bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and characterization of suppressors of plant cell death (SPD) effectors from Magnaporthe oryzae
Authors: Sharpee William , Oh Yeonyee , Yi Mihwa , Franck William , Eyre Alex , Okagaki Laura H. , Valent Barbara , Dean Ralph A. 
Published: June 2016

SummaryPhytopathogenic microorganisms, including the fungal pathogen Magnaporthe oryzae, secrete a myriad of effector proteins to facilitate infection. Utilizing the transient expression of candidate effectors in the leaves of the model plant Nicotiana benthamiana, we identified 11 suppressors of plant cell death (SPD) effectors from M. oryzae that were able to block the host cell death reaction induced by Nep1. Ten of these 11 were also able to suppress BAX‐mediated plant cell death. Five of the 11 SPD genes have been identified previously as either essential for the pathogenicity of M. oryzae, secreted into the plant during disease development, or as suppressors or homologues of other characterized suppressors. In addition, of the remaining six, we showed that SPD8 (previously identified as BAS162) was localized to the rice cytoplasm in invaded and surrounding uninvaded cells during biotrophic invasion. Sequence analysis of the 11 SPD genes across 43 re‐sequenced M. oryzae genomes revealed that SPD2, SPD4 and SPD7 have nucleotide polymorphisms amongst the isolates. SPD4 exhibited the highest level of nucleotide diversity of any currently known effector from M. oryzae in addition to the presence/absence polymorphisms, suggesting that this gene is potentially undergoing selection to avoid recognition by the host. Taken together, we have identified a series of effectors, some of which were previously unknown or whose function was unknown, that probably act at different stages of the infection process and contribute to the virulence of M. oryzae.
Role of the nitrergic pathway in motor effects of oxytocin in rat proximal colon
Authors: Wang R. , Guo L. Y. , Suo M. Y. , Sun Y. , Wu J. Y. , Zhang X. Y. , Liu C. Y. 
Published: June 2016

AbstractBackgroundOxytocin (OT) reduces rat duodenal tone and mouse intestinal transit; however, the underlying mechanisms are not totally understood. Consequently, this study was designed to investigate the influence of OT on spontaneous mechanical activity and neurally evoked responses, to characterize the mechanisms of the action, and to determine the distribution of the OT receptor (OTR) in rat proximal colonic muscle strips.MethodsThe organ bath technique with electrical field stimulation, western blotting, and immunofluorescence were used.Key ResultsIn rat proximal colon, exogenous OT induced a concentration‐dependent reduction of the spontaneous mechanical activity without affecting the resting basal tone, which was abolished by atosiban, an OTR antagonist, by tetrodotoxin (TTX), a neural blocker or by Nω‐propyl‐l‐arginine hydrochloride, an inhibitor of neuronal nitric oxide synthase (nNOS). The inhibitory effects of OT were not affected by atropine or the vasoactive intestinal peptide (VIP) receptor antagonist [Lys1, Pro2,5, Arg3,4, Tyr6]‐VIP (VIPHyb). Proximal colon responses to electrical field stimulation were characterized by nonadrenergic, noncholinergic (NANC) relaxation, which was followed by an off‐contraction. Oxytocin enhanced only NANC relaxation. Oxytocin stimulated spontaneous NO release from the longitudinal muscle myenteric plexus preparation of rat proximal colon. Western blot and immunohistochemistry experiments showing the presence of the OTR in proximal colon, and its co‐localization with nNOS established that myenteric nitrergic neurons express OTR.Conclusions & InferencesThe activation of OTR located on nitrergic neurons may negatively modulate colonic spontaneous contraction and enhance electrically evoked NANC relaxation through excitation of NO release.
Scots pine fine roots adjust along a 2000‐km latitudinal climatic gradient
Authors: Zadworny Marcin , McCormack M. Luke , Mucha Joanna , Reich Peter B. , Oleksyn Jacek 
Published: June 2016

Summary

Patterns of plant biomass allocation and functional adjustments along climatic gradients are poorly understood, particularly belowground. Generally, low temperatures suppress nutrient release and uptake, and forests under such conditions have a greater proportion of their biomass in roots. However, it is not clear whether ‘more roots’ means better capacity to acquire soil resources.

Herein we quantified patterns of fine‐root anatomy and their biomass distribution across Scots pine (Pinus sylvestris) populations both along a 2000‐km latitudinal gradient and within a common garden experiment with a similar range of populations.

We found that with decreasing mean temperature, a greater percentage of Scots pine root biomass was allocated to roots with higher potential absorptive capacity. Similar results were seen in the common experimental site, where cold‐adapted populations produced roots with greater absorptive capacity than populations originating from warmer climates.

These results demonstrate that plants growing in or originated from colder climates have more acquisitive roots, a trait that is likely adaptive in the face of the low resource availability typical of cold soils.
Decaying in different clays: implications for soft‐tissue preservation
Authors: Naimark Elena , Kalinina Maria , Shokurov Alexander , Boeva Natalia , Markov Alexander , Zaytseva Liubov 
Published: June 2016

AbstractLagerstätten, places where soft‐bodied organisms became mineralized, provide a substantial bulk of palaeobiological information, but the detailed mechanisms of how soft‐tissue preservation takes place remain debatable. An experimental taphonomy approach, which allows for direct study of decay and mineralization, offers a means to study the preservational potential of different soft‐bodied organisms under controlled conditions. Here we compare the preservational capacity of two types of clay (kaolinite and montmorillonite) through a long‐term (24 month) experiment involving the burial and decay of small crustaceans. Our experimental design is innovative in that it models catastrophic sedimentation in fine‐grained colloidal suspension, which is believed to form Lagerstätten deposits. We demonstrated better preservation of buried organisms in clays compared to water, and in kaolinite compared to montmorillonite. As aluminium cations were present in high concentrations in kaolinite sediment but not in montmorillonite, the better preservation in kaolinite is attributed to the tanning properties of aluminium, which catalyses cross‐linking in proteins, protecting them from bacterial degradation. Anaerobic environments and acidification also slow down decay, but they are less effective than tanning. Kaolinite and montmorillonite replaced the crustacean integuments differently: in the remains buried in kaolinite, Al and Si were detected in equal proportions, while in those buried in montmorillonite, the Si content appeared to be much higher even in comparison with the initial sample of the clay. These variations probably arose from the different dynamics of acidic hydrolysis in the two clays associated with anaerobic decomposition of organic matter. Our results show that the preservation mechanism includes multi‐component interactions between the solution, mineral, sediment and organic remains; taken separately, any single component explains little. The specific conditions that occur within the colloidal clay sediments can facilitate conservation and start fast mineralization according to chemical properties and elemental content.
An ecophysiological and developmental perspective on variation in vessel diameter
Authors: Hacke Uwe G. , Spicer Rachel , Schreiber Stefan G. , Plavcová Lenka 
Published: June 2016

AbstractVariation in xylem vessel diameter is one of the most important parameters when evaluating plant water relations. This review provides a synthesis of the ecophysiological implications of variation in lumen diameter together with a summary of our current understanding of vessel development and its endogenous regulation. We analyzed inter‐specific variation of the mean hydraulic vessel diameter (Dv) across biomes, intra‐specific variation of Dv under natural and controlled conditions, and intra‐plant variation. We found that the Dv measured in young branches tends to stay below 30 µm in regions experiencing winter frost, whereas it is highly variable in the tropical rainforest. Within a plant, the widest vessels are often found in the trunk and in large roots; smaller diameters have been reported for leaves and small lateral roots. Dv varies in response to environmental factors and is not only a function of plant size. Despite the wealth of data on vessel diameter variation, the regulation of diameter is poorly understood. Polar auxin transport through the vascular cambium is a key regulator linking foliar and xylem development. Limited evidence suggests that auxin transport is also a determinant of vessel diameter. The role of auxin in cell expansion and in establishing longitudinal continuity during secondary growth deserve further study.
Target‐controlled versus fractionated propofol sedation in flexible bronchoscopy: A randomized noninferiority trial
Authors: Franzen Daniel , Bratton Daniel J. , Clarenbach Christian F. , Freitag Lutz , Kohler Malcolm 
Published: June 2016

AbstractBackground and objectiveFractionated propofol administration (FPA) in flexible bronchoscopy (FB) may lead to oversedation and an increased risk of adverse events, because a stable plasma concentration of propofol is not maintainable. The purpose of this randomized noninferiority trial was to evaluate whether target‐controlled infusion (TCI) of propofol is noninferior to FPA in terms of safety in FB.MethodsCoprimary outcomes were the mean lowest arterial oxygen saturation (SpO2) during FB and the number of propofol dose adjustments in relation to procedure duration. Secondary outcomes were the number of occasions with SpO2 < 90% and/or oxygen desaturations of >4% from baseline, number of occasions with systolic blood pressure < 90 mm Hg, cough frequency, cumulative propofol dose, recovery time, maximum transcutaneous CO2, mean SpO2 and O2 delivery during FB.ResultsSeventy‐seven patients were included. TCI was noninferior to FPA in terms of mean (standard deviation) lowest SpO2 during the procedure (88.3% (5.4%) vs 86.9% (7.3%)) and required fewer dose adjustments (0.04/min vs 0.28/min, P < 0.001) but a higher cumulative propofol dose (264 vs 194 mg, P = 0.003). All other secondary outcomes were comparable between the groups.ConclusionWe suggest that TCI of propofol is a favourable sedation technique for FB with equal safety issues and fewer dose adjustments compared with FPA.
Arabidopsis miR827 mediates post‐transcriptional gene silencing of its ubiquitin E3 ligase target gene in the syncytium of the cyst nematode Heterodera schachtii to enhance susceptibility
Authors: Hewezi Tarek , Piya Sarbottam , Qi Mingsheng , Balasubramaniam Muthukumar , Rice J. Hollis , Baum Thomas J. 
Published: June 2016

SummaryMicroRNAs (miRNAs) are a major class of small non‐coding RNAs with emerging functions in biotic and abiotic interactions. Here, we report on a new functional role of Arabidopsis miR827 and its NITROGEN LIMITATION ADAPTATION (NLA) target gene in mediating plant susceptibility to the beet cyst nematode Heterodera schachtii. Cyst nematodes are sedentary endoparasites that induce the formation of multinucleated feeding structures termed syncytia in the roots of host plants. Using promoter:GUS fusion assays we established that miR827 was activated in the initial feeding cells and this activation was maintained in the syncytium during all sedentary stages of nematode development. Meanwhile, the NLA target gene, which encodes an ubiquitin E3 ligase enzyme, was post‐transcriptionally silenced in the syncytium to permanently suppress its activity during all nematode parasitic stages. Overexpression of miR827 in Arabidopsis resulted in hyper‐susceptibility to H. schachtii. In contrast, inactivation of miR827 activity through target mimicry or by overexpression a miR827‐resistant cDNA of NLA produced the opposite phenotype of reduced plant susceptibility to H. schachtii. Gene expression analysis of several pathogenesis‐related genes together with Agrobacterium‐mediated transient expression in Nicotiana benthamiana provided strong evidence that miR827‐mediated downregulation of NLA to suppress basal defense pathways. In addition, using yeast two‐hybrid screens we identified several candidates of NLA‐interacting proteins that are involved in a wide range of biological processes and molecular functions, including three pathogenesis‐related proteins. Taken together, we conclude that nematode‐activated miR827 in the syncytium is necessary to suppress immune responses in order to establish infection and cause disease.
Comparison of the effects of intranasal and intramuscular administrations of zolazepam–tiletamine combination on intraocular pressure in cats
Authors: Yanmaz Latif Emrah , Dogan Elif , Okur Sitkican , Okumus Zafer , Ersoz Ugur 
Published: June 2016

AbstractObjectiveTo determine the effect of intranasal (IN) and intramuscular (IM administration of zolazepam‐tiletamine (ZT) combination on intraocular pressure (IOP).Animals studiedBoth eyes of 8 clinically normal cats were used.ProceduresThe animals received 10 mg/kg dose of ZT combination by IN and IM routes with a 7‐day interval between treatments. IOP values were measured at baseline (T0) and at 10, 15, 20, 25, 30, and 45 min in both treatment groups.ResultsThere were no statistically significant differences between baseline and post‐treatment IOP measurements. The IOP did not change over time regardless of administration route.ConclusionsZT combination did not have a significant effect on IOP in cats, when administered by IM or IN routes.
Molecular data and ecological niche modelling reveal the evolutionary history of the common and Iberian moles (Talpidae) in Europe
Authors: Nicolas Violaine , Martínez‐Vargas Jessica , Hugot Jean‐Pierre 
Published: June 2016

According to mitochondrial data, the common mole, Talpa europaea, is paraphyletic. This could be explained by either an ancient introgression of mtDNA from the Iberian blind mole T. occidentalis to T. europaea, or the existence of a differentiated taxonomic entity in northern Spain that needs to be described. In this study, we combined mitochondrial (Cytb) and nuclear (HDAC2) data to investigate these two alternative hypotheses. Based on both mitochondrial and nuclear data and an extensive geographical sampling (399 sequenced individuals), we show that the populations of T. europaea from Spain and south‐western France (south of the Loire River) are phylogenetically closer to T. occidentalis than to T. europaea. The Spanish–French lineage has some morphological characters resembling more to T. occidentalis (e.g. eyes) and others resembling more to T. europaea (external measurements, mesostyle of the first upper molar). It also seems to have several distinctive dental characters, suggesting that it should be recognized as a new species. Within the three lineages, we found a marked phylogeographical pattern, with several allopatric or parapatric lineages, dating from the Pleistocene. Our genetic data combined with species distribution models support the presence of several putative glacial refugia during glacial maxima for each species.
Hubs and spokes of the lateral hypothalamus: cell types, circuits and behaviour
Authors: Bonnavion Patricia , Mickelsen Laura E. , Fujita Akie , de Lecea Luis , Jackson Alexander C. 
Published: June 2016

AbstractThe hypothalamus is among the most phylogenetically conserved regions in the vertebrate brain, reflecting its critical role in maintaining physiological and behavioural homeostasis. By integrating signals arising from both the brain and periphery, it governs a litany of behaviourally important functions essential for survival. In particular, the lateral hypothalamic area (LHA) is central to the orchestration of sleep–wake states, feeding, energy balance and motivated behaviour. Underlying these diverse functions is a heterogeneous assembly of cell populations typically defined by neurochemical markers, such as the well‐described neuropeptides hypocretin/orexin and melanin‐concentrating hormone. However, anatomical and functional evidence suggests a rich diversity of other cell populations with complex neurochemical profiles that include neuropeptides, receptors and components of fast neurotransmission. Collectively, the LHA acts as a hub for the integration of diverse central and peripheral signals and, through complex local and long‐range output circuits, coordinates adaptive behavioural responses to the environment. Despite tremendous progress in our understanding of the LHA, defining the identity of functionally discrete LHA cell types, and their roles in driving complex behaviour, remain significant challenges in the field. In this review, we discuss advances in our understanding of the neurochemical and cellular heterogeneity of LHA neurons and the recent application of powerful new techniques, such as opto‐ and chemogenetics, in defining the role of LHA circuits in feeding, reward, arousal and stress. From pioneering work to recent developments, we review how the interrogation of LHA cells and circuits is contributing to a mechanistic understanding of how the LHA coordinates complex behaviour.
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Ion recombination correction in carbon ion beams
Authors: Rossomme S. , Hopfgartner J. , Lee N. D. , Delor A. , Thomas R. A. S. , Romano F. , Fukumura A. , Vynckier S. , Palmans H. 
Published: June 2016

Purpose:In this work, ion recombination is studied as a function of energy and depth in carbon ion beams.Methods:Measurements were performed in three different passively scattered carbon ion beams with energies of 62 MeV/n, 135 MeV/n, and 290 MeV/n using various types of plane‐parallel ionization chambers. Experimental results were compared with two analytical models for initial recombination. One model is generally used for photon beams and the other model, developed by Jaffé, takes into account the ionization density along the ion track. An investigation was carried out to ascertain the effect on the ion recombination correction with varying ionization chamber orientation with respect to the direction of the ion tracks. The variation of the ion recombination correction factors as a function of depth was studied for a Markus ionization chamber in the 62 MeV/n nonmodulated carbon ion beam. This variation can be related to the depth distribution of linear energy transfer.Results:Results show that the theory for photon beams is not applicable to carbon ion beams. On the other hand, by optimizing the value of the ionization density and the initial mean‐square radius, good agreement is found between Jaffé's theory and the experimental results. As predicted by Jaffé's theory, the results confirm that ion recombination corrections strongly decrease with an increasing angle between the ion tracks and the electric field lines. For the Markus ionization chamber, the variation of the ion recombination correction factor with depth was modeled adequately by a sigmoid function, which is approximately constant in the plateau and strongly increasing in the Bragg peak region to values of up to 1.06. Except in the distal edge region, all experimental results are accurately described by Jaffé's theory.Conclusions:Experimental results confirm that ion recombination in the investigated carbon ion beams is dominated by initial recombination. Ion recombination corrections are found to be significant and cannot be neglected for reference dosimetry and for the determination of depth dose curves in carbon ion beams.
A comprehensive formulation for volumetric modulated arc therapy planning
Authors: Nguyen Dan , Lyu Qihui , Ruan Dan , O'Connor Daniel , Low Daniel A. , Sheng Ke 
Published: June 2016

Purpose:Volumetric modulated arc therapy (VMAT) is a widely employed radiation therapy technique, showing comparable dosimetry to static beam intensity modulated radiation therapy (IMRT) with reduced monitor units and treatment time. However, the current VMAT optimization has various greedy heuristics employed for an empirical solution, which jeopardizes plan consistency and quality. The authors introduce a novel direct aperture optimization method for VMAT to overcome these limitations.Methods:The comprehensive VMAT (comVMAT) planning was formulated as an optimization problem with an L2‐norm fidelity term to penalize the difference between the optimized dose and the prescribed dose, as well as an anisotropic total variation term to promote piecewise continuity in the fluence maps, preparing it for direct aperture optimization. A level set function was used to describe the aperture shapes and the difference between aperture shapes at adjacent angles was penalized to control MLC motion range. A proximal‐class optimization solver was adopted to solve the large scale optimization problem, and an alternating optimization strategy was implemented to solve the fluence intensity and aperture shapes simultaneously. Single arc comVMAT plans, utilizing 180 beams with 2° angular resolution, were generated for a glioblastoma multiforme case, a lung (LNG) case, and two head and neck cases—one with three PTVs (H&N3PTV) and one with foue PTVs (H&N4PTV)—to test the efficacy. The plans were optimized using an alternating optimization strategy. The plans were compared against the clinical VMAT (clnVMAT) plans utilizing two overlapping coplanar arcs for treatment.Results:The optimization of the comVMAT plans had converged within 600 iterations of the block minimization algorithm. comVMAT plans were able to consistently reduce the dose to all organs‐at‐risk (OARs) as compared to the clnVMAT plans. On average, comVMAT plans reduced the max and mean OAR dose by 6.59% and 7.45%, respectively, of the prescription dose. Reductions in max dose and mean dose were as high as 14.5 Gy in the LNG case and 15.3 Gy in the H&N3PTV case. PTV coverages measured by D95, D98, and D99 were within 0.25% of the prescription dose. By comprehensively optimizing all beams, the comVMAT optimizer gained the freedom to allow some selected beams to deliver higher intensities, yielding a dose distribution that resembles a static beam IMRT plan with beam orientation optimization.Conclusions:The novel nongreedy VMAT approach simultaneously optimizes all beams in an arc and then directly generates deliverable apertures. The single arc VMAT approach thus fully utilizes the digital Linac's capability in dose rate and gantry rotation speed modulation. In practice, the new single VMAT algorithm generates plans superior to existing VMAT algorithms utilizing two arcs.