bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Diversity Study of Fusarium culmorum: Causal agent of wheat crown rot in Iraq
Authors: Matny O. N. , Shamsallah S. A. , Haas M. 
Published: June 2018

ABSTRACTFusarium crown rot (FCR), caused by Fusarium culmorum (Wm.G.Sm) Sacc., is an important disease of wheat both in Iraq and other regions of wheat production worldwide. Changes in environmental conditions and cultural practices such as crop rotation generate stress on pathogen populations leading to the evolution of new strains that can tolerate more stressful environments. This study aims to investigate the genetic diversity among isolates of F. culmorum in Iraq. Twenty-nine samples were collected from different regions of wheat cultivation in Iraq to investigate the pathogenicity and genetic diversity of F. culmorum using the REP-PCR technique. Among the twenty-nine isolates of F. culmorum examined for pathogenicity, 96% were pathogenic to wheat at the seedling stage. The most aggressive isolate, from Baghdad, was IF 0021 at 0.890 on the FCR severity index. Three primer sets were used to assess the genotypic diversity via REP, ERIC and BOX elements. The amplicon sizes ranged from 200-800 bp for BOX-ERIC2, 110-1100 bp for ERIC-ERIC2 and 200-1300 bp for REP. In total, 410 markers were polymorphic, including 106 for BOX, 175 for ERIC and 129 for the REP. Genetic similarity was calculated by comparing markers according to minimum variance (Squared Euclidean). Clustering analysis generated two major groups, group 1 with two subgroup 1a and 1b with 5 and 12 isolates respectively, and group 2 with two subgroups 2a and 2b with 3 and 9 isolates respectively. This is the first study in this field that has been reported in Iraq.
Thresholding of sensory inputs by extrasynaptic glutamate receptors in olfactory bulb glomeruli
Authors: Gire D.H. , Zak J.D. , Bourne J.N. , Goodson N.B. , Lynch B.E. , Dulla C.G. , Schoppa N.E. 
Published: June 2018

AbstractThe mammalian olfactory bulb has presented a challenging system for understanding information processing, in part because the bulb largely lacks the topographical ordering of neurons that promotes processes such as lateral inhibition. Here we have used dual and triple-cell recordings in rodent bulb slices combined with ultrastructural methods to provide the first experimental evidence for a processing mechanism circumventing this problem that operates at the level of single glomeruli, the bulb’s odorant receptor-specific modules. A key feature is non-traditional, extrasynaptic glutamatergic signaling derived from excitatory interneurons and what it means for the local balance between excitation (E) and inhibition (I). We found that the distinct dynamic properties of extrasynaptic excitation versus synaptic inhibition create a thresholding effect whereby only strong stimuli produce a favorable E/I balance enabling an output. This single-glomerulus threshold could have a number of important functions during natural odor responses, for example enhancing stimulus tuning.
Hierarchical Heterogeneity Across Human Cortex Shapes Large-Scale Neural Dynamics
Authors: Demirtaş Murat , Burt Joshua B. , Helmer Markus , Ji Jie Lisa , Adkinson Brendan D. , Glasser Matthew F. , Van Essen David C. , Sotiropoulos Stamatios N. , Anticevic Alan , Murray John D. 
Published: June 2018

SummaryThe large-scale organization of dynamical neural activity across cortex emerges through long-range interactions among local circuits. We hypothesized that large-scale dynamics are also shaped by heterogeneity of intrinsic local properties across cortical areas. One key axis along which microcircuit properties are specialized relates to hierarchical levels of cortical organization. We developed a large-scale dynamical circuit model of human cortex that incorporates heterogeneity of local synaptic strengths, following a hierarchical axis inferred from MRI-derived T1w/T2w mapping, and fit the model using multimodal neuroimaging data. We found that incorporating hierarchical heterogeneity substantially improves the model fit to fMRI-measured resting-state functional connectivity and captures sensory-association organization of multiple fMRI features. The model predicts hierarchically organized high-frequency spectral power, which we tested with resting-state magnetoencephalography. These findings suggest circuit-level mechanisms linking spatiotemporal levels of analysis and highlight the importance of local properties and their hierarchical specialization on the large-scale organization of human cortical dynamics.
Neuroligin dependence of pharyngeal pumping reveals an extrapharyngeal modulation ofCaenorhabditis elegansfeeding
Authors: Calahorro Fernando , Keefe Francesca , Dillon James , Holden-Dye Lindy , O’Connor Vincent 
Published: June 2018

ABSTRACTThe integration of distinct sensory modalities is essential for behavioural decision making. InC. elegansthis process is coordinated by neural circuits that integrate sensory cues from the environment to generate an appropriate behaviour at the appropriate output muscles. Food is a multimodal cue that impacts on the microcircuits to modulating feeding and foraging drivers at the level of the pharyngeal and body wall muscle respectively. When food triggers an upregulation in pharyngeal pumping it allows the effective ingestion of food. Here we show that aC.elegansmutant in the single orthologous gene of human neuroligins,nlg-1are defective in food induced pumping. This is not explained by an inability to sense food, asnlg-1mutants are not defective in chemotaxis towards bacteria. In addition, we show that neuroligin is widely expressed in the nervous system including AIY, ADE, ALA, URX and HSN neurones. Interestingly, despite the deficit in pharyngeal pumping neuroligin is not expressed within the pharyngeal neuromuscular network, which suggests an extrapharyngeal regulation of this circuit. We resolve electrophysiologically the neuroligin contribution to the pharyngeal circuit by mimicking a food-dependent pumping, and show that thenlg-1phenotype is similar to mutants impaired in GABAergic and/or glutamatergic signalling. We suggest that neuroligin organizes extrapharyngeal circuits that regulate the pharynx. These observations based on the molecular and cellular determinants of feeding are consistent with the emerging role of neuroligin in discretely impacting functional circuits underpinning complex behaviours.
Boundary Strength Analysis: Combining colour pattern geometry and coloured patch visual properties for use in predicting behaviour and fitness
Authors: Endler John A. , Cole Gemma L. , Kranz Alexandrea 
Published: June 2018

AbstractColour patterns are used by many species to make decisions that ultimately affect their Darwinian fitness. Colour patterns consist of a mosaic of patches that differ in geometry and visual properties. Although traditionally pattern geometry and colour patch visual properties are analysed separately, these components are likely to work together as a functional unit. Despite this, the combined effect of patch visual properties, patch geometry, and the effects of the patch boundaries on animal visual systems, behaviour and fitness are relatively unexplored. Here we describe Boundary Strength Analysis (BSA), a novel way to combine the geometry of the edges (boundaries among the patch classes) with the receptor noise estimate (ΔS) of the intensity of the edges. The method is based upon known properties of vertebrate and invertebrate retinas. The mean and SD of ΔS (mΔS, sΔS) of a colour pattern can be obtained by weighting each edge class ΔS by its length, separately for chromatic and achromatic ΔS. This assumes those colour patterns, or parts of the patterns used in signalling, with larger mΔS and sΔS are more stimulating and hence more salient to the viewers. BSA can be used to examine both colour patterns and visual backgrounds. BSA was successful in assessing the estimated conspicuousness of colour pattern variants in two species, guppies (Poecilia reticulata) and Gouldian finches (Erythrura gouldiae), both polymorphic for patch colour, luminance and geometry. The pattern difference between chromatic and achromatic edges in both species reveals the possibility that chromatic and achromatic edges could function differently. BSA can be applied to any colour pattern used in intraspecific and interspecific behaviour. Seven predictions and four questions about colour patterns are presented.
Dauer diapause has transgenerational effects on starvation survival and gene expression plasticity
Authors: Webster Amy K. , Jordan James M. , Hibshman Jonathan D. , Chitrakar Rojin , Ryan Baugh L. 
Published: June 2018

ABSTRACTPhenotypic plasticity is facilitated by epigenetic regulation, and remnants of such regulation may persist after plasticity-inducing cues are gone. However, the relationship between plasticity and transgenerational epigenetic memory is not understood. Dauer diapause in Caenorhabditis elegans provides an opportunity to determine how a plastic response to the early-life environment affects traits later in life and in subsequent generations. We report that after extended diapause, post-dauer worms initially exhibit reduced reproductive success and greater inter-individual variation. In contrast, F3 progeny of post-dauers display increased starvation resistance and lifespan, revealing potentially adaptive transgenerational effects. Transgenerational effects are dependent on the duration of diapause, indicating an effect of extended starvation. In agreement, RNA-seq demonstrates a transgenerational effect on nutrient-responsive genes. Further, post-dauer F3 progeny exhibit reduced gene expression plasticity, suggesting a trade-off between plasticity and epigenetic memory. This work reveals complex effects of nutrient stress over different time scales in an animal that evolved to thrive in feast and famine.
Sublethal β-lactam antibiotics induce PhpP phosphatase expression and StkP kinase phosphorylation in PBP-independent β-lactam antibiotic resistance ofStreptococcus pneumoniae
Authors: Huang Yan-Ying , Sun Yan-Hong , Du Peng , Liu Xiao-Xiang , Yan Jie , Sun Ai-Hua 
Published: June 2018

AbstractStkP and PhpP ofStreptococcus pneumoniaehave been confirmed to compose a signaling couple, in which the former is a serine/threonine (Ser/Thr) kinase while the latter was annotated as a phosphotase. StkP has been reported to be involved in penicillin-binding protein (PBP)-independent penicillin resistance ofS. pneumoniae. However, the enzymatic characterization of PhpP and the role of PhpP in StkP-PhpP couple remain poorly understood. Here we showed that 1/4 minimal inhibitory concentration (MIC) of penicillin (PCN) or cefotaxime (CTX), the representatives of β-lactam antibiotics, could induce the expression ofstkPandphpPgenes and phosphorylation of StkP in PCN/CTX-sensitive strain ATCC6306 and three isolates ofS. pneumoniae(MICs: 0.02-0.5 μg/ml). The product ofphpPgene hydrolyzed PP2C type Ser/Thr phosphotase-specific RRA(pT)VA phosphopeptide substrate with the Km and Kcat values of 277.35 μmol/L and 0.71 S−1, and the hydrolytic activity was blocked by sodium fluoride, a PP2C type Ser/Thr phosphatase inhibitor. The phosphorylation levels of StkP in the fourphpPgene-knockout (ΔphpP) mutants were significantly higher than that in the wild-type strains. In particular, the MICs of PCN and CTX against the ΔphpPmutants were significantly elevated as 4-16 μg/ml. Therefore, our findings confirmed that sublethal PCN and CTX act as environmental inducers to cause the increase ofphpPandstkPgene expression and StkP phosphorylation. PhpP is a PP2C type Ser/Thr protein phosphatase responsible for dephosphorylation of StkP. Knockout of thephpPgene results in a high level of StkP phosphorylation and PBP-independent PCN/CTX resistance ofS. pneumoniae.ImportanceStreptococcus pneumoniaeis a common pathogen in human populations in many countries and areas due to the prevalence of β-lactam antibiotic-resistant pneumococcal strains. Production of β-lactamases and mutation of penicillin-binding proteins (PBP) have been considered as the major β-lactam antibiotic-resistant mechanisms in bacteria, butS. pneumoniaehas not been confirmed to produce any β-lactamases and many pneumococcal strains present PBP mutation-independent β-lactam antibiotic resistance. StkP is a Ser/Thr kinase ofS. pneumoniaeto compose a signal-couple with PhpP protein. The present study demonstrated that the PhpP is a PP2C-type phosphotase for dephosphorylation of StkP and the sublethal penicillin (PCN) or cefotaxime (CTX) acted as environmental signal molecules to induce the expression of PhpP. The knockout of PhpP-encoding gene caused the PCN/CTX resistance generation of PCN/CTX-sensitive pneumococcal strains. All the data indicate that StkP-PhpP couple ofS. pneumoniaeis involved in PBP mutation-independent β-lactam antibiotic resistance by phosphorylation of StkP.
In vivogene expression analyses provide unique insights onP. vivaxgametocytogenesis and chloroquine response
Authors: Kim Adam , Popovici Jean , Menard Didier , Serre David 
Published: June 2018

AbstractStudies of gene expression have provided insights on the regulation ofPlasmodiumparasites. However, few studies have targetedP. vivax, the cause of one third of all human malaria cases outside Africa, due to the lack ofin vitroculture system and the difficulties associated with studying clinical samples. Here, we describe robust RNA-seq profiles ofP. vivaxparasites generated directly from infected patient blood. Gene expression deconvolution analysis reveals that most parasite mRNAs derive from trophozoites and that the asynchronicity ofP. vivaxinfections is unlikely to confound gene expression studies. We also show that gametocyte genes form two clusters of co-regulated genes, possibly indicating the independent regulation of male and female gametocytogeneses. Finally, despite a large effect on parasitemia, we find that chloroquine does not alter trophozoite gene expression. Overall, our study highlights the biological knowledge that can be gathered by directly studyingP. vivaxpatient infections.ImportancePlasmodium vivaxis the second most common cause of human malaria worldwide but, since it cannot be cultured in the laboratory, its biology remains poorly understood. In this study, we describe the analysis of the parasite gene expression profiles generated from 26 patient infections. We show that the proportion of male and female parasites varies greatly among infections, suggesting that they are independently regulated. We also compare the gene expression profiles of the same infections before and after treatment with chloroquine, a common antimalarial, and show that the drug efficiently kills mostP. vivaxparasites but appears to have little effect on one specific parasite stage, the trophozoites, in contrast with the effect of the drug onP. falciparum. Overall, our study exemplifies the biological insights that can be gained from applying modern genomic tools to study this difficult human pathogen.
The effects of psychiatric history and age on self-regulation of the default mode network
Authors: Skouras Stavros , Scharnowski Frank 
Published: June 2018

AbstractReal-time neurofeedback enables human subjects to learn to regulate their brain activity, effecting behavioral changes and improvements of psychiatric symptomatology. Neurofeedback up-regulation and down-regulation have been assumed to share common neural correlates. Neuropsychiatric pathology and aging incur suboptimal functioning of the default mode network. Despite the exponential increase in real-time neuroimaging studies, the effects of aging, pathology and the direction of regulation on neurofeedback performance remain largely unknown. Using open-access analyses and real-time fMRI data shared through the Rockland Sample Real-Time Neurofeedback project (N=136), we first modeled neurofeedback performance and learning in a group of subjects with psychiatric history (na=74) and a healthy control group (nb=62). Subsequently, we examined the relationship between up-regulation and down-regulation learning, the relationship between age and neurofeedback performance in each group and differences in neurofeedback performance between the two groups. Results show that in an initial session of default mode network neurofeedback with real-time fMRI, up-regulation and down-regulation learning scores are negatively correlated. Moreover, age correlates negatively with default mode network neurofeedback performance, only in absence of psychiatric history. Finally, adults with psychiatric history outperform healthy controls in default mode network up-regulation. Interestingly, the performance difference is related to no up-regulation learning in controls.
SHANK3 downregulation in the VTA accelerates the extinction of contextual associations induced by non-familiar conspecific interaction
Authors: Bariselli Sebastiano , Contestabile Alessandro , Tzanoulinou Stamatina , Bellone Camilla 
Published: June 2018

AbstractConditioned place preference (CPP) paradigms, traditionally adopted to study the reinforcing properties of drugs of abuse, have been developed to investigate the neurobiological mechanisms underlying the reinforcing properties of social stimuli. These protocols are largely based on single-housing before and/or during the social stimulus-contextual cues acquisition phase. Here, based on previously established social interaction-induced CPP paradigms, we characterize a place preference task relying on the reinforcing properties of free interaction with a non-familiar (novel) conspecific. The formation of contextual associations induced by the interaction with a novel social stimulus does not require single-housing, necessitates dopamine (DA) receptor 2/3 (D2/3R) activation and undergoes extinction. Interestingly, while extinction of CPP responses is reduced by single-housing, it is accelerated by the downregulation of the autism spectrum disorder (ASD)-related protein SHANK3 in the ventral tegmental area (VTA). Thus, inspired by the literature on drug of abuse-induced contextual learning, we propose that acquisition and extinction of CPP might be used as behavioral assays to assess social-induced contextual association and “social-seeking” dysfunctions in animal models of psychiatric disorders.
Manipulation of subcortical and deep cortical activity in the primate brain using transcranial focused ultrasound stimulation
Authors: Folloni Davide , Verhagen Lennart , Mars Rogier B. , Fouragnan Elsa , Constans Charlotte , Aubry Jean-François , Rushworth Matthew F.S. , Sallet Jérôme 
Published: June 2018

SummaryThe causal role of an area within a neural network can be determined by interfering with its activity and measuring the impact. Many current reversible manipulation techniques have limitations preventing their focal application particularly in deep areas of the primate brain. Here we demonstrate a transcranial focused ultrasound stimulation (TUS) protocol that manipulates activity even in deep brain areas: a subcortical brain structure, the amygdala (experiment 1), and a deep cortical region, anterior cingulate cortex (ACC, experiment 2), in macaques. TUS neuromodulatory effects were measured by examining relationships between activity in each area and the rest of the brain using functional magnetic resonance imaging (fMRI). In control conditions without sonication, activity in a given area is related to activity in interconnected regions but such relationships are reduced after sonication. Dissociable and focal effects on neural activity could not be explained by auditory artefacts.
Offline impact of transcranial focused ultrasound on cortical activation in primates
Authors: Verhagen Lennart , Gallea Cécile , Folloni Davide , Constans Charlotte , Jensen Daria EA , Ahnine Harry , Roumazeilles Léa , Santin Mathieu D , Ahmed Bashir , Lehericy Stéphane , Klein-Flügge Miriam , Krug Kristine , Mars Rogier B , Rushworth Matthew FS , Pouget Pierre , Aubry Jean-François , Sallet Jérôme 
Published: June 2018

AbstractTo understand brain circuits it is necessary both to record and manipulate their activity. Transcranial ultrasound (TUS) is a promising non-invasive brain stimulation technique. To date, investigations have focused on short-lived neuromodulatory effects, but to deliver on its full potential for research and therapy, ultrasound protocols are required that induce longer-lasting ‘offline’ changes. Here, we present a TUS protocol that modulates brain activation in macaques for more than one hour after 40 seconds of stimulation, while circumventing auditory confounds. Normally activity in brain areas reflects activity in interconnected regions but TUS’ impact can be demonstrated by showing such patterns change for stimulated areas. We report regionally specific TUS effects for two medial frontal brain regions – supplementary motor area and frontal polar cortex. Independently of these site-specific effects, TUS also induced signal changes in the meningeal compartment. TUS effects were temporary and not associated with microstructural changes.
TOL proteins mediate vacuolar sorting of the borate transporter BOR1 in Arabidopsis thaliana
Authors: Yoshinari Akira , Korbei Barbara , Takano Junpei 
Published: June 2018

ABSTRACTBoron (B) is an essential micronutrient for plants, however, it shows cytotoxicity at high concentrations. A borate transporter BOR1 is required for efficient transport of boron (B) toward the root stele in Arabidopsis thaliana. BOR1 shows polar localization in the plasma membrane of various root cells toward the stele-side under B limitation. To avoid over-accumulation of B, BOR1 in the plasma membrane is rapidly internalized and transported into the vacuole for proteolysis after high-B supply in an ubiquitination-dependent manner. Although BOR1 has been predicted to be transported into multi-vesicular bodies/late endosomes (MVB/LEs) via the endosomal sorting complex required for transport (ESCRT) machinery, experimental evidence was absent so far. In this study, we investigated the intracellular localization of BOR1 by visualizing endomembrane compartments, and tested the involvement of ESCRT-0-like proteins TOM1-LIKEs (TOLs) in the vacuolar sorting of BOR1. Under low-B conditions, a large portion of cytoplasmic BOR1 was localized in the trans-Golgi networks/early endosomes (TGN/EEs) labeled with VHA-a1 subunit. Pharmacological interference of endosomal recycling using brefeldin A induced colocalization of BOR1 with RabA5D, which labels recycling vesicles associated with the TGN. These data suggest that BOR1 cycles between plasma membrane and TGN/EE via RabA5D-positive endomembrane compartments under low-B conditions. On the other hand, under high-B conditions, BOR1 was localized in the inside of TOL5-positive MVB/LEs. To examine the roles of TOL proteins in intracellular trafficking of BOR1, we analyzed BOR1-GFP localization in the TOL quintuple mutant (tolQ; tol2-1tol3-1tol5-1tol6-1tol9-1) after high-B supply. In the tolQ mutant, vacuolar sorting of BOR1 was delayed, while the polar localization of BOR1 was not disturbed. Taken together, BOR1 is constantly transported to the TGN/EE by endocytosis and recycled to the plasma membrane likely via RabA5D-positive endomembrane compartments under low-B conditions. On the other hand, BOR1 is transported to the vacuole via TOL5-positive MVB/LEs under high-B conditions. TOL proteins are required for sorting of ubiquitinated BOR1 into MVB/LE for vacuolar degradation but not for the polar trafficking of BOR1.