bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetic mechanisms of fast glutamate sensing by fluorescent protein probes
Authors: Coates C. , Kerruth S. , Helassa N. , Török K. 
Published: June 2019

ABSTRACTProtein-based fluorescent glutamate sensors have the potential for real-time monitoring of synaptic and cellular glutamate concentration changes, however even the fastest currently available sensors’ response times of 2-3 ms are too slow for accurate reporting of the post-synaptic AMPA receptor function in physiological conditions. We have developed probes based on the bacterial periplasmic glutamate/aspartate binding protein with either an endogenously fluorescent protein or a synthetic fluorophore as the indicator of glutamate binding: affinity variants of iGluSnFR termed iGluh, iGlumand iGlulcovering a range ofKd−s (5.8 μM, 2.1 mM and 50 mM, respectively) and a novel fluorescently labelled indicator, Fl-GluBP with aKdof 9.7 μM are presented. The fluorescence response kinetics of all the probes are consistent with two-step mechanisms involving ligand binding and rate limiting isomerisation, however the contribution in each step to the total fluorescence enhancement and kinetic paths to the final state are diverse. In contrast to the previously characterised ultrafast indicators iGluuand iGluf, for which fluorescence enhancement occurred only in the rate limiting isomerisation step, the sensors described here all have biphasic binding kinetics with a significant fraction of the fluorescence increase evoked by glutamate binding which, in the case of iGluhand Fl-GluBP, occurs with a diffusion limited rate constant. The above genetically encoded and chemically labelled fluorescent glutamate sensor variants demonstrate how single amino acid changes around the binding site introduce structural heterogeneity affecting the kinetic mechanism of interactions with glutamate. Through their broad affinity range and mechanistic variety, the probes contribute to a novel toolkit for monitoring processes of glutamate neurotransmission and cellular homeostasis.STATEMENT OF SIGNIFICANCEGlutamate is a major excitatory neurotransmitter, important in synaptic plasticity e.g. memory formation. Although predicted to clear rapidly from the synaptic cleft following presynaptic release, optical monitoring of glutamate neurotransmission has only become possible with the advent of fluorescent, protein-based indicators. Understanding their biophysical properties is important for quantification of the observed processes. Here we report the biophysical characterisation of a number of glutamate indicator variants based on the bacterial periplasmic glutamate/aspartate binding protein, revealing the subtle differences in their kinetic pathway caused by structural alteration of the glutamate binding protein by point mutations. Diffusion limited glutamate binding indicated by a novel chemically labelled probe hints at the mechanism that underlies the rapid response of the AMPA receptor.
The p38MAPK-MK2-HSP27 Pathway Regulates the mRNA Stability of the Senescence-Associated Secretory Phenotype
Authors: Moore Hayley R. , Alspach Elise , Hirsch Jeffrey L. , Monahan Joseph , Stewart Sheila A. 
Published: June 2019

AbstractAge is a significant risk factor for the development of cancer. Both age-dependent accumulation of cell autonomous mutations within preneoplastic cells and increases in senescent stromal cells within the tumor microenvironment are thought to collaborate to drive tumorigenesis. Senescent cells express pro-tumorigenic factors termed the senescence-associated secretory phenotype (SASP), subject to a variety of regulatory mechanisms that are not fully elucidated. Previous work demonstrated that p38 mitogen-activated protein kinase (p38MAPK)-dependent regulation of AUF1 occupancy on SASP factor mRNAs post-transcriptionally stabilizes many SASP mRNAs and contributes to their increased expression. Here, we address the mechanism by which p38MAPK regulates AUF1’s occupancy and activity on SASP factor mRNAs. We found that the p38MAPK-MK2-HSP27 pathway regulates both mRNA stability and AUF1 occupancy in cells induced to senesce. Furthermore, the tumor-promoting abilities of senescent stromal cells were lost upon inhibition of MK2, suggesting that this pathway is a viable therapeutic target within the tumor microenvironment.
RanGTP induces an effector gradient of XCTK2 and importin α/β for spindle microtubule cross-linking
Authors: Ems-McClung Stephanie C. , Emch Mackenzie , Zhang Stephanie , Mahnoor Serena , Weaver Lesley N. , Walczak Claire E. 
Published: June 2019

AbstractHigh RanGTP around chromatin is important for governing spindle assembly during meiosis and mitosis by releasing the inhibitory effects of importin α/β. Here we examine how the Ran gradient regulates Kinesin-14 function to control spindle organization. We show thatXenopusKinesin-14, XCTK2, and importin α/β form an effector gradient, which is highest at the poles that diminishes toward the chromatin and is inverse of the RanGTP gradient. Importin α/β preferentially inhibit XCTK2 anti-parallel microtubule cross-linking and sliding by decreasing the microtubule affinity of the XCTK2 tail domain. This change in microtubule affinity enables RanGTP to target endogenous XCTK2 to the spindle. We propose that these combined actions of the Ran pathway are critical to promote Kinesin-14 parallel microtubule cross-linking at the spindle poles to cluster centrosomes in cancer cells. Furthermore, our work illustrates that RanGTP regulation in the spindle is not simply a switch, but rather generates effector gradients where RanGTP gradually tunes the activities of spindle assembly factors.SummaryEms-McClung et al. visualize a RanGTP effector gradient of association between XCTK2 and importin α/β in the spindle. The importins preferentially inhibit XCTK2-mediate anti-parallel microtubule cross-linking and sliding, which allows XCTK2 to cross-link parallel microtubules and help focus spindle poles.
Gastruloid development competence discriminates different states of pluripotency between naïve and primed
Authors: Cermola Federica , D’Aniello Cristina , Tatè Rosarita , De Cesare Dario , Martinez-Arias Alfonso , Minchiotti Gabriella , Patriarca Eduardo Jorge 
Published: June 2019

ABSTRACTFloating spheroidal aggregates (aggregomes) of mouse embryonic stem cells (mESCs) can develop into polarized/elongated organoids, namely gastruloids. Here we report a high-performing assay to measure gastruloids formation efficiency (GFE), i.e. the fraction of gastruloid-developing aggregomes. By exploiting this procedure, we provide morphological and molecular evidence that gastruloid development relies on Cripto. We also demonstrate that GFE decreases as pluripotency progresses from naïve to primed state. Indeed, naïve ESC-derived aggregomes efficiently elongate (GFE≥95%), while primed EpiSCs fail to aggregate and consequently to generate gastruloids (GFE=0%). Conversely, while early-primed EpiLCs properly aggregate, EpiLC-derived aggregomes are mostly abortive (GFE=0%). Unlike EpiLCs, L-Proline-treated ESCs (PiCs) generate productive aggregomes (GFE≥50%), which however begin to elongate earlier and generate smaller gastruloids that appear more differentiated. Like EpiLCs, PiCs are competent to differentiate into primordial germ cell-like cells (PGCLCs), suggesting that PiCs capture an EpiLC-like state with unique competence for both gastruloid formation and differentiation into PGCLCs. Thus we propose GFE assay as a simple and robust in vitro method to discriminate different phenotypic/functional states of the pluripotency continuum.
Genomic architecture of Shh dependent cochlear morphogenesis
Authors: Muthu Victor , Rohacek Alex. M. , Yao Yao , Rakowiecki Staci M. , Brown Alexander S. , Zhao Ying-Tao , Meyers James , Won Kyoung-Jae , Ramdas Shweta , Brown Christopher D. , Peterson Kevin A. , Epstein Douglas J. 
Published: June 2019

ABSTRACTThe mammalian cochlea develops from a ventral outgrowth of the otic vesicle in response to Shh signaling. Mouse embryos lacking Shh or its essential signal transduction components display cochlear agenesis, however, a detailed understanding of the transcriptional network mediating this process is unclear. Here, we describe an integrated genomic approach to identify Shh dependent genes and associated regulatory sequences that promote cochlear duct morphogenesis. A comparative transcriptome analysis of otic vesicles from mouse mutants exhibiting loss (Smoecko) and gain (Shh-P1) of Shh signaling revealed a set of Shh responsive genes partitioned into four expression categories in the ventral half of the otic vesicle. This target gene classification scheme provided novel insights into several unanticipated roles for Shh, including priming the cochlear epithelium for subsequent sensory development. We also mapped regions of open chromatin in the inner ear by ATAC-seq that, in combination with Gli2 ChIP-seq, identified inner ear enhancers in the vicinity of Shh responsive genes. These datasets are useful entry points for deciphering Shh dependent regulatory mechanisms involved in cochlear duct morphogenesis and establishment of its constituent cell types.SUMMARY STATEMENTAn integrated genomic approach identifies Shh responsive genes and associated regulatory sequences with known and previously uncharacterized roles in cochlear morphogenesis, including genes that prime the cochlea for sensory development.
Socioeconomic status and the structure of the self‐concept
Authors: Easterbrook Matthew J. , Kuppens Toon , Manstead Antony S. R. 
Published: June 2019

Individuals have a myriad of potential identities that they can use to define who they are, yet little research has investigated which types of identities people tend to prioritize within their self‐concepts, and how this may vary across individuals. We analyse data from two large UK social surveys (Ns = 16,966 and 44,903) that assessed the importance respondents attached to various identities within their self‐concepts, and find that social class plays a crucial role. Our results show that respondents attached high importance to identities that are indicative of their social class (income, education, and professional), and at least as much importance as they gave to identities more commonly studied by psychologists (such as ethnicity, nationality, or gender). Furthermore, respondents’ objective social class was one of the strongest predictors of the importance they attached to different types of identities: Higher class respondents placed greater importance on identities that are indicative of their social class, but less importance on identities based on basic demographics, chosen communities, or their sociocultural orientation. Our results suggest that social class plays an important role in structuring the self‐concept, and that researchers should pay more attention to the importance of social class to self and identity processes.
Clinicopathological significance of heterogeneic ezrin expression in poorly differentiated clusters of colorectal cancers
Authors: Aikawa Akane , Fujita Hideto , Kosaka Takeo , Minato Hiroshi , Kiyokawa Etsuko 
Published: June 2019

AbstractMulticellular structures, such as tumor buddings and poorly differentiated clusters (PDC), exist at the invasive front of colorectal cancers (CRC). Although it has been reported that CRC with PDC showed frequent lymph node metastases with a worse prognosis, the molecular markers of PDC that are responsible for prognosis have not been identified. We here noticed for the first time that Ezrin, a regulator of the actin cytoskeleton, is expressed in the corner cells of PDC. We then aimed to verify whether heterogeneous Ezrin expression in PDC predicts the prognosis of CRC patients. We immunohistochemically analyzed Ezrin expression in PDC of 184 patients with completely resected stages I‐III CRC. We established the Ezrin corner score (ECS), which quantifies the tendency of Ezrin‐positive cells to accumulate at the corners of PDC. On the basis of ECS values, 2 indices, the mean ECS and the number of PDC with high ECS, were obtained. Both indices were significantly higher in CRC with lymphatic invasion, higher PDC grade, and presence of micropapillary (MP) PDC. The mean ECS‐high group showed shorter recurrence‐free survival than the mean ECS‐low group but without significance. The other index, the number of ECS‐high PDC, was significantly associated with recurrence‐free survival. These results suggest that Ezrin is involved in PDC progression and lymphatic invasion, and that ECS may be a marker for aggressive PDC.
When Stronger Knowledge Slows You Down: Semantic Relatedness Predicts Children's Co‐Activation of Related Items in a Visual Search Paradigm
Authors: Vales Catarina , Fisher Anna V. 
Published: June 2019

AbstractA large literature suggests that the organization of words in semantic memory, reflecting meaningful relations among words and the concepts to which they refer, supports many cognitive processes, including memory encoding and retrieval, word learning, and inferential reasoning. The co‐activation of related items has been proposed as a mechanism by which semantic knowledge influences cognition, and contemporary accounts of semantic knowledge propose that this co‐activation is graded—that it depends on how strongly related the items are in semantic memory. Prior research with adults yielded evidence supporting this prediction; however, there is currently no evidence of graded co‐activation early in development. This study provides the first evidence that in children the co‐activation of related items depends on their relational strength in semantic memory. Participants (N = 84, age range: 3–9 years) were asked to identify a target (e.g., bone) amid distractors. Children's responses were slowed down by the presence of a related distractor (e.g., puppy) relative to unrelated distractors (e.g., flower)—suggesting that children co‐activated related items upon hearing the name of the target. Importantly, the degree of this co‐activation was predicted by the strength of the target–distractor relation, such that distractors more strongly related to the targets slowed down children to a larger extent. These findings have important implications for understanding how organized semantic knowledge affects other cognitive processes across development.
Relapse risk factors in anti‐N‐methyl‐D‐aspartate receptor encephalitis
Authors: Nosadini Margherita , Granata Tiziana , Matricardi Sara , Freri Elena , Ragona Francesca , Papetti Laura , Suppiej Agnese , Valeriani Massimiliano , Sartori Stefano ,   Italian Working Group on Paediatric Anti‐N‐methyl‐D‐aspartate Receptor Encephalitis
Published: June 2019

AimTo identify factors that may predict and affect the risk of relapse in anti‐N‐methyl‐D‐aspartate receptor (NMDAR) encephalitis.MethodThis was a retrospective study of an Italian cohort of patients with paediatric (≤18y) onset anti‐NMDAR encephalitis.ResultsOf the 62 children included (39 females; median age at onset 9y 10mo, range 1y 2mo–18y; onset between 2005 and 2018), 21 per cent relapsed (median two total events per relapsing patient, range 2–4). Time to first relapse was median 31.5 months (range 7–89mo). Severity at first relapse was lower than onset (median modified Rankin Scale [mRS] 3, range 2–4, vs median mRS 5, range 3–5; admission to intensive care unit: 0/10 vs 3/10). At the survival analysis, the risk of relapsing was significantly lower in patients who received three or more different immune therapies at first disease event (hazard ratio 0.208, 95% confidence interval 0.046–0.941; p=0.042). Neurological outcome at follow‐up did not differ significantly between patients with relapsing and monophasic disease (mRS 0–1 in 39/49 vs 12/13; p=0.431), although follow‐up duration was significantly longer in relapsing (median 84mo, range 14–137mo) than in monophasic patients (median 32mo, range 4–108mo; p=0.002).InterpretationRelapses may occur in about one‐fifth of children with anti‐NMDAR encephalitis, are generally milder than at onset, and may span over a long period, although they do not seem to be associated with severity in the acute phase or with outcome at follow‐up. Aggressive immune therapy at onset may reduce risk of relapse.What this paper adds

Relapses of anti‐N‐methyl‐D‐aspartate receptor encephalitis may span over a long period.

Relapses were not associated with severity in the acute phase or outcome at follow‐up.

Aggressive immune therapy at onset appears to decrease risk of relapse.
Treatments in Aicardi–Goutières syndrome
Authors: Crow Yanick J , Shetty Jayakara , Livingston John H 
Published: June 2019

Comprehensive reviews of the clinical characteristics and pathogenesis of Aicardi–Goutières syndrome (AGS), particularly its contextualization within a putative type I interferonopathy framework, already exist. However, recent reports of attempts at treatment suggest that an assessment of the field from a therapeutic perspective is warranted at this time. Here, we briefly summarize the neurological phenotypes associated with mutations in the seven genes so far associated with AGS, rehearse current knowledge of the pathology as it relates to possible treatment approaches, critically appraise the potential utility of therapies, and discuss the challenges in assessing clinical efficacy.What this paper adds

Progress in understanding AGS disease pathogenesis has led to the first attempts at targeted treatment.

Further rational therapies are expected to become available in the short‐ to medium‐term.
Alpha diversity of vascular plants in European forests
Authors: Večeřa Martin , Divíšek Jan , Lenoir Jonathan , Jiménez‐Alfaro Borja , Biurrun Idoia , Knollová Ilona , Agrillo Emiliano , Campos Juan Antonio , Čarni Andraž , Crespo Jiménez Guillermo , Ćuk Mirjana , Dimopoulos Panayotis , Ewald Jörg , Fernández‐González Federico , Gégout Jean‐Claude , Indreica Adrian , Jandt Ute , Jansen Florian , Kącki Zygmunt , Rašomavičius Valerijus , Řezníčková Marcela , Rodwell John S. , Schaminée Joop H.J. , Šilc Urban , Svenning Jens‐Christian , Swacha Grzegorz , Vassilev Kiril , Venanzoni Roberto , Willner Wolfgang , Wohlgemuth Thomas , Chytrý Milan 
Published: June 2019

AbstractAimThe former continental‐scale studies modelled coarse‐grained plant species‐richness patterns (gamma diversity). Here we aim to refine this information for European forests by (a) modelling the number of vascular plant species that co‐occur in local communities (alpha diversity) within spatial units of 400 m2; and (b) assessing the factors likely determining the observed spatial patterns in alpha diversity.LocationEurope roughly within 12°W–30°E and 35–60°N.TaxonVascular plants.MethodsThe numbers of co‐occurring vascular plant species were counted in 73,134 georeferenced vegetation plots. Each plot was classified by an expert system into deciduous broadleaf, coniferous or sclerophyllous forest. Random Forest models were used to map and explain spatial patterns in alpha diversity for each forest type separately using 19 environmental, land‐use and historical variables.ResultsOur models explained from 51.0% to 70.9% of the variation in forest alpha diversity. The modelled alpha‐diversity pattern was dominated by a marked gradient from species‐poor north‐western to species‐rich south‐eastern Europe. The most prominent richness hotspots were identified in the Calcareous Alps and adjacent north‐western Dinarides, the Carpathian foothills in Romania and the Western Carpathians in Slovakia. Energy‐related factors, bedrock types and terrain ruggedness were identified as the main variables underlying the observed richness patterns. Alpha diversity increases especially with temperature seasonality in deciduous broadleaf forests, on limestone bedrock in coniferous forests and in areas with low annual actual evapotranspiration in sclerophyllous forests.Main conclusionsWe provide the first predictive maps and analyses of environmental factors driving the alpha diversity of vascular plants across European forests. Such information is important for the general understanding of European biodiversity. This study also demonstrates a high potential of vegetation‐plot databases as sources for robust estimation of the number of vascular plant species that co‐occur at fine spatial grains across large areas.
North Atlantic Gateway: Test bed of deep‐sea macroecological patterns
Authors: Jöst Anna B. , Yasuhara Moriaki , Wei Chih‐Lin , Okahashi Hisayo , Ostmann Alexandra , Martínez Arbizu Pedro , Mamo Briony , Svavarsson Jörundur , Brix Saskia 
Published: June 2019

AbstractAimThe deep waters around Iceland, known as the North Atlantic Gateway, constitute an ideal location to investigate deep‐sea ecological hypotheses. We constructed a comprehensive deep‐sea macroecological dataset of the North Atlantic Gateway region and investigated the controlling factors of large‐scale, deep‐sea species diversity patterns.LocationSub‐polar North Atlantic Ocean.Time periodModern.Major taxa studiedOstracoda (Crustacea).MethodsWe investigated deep‐sea biodiversity patterns and applied ecological modelling (multiple regression and model averaging) to test whether these patterns are governed by environmental factors such as temperature, surface primary productivity, and seasonality. Beta diversity analyses were applied to evaluate the effect of a geographical barrier (Greenland‐Iceland‐Faeroe Ridge) on deep‐sea benthic faunal distributions.ResultsWe constructed a deep‐sea macroecological dataset with 32 stations, 5,676 specimens, and >122 species. We confirmed a linear latitudinal diversity gradient with higher diversity in the North Atlantic proper than in the Nordic Seas. We report a unimodal depth diversity gradient south of the ridge, but a linear diversity‐decline with depth north of the ridge. The turnover component of beta diversity increased towards the ridge.Main conclusionsWe found both temperature and surface primary production are important for deep‐sea biodiversity. For the first time, we report a significant diversity‐temperature relationship in both macroecological (spatial; this study) and existing paleoecological (time‐series) data for the same taxa. In addition to temperature and surface primary production, bathymetric features such as a shallow ridge acting as a barrier are an important factor for deep‐sea biodiversity distribution. The low diversity of the Nordic Seas is likely due to a combination of low temperatures and bathymetric barriers. These results substantially expand our understanding of the well‐known yet poorly understood Greenland‐Iceland‐Faeroe Ridge faunal transition with possible insight to its cause.