox biology, we aim to provide an interdisciplinary understanding of the influence of such mediators of interspecies communication on the evolution and stability of symbioses, which in turn can shape ecosystems and play a role in health and disease.
Sexual conflict over mating in
Gnatocerus cornutus
? Females prefer lovers not fighters
Authors: Okada Kensuke , Katsuki Masako , Sharma Manmohan D. , House Clarissa M. , Hosken David J.
Published: May 2014

Female mate choice and male–male competition are the typical mechanisms of sexual selection. However, these two mechanisms do not always favour the same males. Furthermore, it has recently become clear that female choice can sometimes benefit males that reduce female fitness. So whether male–male competition and female choice favour the same or different males, and whether or not females benefit from mate choice, remain open questions. In the horned beetle,
Gnatocerus cornutus,
males have enlarged mandibles used to fight rivals, and larger mandibles provide a mating advantage when there is direct male–male competition for mates. However, it is not clear whether females prefer these highly competitive males. Here, we show that female choice targets male courtship rather than mandible size, and these two characters are not phenotypically or genetically correlated. Mating with attractive, highly courting males provided indirect benefits to females but only via the heritability of male attractiveness. However, mating with attractive males avoids the indirect costs to daughters that are generated by mating with competitive males. Our results suggest that male–male competition may constrain female mate choice, possibly reducing female fitness and generating sexual conflict over mating.
Can environmental conditions experienced in early life influence future generations?
Authors: Burton Tim , Metcalfe Neil B.
Published: May 2014

The consequences of early developmental conditions for performance in later life are now subjected to convergent interest from many different biological sub-disciplines. However, striking data, largely from the biomedical literature, show that environmental effects experienced even before conception can be transmissible to subsequent generations. Here, we review the growing evidence from natural systems for these cross-generational effects of early life conditions, showing that they can be generated by diverse environmental stressors, affect offspring in many ways and can be transmitted directly or indirectly by both parental lines for several generations. In doing so, we emphasize why early life might be so sensitive to the transmission of environmentally induced effects across generations. We also summarize recent theoretical advancements within the field of developmental plasticity, and discuss how parents might assemble different ‘internal’ and ‘external’ cues, even from the earliest stages of life, to instruct their investment decisions in offspring. In doing so, we provide a preliminary framework within the context of adaptive plasticity for understanding inter-generational phenomena that arise from early life conditions.
The use of network analysis to study complex animal communication systems: a study on nightingale song
Authors: Weiss Michael , Hultsch Henrike , Adam Iris , Scharff Constance , Kipper Silke
Published: May 2014

The singing of song birds can form complex signal systems comprised of numerous subunits sung with distinct combinatorial properties that have been described as syntax-like. This complexity has inspired inquiries into similarities of bird song to human language; but the quantitative analysis and description of song sequences is a challenging task. In this study, we analysed song sequences of common nightingales (
Luscinia megarhynchos
) by means of a network analysis. We translated long nocturnal song sequences into networks of song types with song transitions as connectors. As network measures, we calculated shortest path length and transitivity and identified the ‘small-world’ character of nightingale song networks. Besides comparing network measures with conventional measures of song complexity, we also found a correlation between network measures and age of birds. Furthermore, we determined the numbers of in-coming and out-going edges of each song type, characterizing transition patterns. These transition patterns were shared across males for certain song types. Playbacks with different transition patterns provided first evidence that these patterns are responded to differently and thus play a role in singing interactions. We discuss potential functions of the network properties of song sequences in the framework of vocal leadership. Network approaches provide biologically meaningful parameters to describe the song structure of species with extremely large repertoires and complex rules of song retrieval.
Harnessing ant defence at fruits reduces bruchid seed predation in a symbiotic ant–plant mutualism
Authors: Pringle Elizabeth G.
Published: May 2014

In horizontally transmitted mutualisms, mutualists disperse separately and reassemble in each generation with partners genetically unrelated to those in the previous generation. Because of this, there should be no selection on either partner to enhance the other's reproductive output directly. In symbiotic ant–plant mutualisms, myrmecophytic plants host defensive ant colonies, and ants defend the plants from herbivores. Plants and ants disperse separately, and, although ant defence can indirectly increase plant reproduction by reducing folivory, it is unclear whether ants can also directly increase plant reproduction by defending seeds. The neotropical tree
Cordia alliodora
hosts colonies of
Azteca pittieri
ants. The trees produce domatia where ants nest at stem nodes and also at the node between the peduncle and the rachides of the infloresence. Unlike the stem domatia, these reproductive domatia senesce after the tree fruits each year. In this study, I show that the tree's resident ant colony moves into these ephemeral reproductive domatia, where they tend honeydew-producing scale insects and patrol the nearby developing fruits. The presence of ants significantly reduced pre-dispersal seed predation by
Amblycerus
bruchid beetles, thereby directly increasing plant reproductive output.
Morphological and functional diversity in therizinosaur claws and the implications for theropod claw evolution
Authors: Lautenschlager Stephan
Published: May 2014

Therizinosaurs are a group of herbivorous theropod dinosaurs from the Cretaceous of North America and Asia, best known for their iconically large and elongate manual claws. However, among Therizinosauria, ungual morphology is highly variable, reflecting a general trend found in derived theropod dinosaurs (Maniraptoriformes). A combined approach of shape analysis to characterize changes in manual ungual morphology across theropods and finite-element analysis to assess the biomechanical properties of different ungual shapes in therizinosaurs reveals a functional diversity related to ungual morphology. While some therizinosaur taxa used their claws in a generalist fashion, other taxa were functionally adapted to use the claws as grasping hooks during foraging. Results further indicate that maniraptoriform dinosaurs deviated from the plesiomorphic theropod ungual morphology resulting in increased functional diversity. This trend parallels modifications of the cranial skeleton in derived theropods in response to dietary adaptation, suggesting that dietary diversification was a major driver for morphological and functional disparity in theropod evolution.
The Plant Membrane-Associated REMORIN1.3 Accumulates in Discrete Perihaustorial Domains and Enhances Susceptibility to Phytophthora infestans
Authors: Bozkurt Tolga O. , Richardson Annis , Dagdas Yasin F. , Mongrand Sébastien , Kamoun Sophien , Raffaele Sylvain
Published: May 2014

Filamentous pathogens such as the oomycete Phytophthora infestans infect plants by developing specialized structures termed haustoria inside the host cells. Haustoria are thought to enable the secretion of effector proteins into the plant cells. Haustorium biogenesis, therefore, is critical for pathogen accommodation in the host tissue. Haustoria are enveloped by a specialized host-derived membrane, the extrahaustorial membrane (EHM), which is distinct from the plant plasma membrane. The mechanisms underlying the biogenesis of the EHM are unknown. Remarkably, several plasma membrane-localized proteins are excluded from the EHM, but the remorin REM1.3 accumulates around P. infestans haustoria. Here, we used overexpression, colocalization with reporter proteins, and superresolution microscopy in cells infected by P. infestans to reveal discrete EHM domains labeled by REM1.3 and the P. infestans effector AVRblb2. Moreover, SYNAPTOTAGMIN1, another previously identified perihaustorial protein, localized to subdomains that are mainly not labeled by REM1.3 and AVRblb2. Functional characterization of REM1.3 revealed that it is a susceptibility factor that promotes infection by P. infestans. This activity, and REM1.3 recruitment to the EHM, require the REM1.3 membrane-binding domain. Our results implicate REM1.3 membrane microdomains in plant susceptibility to an oomycete pathogen.
CYTOKININ OXIDASE/DEHYDROGENASE4 Integrates Cytokinin and Auxin Signaling to Control Rice Crown Root Formation
Authors: Gao Shaopei , Fang Jun , Xu Fan , Wang Wei , Sun Xiaohong , Chu Jinfang , Cai Baodong , Feng Yuqi , Chu Chengcai
Published: May 2014

Crown roots constitute the majority of the rice (Oryza sativa) root system and play an important role in rice growth and development. However, the molecular mechanism of crown root formation in rice is not well understood. Here, we characterized a rice dominant mutant, root enhancer1 (ren1-D), which was observed to exhibit a more robust root system, increased crown root number, and reduced plant height. Molecular and genetic analyses revealed that these phenotypes are caused by the activation of a cytokinin oxidase/dehydrogenase (CKX) family gene, OsCKX4. Subcellular localization demonstrated that OsCKX4 is a cytosolic isoform of CKX. OsCKX4 is predominantly expressed in leaf blades and roots. It is the dominant CKX, preferentially expressed in the shoot base where crown root primordia are produced, underlining its role in root initiation. OsCKX4 is induced by exogenous auxin and cytokinin in the roots. Furthermore, one-hybrid assays revealed that OsCKX4 is a direct binding target of both the auxin response factor OsARF25 and the cytokinin response regulators OsRR2 and OsRR3. Overexpression and RNA interference of OsCKX4 confirmed that OsCKX4 plays a positive role in crown root formation. Moreover, expression analysis revealed a significant alteration in the expression of auxin-related genes in the ren1-D mutants, indicating that the OsCKX4 mediates crown root development by integrating the interaction between cytokinin and auxin. Transgenic plants harboring OsCKX4 under the control of the root-specific promoter RCc3 displayed enhanced root development without affecting their shoot parts, suggesting that this strategy could be a powerful tool in rice root engineering.
Phosphoproteomic Analyses Reveal Early Signaling Events in the Osmotic Stress Response
Authors: E. Stecker Kelly , Minkoff Benjamin B. , Sussman Michael R.
Published: May 2014

Elucidating how plants sense and respond to water loss is important for identifying genetic and chemical interventions that may help sustain crop yields in water-limiting environments. Currently, the molecular mechanisms involved in the initial perception and response to dehydration are not well understood. Modern mass spectrometric methods for quantifying changes in the phosphoproteome provide an opportunity to identify key phosphorylation events involved in this process. Here, we have used both untargeted and targeted isotope-assisted mass spectrometric methods of phosphopeptide quantitation to characterize proteins in Arabidopsis (Arabidopsis thaliana) whose degree of phosphorylation is rapidly altered by hyperosmotic treatment. Thus, protein phosphorylation events responsive to 5 min of 0.3 m mannitol treatment were first identified using 15N metabolic labeling and untargeted mass spectrometry with a high-resolution ion-trap instrument. The results from these discovery experiments were then validated using targeted Selected Reaction Monitoring mass spectrometry with a triple quadrupole. Targeted Selected Reaction Monitoring experiments were conducted with plants treated under nine different environmental perturbations to determine whether the phosphorylation changes were specific for osmosignaling or involved cross talk with other signaling pathways. The results indicate that regulatory proteins such as members of the mitogen-activated protein kinase family are specifically phosphorylated in response to osmotic stress. Proteins involved in 5′ messenger RNA decapping and phosphatidylinositol 3,5-bisphosphate synthesis were also identified as targets of dehydration-induced phosphoregulation. The results of these experiments demonstrate the utility of targeted phosphoproteomic analysis in understanding protein regulation networks and provide new insight into cellular processes involved in the osmotic stress response.
Strigolactone Hormones and Their Stereoisomers Signal through Two Related Receptor Proteins to Induce Different Physiological Responses in Arabidopsis
Authors: Scaffidi Adrian , Waters Mark T. , Sun Yueming K. , Skelton Brian W. , Dixon Kingsley W. , Ghisalberti Emilio L. , Flematti Gavin R. , Smith Steven M.
Published: May 2014

Two α/β-fold hydrolases, KARRIKIN INSENSITIVE2 (KAI2) and Arabidopsis thaliana DWARF14 (AtD14), are necessary for responses to karrikins (KARs) and strigolactones (SLs) in Arabidopsis (Arabidopsis thaliana). Although KAI2 mediates responses to KARs and some SL analogs, AtD14 mediates SL but not KAR responses. To further determine the specificity of these proteins, we assessed the ability of naturally occurring deoxystrigolactones to inhibit Arabidopsis hypocotyl elongation, regulate seedling gene expression, suppress outgrowth of secondary inflorescences, and promote seed germination. Neither 5-deoxystrigol nor 4-deoxyorobanchol was active in KAI2-dependent seed germination or hypocotyl elongation, but both were active in AtD14-dependent hypocotyl elongation and secondary shoot growth. However, the nonnatural enantiomer of 5-deoxystrigol was active through KAI2 in growth and gene expression assays. We found that the four stereoisomers of the SL analog GR24 had similar activities to their deoxystrigolactone counterparts. The results suggest that AtD14 and KAI2 exhibit selectivity to the butenolide D ring in the 2′R and 2′S configurations, respectively. However, we found, for nitrile-debranone (CN-debranone, a simple SL analog), that the 2′R configuration is inactive but that the 2′S configuration is active through both AtD14 and KAI2. Our results support the conclusion that KAI2-dependent signaling does not respond to canonical SLs. Furthermore, racemic mixtures of chemically synthesized SLs and their analogs, such as GR24, should be used with caution because they can activate responses that are not specific to naturally occurring SLs. In contrast, the use of specific stereoisomers might provide valuable information about the specific perception systems operating in different plant tissues, parasitic weed seeds, and arbuscular mycorrhizae.
Nickel hexayttrium decaiodide, [NiY6]I10
Authors: Steinberg Simon , Meyer Gerd
Published: May 2014

Comproportionation reactions of yttrium triiodide, yttrium and nickel led to the formation of the compound [NiY6]I10, which is isostructural with the prototypical [RuY6]I10. In particular, [NiY6]I10is composed of isolated nickel centered yttrium octahedra (site symmetry -1) that are further surrounded by iodide ligands to construct a three-dimensional cluster complex framework. Although this compound has been previously detected by powder X-ray diffraction techniques [Payne & Corbett (1990).Inorg. Chem.29, 2246–2251], details of the crystal structure for triclinic [NiY6]I10were not provided.
4-Azaniumyl-2,2,6,6-tetramethylpiperidin-1-ium dinitrate
Authors: Chebbi Hammouda , Ben Smail Ridha , Zid Mohamed Faouzi
Published: May 2014

In the crystal structure of the title salt, C9H22N22+·2NO3−, the piperidine ring of the dication adopts a chair conformation and the orientation of the C—NH3bond is equatorial. The ions are linked by normal and bifurcated N—H...O hydrogen bonds inR22(6), twoR42(8) andR34(14) graf-set motifs, generating a three-dimensional network.
Bis(1-methylpiperazine-1,4-diium) di-μ-bromido-bis[tetrabromidobismuthate(III)] dihydrate
Authors: Essid Manel , Roisnel Thierry , Marouani Houda
Published: May 2014

In the title hydrated salt, (C5H14N2)2[Bi2Br10]·2H2O, the complete [Bi2Br10]4−bioctahedron is generated by crystallographic inversion symmetry. The diprotonated piperazine ring adopts a chair conformation, with the methyl group occupying an equatorial position. In the crystal, the tetraanions and water molecules are linked by O—H...Br and O—H...(Br,Br) hydrogen bonds to generate [100] chains. The chains are crosslinked by N—H...Br, N—H...O and C—H...Br hydrogen bonds originating from the piperazinediium dications, thereby forming a three-dimensional network.
4-Phenyl-1,2,4-triazaspiro[4.6]undec-1-ene-3-thione
Authors: Mohamed Shaaban K. , Mague Joel T. , Akkurt Mehmet , Hassan Alaa A. , Albayati Mustafa R.
Published: May 2014

In the title compound, C14H17N3S, the plane of the phenyl ring makes a dihedral angle of 74.90 (4)° with that of the triazathione ring (r.m.s. deviation = 0.001 Å), while the seven-membered ring adopts a twist-chair conformation. No specific intermolecular interactions are discerned in the crystal packing.
3-Iodo-1H-pyrazolo[3,4-b]pyridine
Authors: Huang Ping-Hsin , Wen Yuh-Sheng , Shen Jiun-Yi
Published: May 2014

The title compound, C6H4IN3, is essentially planar, with a dihedral angle of 0.82 (3)° between the planes of the pyridine and pyrazole rings. In the crystal, pairs of molecules are connected into inversion dimers through N—H...N hydrogen bonds. C—I...N halogen bonds link the dimers into zigzag chains parallel to theb-axis direction. The packing also features π–π stacking interactions along (110) with interplanar distances of 3.292 (1) and 3.343 (1) Å, and centroid–centroid distances of 3.308 (1) and 3.430 (1) Å.
Deacetylcinobufalactam monohydrate
Authors: Tang Hong-Jin , Yuan Xiao-Feng , Tian Hai-Yan , Ruan Li-Jun , Jiang Ren-Wang
Published: May 2014

The title compound, C24H33NO4·H2O, the reaction product of deacetylcinobufagin with ammonium acetate, consists of three cyclohexane rings (A,BandC), one five-membered ring (D), one six-membered lactone ring (E) and an epoxide ring (F). The stereochemistry of the ring junctures areA/B cis,B/C trans,C/D cisandD/F cis. Cyclohexane ringsA,BandChave normal chair conformations. The five-membered ringDadopts an envelope conformation (with the C atom bearing the lactone ring as the flap) and the lactone ringEis planar. In the crystal, hydroxy and water O—H...O and amine N—H...O hydrogen bonds involving carbonyl, hydroxy and water O-atom acceptors link the molecules into a three-dimensional network.
Diethyl 7,7′-dichloro-4-oxo-4H-[1,4′-biquinoline]-3,3′-dicarboxylate
Authors: Ishikawa Yoshinobu , Sugisawa Yasuhiro
Published: May 2014

In the title compound, C24H18Cl2N2O5, the quinoline and quinolinone moieties are nearly perpendicular to each other, forming a dihedral angle of 82.36 (3)°. In the crystal, molecules form a halogen bond between a Cl atom of a quinolinone moiety and the N atom of the quinoline moiety of the inversion equivalent [Cl...N = 3.106 (3) Å]. The molecules also form two kinds of C—H...O hydrogen-bonded centrosymmetric inversion dimers, making chains along thec-axis direction which are further interlinked by the halogen bonds into layers parallel to thebcplane.
Favre–Racouchot syndrome concurrent with chronic granulomatous reaction
Authors: Zheng Li‐qiang , Han Xiang‐chun , Huang Yong , Li Hong‐wei , Niu Xiao‐dong
Published: May 2014

Favre–Racouchot syndrome (FRS) is a disorder consisting of solar elastosis with the presence of multiple cysts and open comedones. Although the exact mechanism of the condition is not known, FRS has been specifically connected to sun exposure, smoking and radiation exposure. The histological changes present in FRS reveal an atrophic epidermis and large masses of keratinous material, causing follicular plugging, as well as solar elastotic changes and possible basophilic degeneration of connective tissue. Herein, we report an unusual case of FRS concurrent with chronic granulomatous reaction and review relevant published works.
Warming decreases thermal heterogeneity of leaf surfaces: implications for behavioural thermoregulation by arthropods
Authors: Caillon Robin , Suppo Christelle , Casas Jérôme , Arthur Woods H. , Pincebourde Sylvain
Published: May 2014

Ectotherms rely heavily on the spatial variance of environmental conditions to thermoregulate. Theoretically, their fitness is maximized when they can find suitable microhabitats by moving over short distances – this condition is met when spatial variance is high at fine spatial scales. Strikingly, despite the diversity of organisms living in leaf microhabitats, little is known about the impact of warming on the spatial variance of climatic conditions at the scale of individual leaf surfaces.

Here, we used experimental manipulation of ambient conditions to quantify the effects of environmental change on the thermal heterogeneity within individual leaf surfaces. We also explored the implications for behavioural thermoregulation by arthropods at a single leaf surface.

Using thermography, we characterized the apple leaf microclimate in terms of span and spatial aggregation of surface temperatures across a range of air temperatures and relative humidities. Then, we assessed how thermal heterogeneity within individual leaves affected behavioural thermoregulation by the two‐spotted spider mite (Tetranychus urticae Koch) under both near‐optimal and sublethal conditions in this microhabitat. We measured the upper lethal temperature threshold of the mite to define sublethal exposure.

Thermal heterogeneity of individual leaves was driven mainly by ambient air temperature. Higher air temperatures gave both smaller ranges and higher spatial aggregation of temperatures at the leaf surface, such that the leaf microclimate was homogenized.

Tetranychus urticae used behavioural thermoregulation at moderate air temperature, when thermal heterogeneity was high at the leaf surface. At higher air temperature, however, heterogeneity declined and spider mites did not perform behavioural thermoregulation.

Warming decreases thermal heterogeneity of leaf surfaces with critical implications for arthropods – behavioural thermoregulation alone is not sufficient to escape the heat in the leaf microhabitat. Information on spatial variance of microclimatic conditions is critical for estimating how readily organisms can buffer global warming by moving.
Functional Properties of Vinegar
Authors: Budak Nilgün H. , Aykin Elif , Seydim Atif C. , Greene Annel K. , Guzel‐Seydim Zeynep B.
Published: May 2014

A variety of natural vinegar products are found in civilizations around the world. A review of research on these fermented products indicates numerous reports of health benefits derived by consumption of vinegar components. Therapeutic effects of vinegar arising from consuming the inherent bioactive components including acetic acid, gallic acid, catechin, ephicatechin, chlorogenic acid, caffeic acid, p‐coumaric acid, and ferulic acid cause antioxidative, antidiabetic, antimicrobial, antitumor, antiobesity, antihypertensive, and cholesterol‐lowering responses. The aims of this article are to discuss vinegar history, production, varieties, acetic acid bacteria, and functional properties of vinegars.
Network analysis in the identification of special mechanisms between small cell lung cancer and non‐small cell lung cancer
Authors: Zhang Weisan , Zhang Qiang , Zhang Mingpeng , Zhang Yun , Li Fengtan , Lei Ping
Published: May 2014

Background

To explore the similar and different pathogenesis between non‐small cell lung cancer (NSCLC) and small cell lung cancer (SCLC).

Methods

This study used bioinformatics methods, including functional enrichment analysis, compared the topological features of SCLC and NSCLC in the human protein interaction network in a system aspect, and analyzed the highly intense modules from an integrated network.

Results

This study included 5082 and 2781 significantly different expression genes for NSCLC and SCLC, respectively. The differently expressed genes of NSCLC are mainly distributed in the extracellular region and synapse. By contrast, the genes of SCLC are located in the organelle, macromolecular complex, membrane‐enclosed lumen, cell part, envelope, and synapse. Compared with SCLC, the differently expressed genes of NSCLC act in the biological regulation, multicellular organismal process, and viral reproduction and locomotion, which show that NSCLC is more likely to cause a wide range of cancer cell proliferation and virus infection than SCLC. The network topological properties of SCLC and NSCLC are similar, except the average shortest path length, which indicates that most of the genes of the two lung cancers play a similar function in the entire body. The commonly expressed genes show that all of the genes in the module may also cause NSCLC and SCLC, simultaneously.

Conclusions

The proteins in module will involve the same or similar biological functions and the interactions among them induce the occurrence of lung cancer. Moreover, a potential biomarker of SCLC is the interaction between APIP and apoptotic protease activating factor (APAF)1, which share a common module.
Preattentive dysfunction in patients with bipolar disorder as revealed by the pitch‐mismatch negativity: a magnetoencephalography (MEG) study
Authors: Shimano Satomi , Onitsuka Toshiaki , Oribe Naoya , Maekawa Toshihiko , Tsuchimoto Rikako , Hirano Shogo , Ueno Takefumi , Hirano Yoji , Miura Tomofumi , Kanba Shigenobu
Published: May 2014

Objectives

Mismatch negativity (MMN) and its magnetic counterpart (MMNm) are thought to reflect an automatic process that detects a difference between an incoming stimulus and the sensory memory trace of preceding stimuli. In patients with schizophrenia, an attenuation of the MMN/MMNm amplitude has been repeatedly reported. Heschl's gyrus (HG) is one of the major generators of MMN and the functional alteration of HG has been reported in patients with bipolar disorder. The present study investigated the pitch‐MMNm in patients with bipolar disorder using whole‐head 306‐ch magnetoencephalography (MEG).

Methods

Twenty‐two patients and 22 healthy controls participated in this study. Subjects were presented with two types of auditory stimulus sequences. One consisted of 1,000 Hz standards (probability = 90%) and 1,200 Hz deviants (probability = 10%), and the other consisted of 1,000 Hz standards (90%) and 1,200 Hz deviants (10%). These two tasks were each performed twice. Event‐related brain responses to standard tones were subtracted from responses to deviant tones.

Results

Patients with bipolar disorder showed a significant bilateral reduction in magnetic global field power (mGFP) amplitudes (p = 0.02) and dipole moments of the MMNm (p = 0.04) compared with healthy controls. Patients with admission experience showed significantly reduced mGFP amplitudes of MMNm compared with patients without admission experience (p = 0.004). Additionally, patients with more severe manic symptoms had smaller mGFP amplitudes of MMNm (ρ = −0.50, p = 0.05).

Conclusions

The results of this study suggest that patients with bipolar disorder may exhibit preattentive auditory dysfunction indexed by reduced pitch‐MMNm responses. Pitch‐MMNm could be a potential trait marker reflecting the global severity of bipolar disorder.