bluuebunny/crossref_metadata_2025_split huggingface dataset:
Granulocyte-Colony Stimulating Factor reduces cocaine-seeking and downregulates glutamatergic synaptic proteins in medial prefrontal cortex
Authors: Hofford Rebecca S. , Euston Tanner J. , Wilson Rashaun S. , Meckel Katherine R. , Peck Emily G. , Godino Arthur , Landry Joseph A. , Calipari Erin S. , Lam TuKiet T. , Kiraly Drew D. 
Published: February 2020

AbstractBackgroundPsychostimulant use disorder is a major public health issue, and despite the scope of the problem there are currently no FDA approved treatments. There would be tremendous utility in development of a treatment that could help patients both achieve and maintain abstinence. Previous work from our group has identified granulocyte-colony stimulating factor (G-CSF) as a neuroactive cytokine that alters behavioral response to cocaine, increases synaptic dopamine release, and enhances cognitive flexibility. Here, we investigate the role of G-CSF in affecting extinction and reinstatement of cocaine-seeking and perform detailed characterization of its proteomic effects in multiple limbic substructures.MethodsSprague-Dawley rats were injected with PBS or G-CSF during (1) extinction or (2) abstinence from cocaine self-administration, and drug seeking behavior was measured. Quantitative assessment of changes in the proteomic landscape in the nucleus accumbens (NAc) and medial prefrontal cortex (mPFC) were performed via data-independent acquisition (DIA) mass spectrometry analysis.ResultsAdministration of G-CSF during extinction accelerated the rate of extinction, and administration during abstinence attenuated cue-induced cocaine-seeking. Analysis of global protein expression demonstrated that G-CSF regulated proteins primarily in mPFC that are critical to glutamate signaling and synapse maintenance.ConclusionTaken together, these findings support G-CSF as a viable translational research target with the potential to reduce drug craving or seeking behaviors. Importantly, recombinant G-CSF exists as an FDA-approved medication which may facilitate rapid clinical translation. Additionally, using cutting-edge multi-region discovery proteomics analyses, these studies identify a novel mechanism underlying G-CSF effects on behavioral plasticity.
Identification of multiple noise sources improves estimation of neural responses across stimulus conditions
Authors: Weber Alison I. , Shea-Brown Eric , Rieke Fred 
Published: February 2020

AbstractMost models of neural responses are constructed to capture the average response to inputs but poorly reproduce the observed response variability. The origins and structure of this variability have significant implications for how information is encoded and processed in the nervous system. Here, we present a new modeling framework that better captures observed features of neural response variability across stimulus conditions by incorporating multiple sources of noise. We use this model to fit responses of retinal ganglion cells at two different ambient light levels and demonstrate that it captures the full distribution of responses. The model reveals light level-dependent changes that could not be seen with previous models. It shows both large changes in rectification of nonlinear circuit elements and systematic differences in the contributions of different noise sources under different conditions. This modeling framework is general and can be applied to a variety of systems outside the retina.
Extraction of Protein Dynamics Information Hidden in Cryogenic Electron Microscopy Maps Using Deep Learning
Authors: Matsumoto Shigeyuki , Ishida Shoichi , Araki Mitsugu , Kato Takayuki , Terayama Kei , Okuno Yasushi 
Published: February 2020

AbstractTechnical breakthroughs in cryogenic electron microscopy (cryo-EM)-based single-particle analysis have enabled the structures of numerous proteins to be solved at atomic or near-atomic resolutions, including extremely large macromolecules whose structures could not be solved by conventional techniques. Determining the dynamics properties of these macromolecules, based on their solved structures, can further improve our understanding of their functional mechanisms. However, such analysis is often hampered by the large molecular size and complex structural assembly, making both experimental and computational approaches to determine dynamics properties challenging. Here, we report a deep learning-based approach, DEFMap, to extract the dynamics information “hidden” in cryo-EM density maps. By relying only on cryo-EM maps, DEFMap successfully provided dynamics information equivalent to that determined from molecular dynamics (MD) simulations and experimental approaches at the atomic and residue levels. Additionally, DEFMap could detect dynamics changes associated with molecular recognition and the accompanying allosteric conformational stabilizations, which trigger various biological events such as signal transduction and enzyme catalysis. This approach will provide new insights into the functional mechanisms of biological molecules, accelerating modern molecular biology researches. Furthermore, this advanced strategy combining experimental data, deep learning approaches, and MD simulations would open a new multidisciplinary science area
Experimentally determined long intrinsically disordered protein regions are now abundant in the Protein Data Bank
Authors: Monzon Alexander Miguel , Necci Marco , Quaglia Federica , Walsh Ian , Piovesan Damiano , Zanotti Giuseppe , Tosatto Silvio C. E. 
Published: February 2020

AbstractIntrinsically disordered protein regions are commonly defined from missing electron density in X-ray structures. Experimental evidence for long disorder regions (LDRs) of at least 30 residues was so far limited to a less than a thousand manually curated proteins. Here, we describe a comprehensive and large-scale analysis of experimental LDRs for 3,133 unique proteins, demonstrating an increasing coverage of intrinsic disorder in the Protein Data Bank (PDB) in the last decade. The results suggest that long missing residue regions are a good quality source to annotate intrinsically disordered regions and perform functional analysis in large data sets. The consensus approach used to define LDRs allows to evaluate context dependent disorder and provide a common definition at the protein level.
Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway
Authors: Gillies Taryn E. , Pargett Michael , Silva Jillian M. , Teragawa Carolyn , McCormick Frank , Albeck John G. 
Published: February 2020

AbstractActivating mutations in RAS are present in ∼30% of human tumors, and the resulting aberrations in ERK/MAPK signaling play a central role in oncogenesis. However, the form of these signaling changes is uncertain, with activating RAS mutants linked to both increased and decreased ERK activationin vivo. Rationally targeting the kinase activity of this pathway requires clarification of the quantitative effects of RAS mutations. Here, we use live-cell imaging in cell lines expressing only one RAS isoform to quantify ERK activity with a new level of accuracy. We find that despite large differences in their biochemical activity, mutant KRAS isoforms within cells have similar ranges of ERK output. We identify roles for pathway-level effects, including variation in feedback strength and feedforward modulation of phosphatase activity, that act to rescale pathway sensitivity independent of expression level, ultimately resisting changes in the dynamic range of ERK activity while preserving responsiveness to growth factor stimuli. Our results reconcile seemingly inconsistent reports within the literature and imply that the initial signaling changes induced by RAS mutations in oncogenesis are subtle.
Systematic quantification of synapses in primary neuronal culture
Authors: Verstraelen Peter , Garcia Gerardo , Verschuuren Marlies , Asselbergh Bob , Nuydens Rony , Larsen Peter , Timmermans Jean-Pierre , De Vos Winnok H. 
Published: February 2020

AbstractA vast set of neurological disorders is associated with impaired synaptic connectivity. Therefore, modulation of synapse formation could have therapeutic relevance. However, the high density and small size of synapses make their quantification a challenging task. To improve the reliability of synapse-oriented drug screens, we evaluated a panel of synapse-targeting antibodies for their labeling specificity on hippocampal and cortical cell cultures using quantitative immunofluorescence microscopy. For those antibodies that passed multiparametric validation, we assessed pairwise colocalization, an often-used readout for established synapses. We found that even when two pan-synaptic markers were used, the overlap was incomplete, and the presence of spurious signals limited the dynamic range. To circumvent this problem, we implemented a proximity ligation-based approach, that only leads to a signal when two pre- and postsynaptic markers are sufficiently close. We demonstrate that this approach can be applied to different synaptic marker combinations and can be successfully used for quantification of synapse density in cultures of different maturity stage in healthy or pathological conditions. Thus, the unbiased analysis of synapse labeling and exploitation of resident protein proximity, allows increasing the sensitivity of synapse quantifications in neuronal culture and therefore represents a valuable extension of the analytical toolset forin vitrosynapse screens.
Stony coral populations are more sensitive to changes in vital rates in disturbed environments
Authors: Hall Tessa E. , Freedman Andrew S. , de Roos André M. , Edmunds Peter J. , Carpenter Robert C. , Gross Kevin 
Published: February 2020

AbstractReef-building corals, like many long-lived organisms, experience environmental change as a combination of separate but concurrent processes, some of which are gradual yet long-lasting, while others are more acute but short-lived. For corals, some chronic environmental stressors, such as rising temperature and ocean acidification, are thought to induce gradual changes in colonies’ vital rates. Meanwhile, other environmental changes, such as the intensification of tropical cyclones, change the disturbance regime that corals experience. Here, we use a physiologically structured population model to explore how chronic environmental stressors that impact the vital rates of individual coral colonies interact with the intensity and magnitude of disturbance to affect coral population dynamics and cover. We find that when disturbances are relatively benign, intraspecific density dependence driven by space competition partially buffers coral populations against gradual changes in vital rates. However, the impact of chronic stressors is amplified in more highly disturbed environments, because disturbance weakens the buffering effect of space competition. We also show that coral cover is more sensitive to changes in colony growth and mortality than to external recruitment, at least in non-self-seeding populations, and that space competition and size structure mediate the extent and pace of coral-population recovery following a large-scale mortality event. Understanding the complex interplay among chronic environmental stressors, mass-mortality events, and population size structure sharpens our ability to project coral dynamics in an increasingly disturbed future.
KD-64 – a new selective A2Aadenosine receptor antagonist has anti-inflammatory activity but contrary to the non-selective antagonist – caffeine does not reduce diet-induced obesity in mice
Authors: Kotańska Magdalena , Dziubina Anna , Szafarz Małgorzata , Mika Kamil , Reguła Karolina , Bednarski Marek , Zygmunt Małgorzata , Drabczyńska Anna , Sapa Jacek , Kieć-Kononowicz Katarzyna 
Published: February 2020

AbstractThe A2adenosine receptors play an important role, among others, in the regulation of inflammatory process and glucose homeostasis in diabetes and obesity. Thus, the presented project evaluated of influence of the selective antagonist of A2Aadenosine receptor – KD-64 as compared to the known non-selective antagonist – caffeine on these two particular processes. Two different inflammation models were induced namely local and systemic inflammation. Obesity was induced in mice by high-fat diet and the tested compounds (KD-64 and caffeine) were administrated for 21 days. KD-64 showed anti-inflammatory effect in both tested inflammation models and administered at the same dose as ketoprofen exerted stronger effect than this reference compound. Elevated levels of IL-6 and TNF-α observed in obese control mice were significantly lowered by the administration of KD-64 and were similar to the values observed in control non-obese mice. Interestingly, caffeine increased the levels of these parameters. In contrast to caffeine which had no influence on AlaT activity, KD-64 administration significantly lowered AlaT activity in the obese mice. Although, contrary to caffeine, KD-64 did not reduce diet-induced obesity in mice, it improved glucose tolerance. Thus, the activity of the selective adenosine A2Areceptor antagonist was quite different from that of the non-selective.
Mechanism of upstream promoter element stimulation of transcription at a ribosomal RNA promoter determined by single-molecule imaging
Authors: Mumm Jeffrey P. , Friedman Larry J. , Gelles Jeff 
Published: February 2020

AbstractDNA elements upstream of transcription promoters play a role in regulating transcription initiation in all organisms. In bacteria, upstream A-T rich sequences called UP elements can stimulate transcription through contact with the α subunit C-terminal domain (αCTD) of core RNA polymerase (RNAP), but the kinetic mechanisms by which they do so remain unclear. We investigated the role of the UP element in stimulating initiation from the strong E. coli 16s rRNA promoter using single-molecule fluorescence microscopy to visualize σ70RNAP holoenzyme binding and the formation nascent RNA by oligonucleotide probe hybridization on individual DNA molecules containing therrnBP1 promoter. By directly detecting initial binding of σ70RNAP to promoter and monitoring the lifetimes of promoter-polymerase complexes, the experiments reveal the kinetic mechanism of polymerase recruitment to the promoter and the subsequent conformational change that stabilizes binding. The presence of UP stimulated the rate of initial binding of polymerase to promoter by at least six-fold, and this stimulation was fully sufficient to account for the increase in initiation rate by UP. Thus, UP likely functions at this strong promoter simply by acting as a binding target for the rapidly reorienting αCTD domain tethered to the core polymerase. In contrast, there were only minor effects of UP on the measured rates of the conformational change or the dissociation rates of the initial σ70RNAP promoter complexes. These studies define a paradigmatic kinetic mechanism for stimulation of transcription initiation by direct αCTD-DNA interactions. This mechanism can serve as a building block of more complex regulatory architectures in which αCTD promotes transcription through interactions with both DNA and protein activators.
AtCIPK16 Mediates Salt Stress Through Phytohormones and Transcription Factors
Authors: Amarasinghe Shanika L. , Huang Wenmian , Watson-Haigh Nathan S. , Gilliham Matthew , Roy Stuart J. , Baumann Ute 
Published: February 2020

AbstractSoil salinity causes large productivity losses for agriculture worldwide. “Next-generation crops” that can tolerate salt stress are required for the sustainability of global food production. Previous research inArabidopsis thalianaaimed at uncovering novel factors underpinning improved plant salinity tolerance identified the protein kinase AtCIPK16. Overexpression ofAtCIPK16enhanced shoot Na+exclusion and increased biomass in both Arabidopsis and barley. Here, a comparative transcriptomic study on Arabidopsis lines expressingAtCIPK16was conducted in the presence and absence of salt stress, using an RNA-Seq approach, complemented by AtCIPK16 interaction and localisation studies. We are now able to provide evidence for AtCIPK16 activity in the nucleus. Moreover, the results manifest the involvement of a transcription factor, AtTZF1, phytohormones and the ability to quickly reach homeostasis as components important for improving salinity tolerance in transgenics overexpressingAtCIPK16. Furthermore, we suggest the possibility of both biotic and abiotic tolerance through AtCIPK16, and propose a model for the salt tolerance pathway elicited through AtCIPK16.
Renal tubule Cpt1a overexpression protects from kidney fibrosis by restoring mitochondrial homeostasis
Authors: Miguel Verónica , Tituaña Jessica , Herrero J.Ignacio , Herrero Laura , Serra Dolors , Cuevas Paula , Barbas Coral , Puyol Diego Rodríguez , Márquez-Expósito Laura , Ruiz-Ortega Marta , Castillo Carolina , Sheng Xin , Susztak Katalin , Ruiz-Canela Miguel , Salas-Salvadó Jordi , González Miguel A. Martínez , Ortega Sagrario , Ramos Ricardo , Lamas Santiago 
Published: February 2020

AbstractChronic kidney disease (CKD) remains a major epidemiological, clinical and biomedical challenge. During CKD, renal tubular epithelial cells (TECs) suffer a persistent inflammatory and profibrotic response. Fatty acid oxidation (FAO), the main source of energy for TECs, is reduced in kidney fibrosis and contributes to its pathogenesis. To determine if FAO gain-of-function (FAO-GOF) could protect from fibrosis, we generated a conditional transgenic mouse model with overexpression of the fatty acid shuttling enzyme carnitine palmitoyl-transferase 1 A (CPT1A) in TECs.Cpt1aknock-in (CPT1A KI) mice subjected to three different models of renal fibrosis (unilateral ureteral obstruction, folic acid nephropathy-FAN and adenine induced nephrotoxicity) exhibited decreased expression of fibrotic markers, a blunted pro-inflammatory response and reduced epithelial cell damage and macrophage influx. Protection from fibrosis was also observed when Cpt1a overexpression was induced after FAN. FAO-GOF restituted oxidative metabolism and mitochondrial number and enhanced bioenergetics increasing palmitate oxidation and ATP levels, changes also recapitulated in TECs exposed to profibrotic stimuli. Studies in patients evidenced decreased CPT1 levels and increased accumulation of short and middle chain acyl-carnitines, reflecting impaired FAO in human CKD. We propose that strategies based on FAO-GOF may constitute powerful alternatives to combat fibrosis inherent to CKD.Graphical abstractOverexpression of CPT1A impedes tubular epithelial renal cell dedifferentiation and a pro-fibrotic phenotype by restoring mitochondrial metabolic bioenergetics.
Twist-chair conformation of the tetraoxepane ring remains unchanged in tetraoxaspirododecane diamines
Authors: Khalilov Leonard M. , Mescheryakova Ekaterina S. , Bikmukhametov Kamil Sh. , Makhmudiyarova Natalia N. , Shangaraev Kamil R. , Tulyabaev Arthur R. 
Published: February 2020

A detailed structural analysis has been performed forN,N′-bis(4-chlorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22Cl2N2O4, (I),N,N′-bis(2-fluorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22F2N2O4, (II), andN,N′-bis(4-fluorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22F2N2O4, (III). The seven-membered ring with two peroxide groups adopts a twist-chair conformation in all three compounds. The lengths of the C—N and O—O bonds are slightly shorter than the average statistical values found in the literature for azepanes and 1,2,4,5-tetraoxepanes. The geometry analysis of compounds (I)–(III), the topological analysis of the electron density at the (3, −1) bond critical points within Bader's quantum theory of `Atoms in molecules' (QTAIM) and NBO (natural bond orbital) analysis at the B3LYP/6-31G(d,2p) level of theory showed that there arenO→σ*(C—O),nN→σ*(C—O) andnO→σ*(C—N) stereoelectronic effects. The molecules of compounds (I) and (III) are packed in the crystals as zigzag chains due to strong N—H...O and C—H...O hydrogen-bond interactions, whereas the molecules of compound (II) form chains in the crystals bound by N—H...O, C—H...π and C—H...O contacts. All these data show that halogen atoms and their positions have a minimal effect on the geometric parameters, stereoelectronic effects and crystal packing of compounds (I)–(III), so that the twist-chair conformation of the tetraoxepane ring remains unchanged.
Monotonicity, linearity and symmetry in the price volatility–volume relationship
Authors: Fousekis Panos , Tzaferi Dimitra 
Published: February 2020

PurposeThis paper aims to investigate the contemporaneous link between price volatility and trading volume in the futures markets of energy.Design/methodology/approachNon-parametric (local linear) regression models and formal statistical tests are used to assess monotonicity, linearity and symmetry. The data are daily price and volumes from five futures markets (West Texas Intermediate, Brent, gasoline, heating oil and natural gas) in the USA.FindingsTrading volume and price volatility have, in all markets, a strong nonlinear relation to each other. There are violations of monotonicity locally but not globally. The qualitative nature of the price shocks may have implications for the trading activity locally.Originality/valueTo the authors’ best knowledge, this is the first manuscript that investigates simultaneously and formally all the three important issues (i.e. monotonicity, linearity and asymmetry) for the price volatility–volume relationship using a highly flexible nonparametric approach.
Demand for global health training and experiences among emergency medicine trainees in Australia and New Zealand
Authors: Mitchell Rob D , Mitchell Rebecca L , Phillips Georgina A , Jayaratnam Skandarupan , Jamieson Jennifer , O'Reilly Gerard M 
Published: February 2020

AbstractObjectiveDemand for global health (GH) training and experiences among emergency medicine trainees is unknown. The primary objective of the Trainee Interest in Global Health Training (TIGHT) study was to quantify the number of trainees interested in completing a rotation in a resource‐limited environment within a low‐ or middle‐income country during their specialty training.MethodsA cross‐sectional study of trainees in seven specialty training programmes was conducted between August and October 2018. Data were collected using a voluntary, anonymous, self‐reporting, web‐based survey. This study describes the results of a planned sub‐group analysis of ACEM trainees.ResultsThere were 203 respondents among 2525 ACEM trainees. Although only a small number (36/198, 18.2%) had undertaken a GH experience as a specialty trainee, 85.6% (167/195) were keen to do so. The vast majority of respondents (179/194, 87.1%) were interested or very interested in having their GH experience accredited for training, but 68.9% (133/193) reported that accessing a suitable placement was a barrier. More than 79% (147/186) expressed interest in undertaking an integrated GH training or fellowship programme as an adjunct to specialty training.ConclusionsNotwithstanding the limitations of a self‐reporting survey with a sub‐optimal response rate, there is significant demand for GH training and experiences among ACEM trainees. These findings should inform the development of safe and effective global emergency care training pathways, underpinned by mutually beneficial, international partnerships with educational and development objectives.