bluuebunny/crossref_metadata_2025_split huggingface dataset:
SirT7 auto-ADP-ribosylation regulates glucose starvation response through macroH2A1.1
Authors: Simonet Nicolás G. , Thackray Joshua K. , Vazquez Berta N. , Ianni Alessandro , Espinosa-Alcantud Maria , Morales-Sanfrutos Julia , Hurtado-Bagès Sarah , Sabidó Eduard , Buschbeck Marcus , Tischfield Jay , de la Torre Carolina , Esteller Manel , Braun Thomas , Olivella Mireia , Serrano Lourdes , Vaquero Alejandro 
Published: August 2019

AbstractSirtuins are key players in the response to oxidative, metabolic and genotoxic stress, and are involved in genome stability, metabolic homeostasis and aging. Originally described as NAD+-dependent deacetylases, some sirtuins are also characterized by a poorly understood mono-ADP-ribosyltransferase (mADPRT) activity. Here we report that the deacetylase SirT7 is a dual sirtuin as it also features auto-mADPRT activity. Molecular and structural evidence suggests that this novel activity occurs at a second previously undefined active site that is physically separated in another domain. Specific abrogation of this activity alters SirT7 chromatin distribution, suggesting a role for this modification in SirT7 chromatin binding specificity. We uncover an epigenetic pathway by which ADP-ribosyl-SirT7 is recognized by the ADP-ribose reader macroH2A1.1, a histone variant involved in chromatin organization, metabolism and differentiation. Glucose starvation (GS) boosts this interaction and promotes SirT7 relocalization to intergenic regions in a macroH2A1-dependent manner. Both SirT7 activities are in turn required to promote GS-dependent enrichment of macroH2A1 in a subset of nearby genes, which results in their specific up- or downregulation. Consistently, the expression changes of these genes associated to calorie restriction (CR) or aging are abrogated in SirT7-/- mice, reinforcing the link between Sirtuins, CR and aging. Our work provides a novel perspective about sirtuin duality and suggests a key role for SirT7/macroH2A1.1 axis in mammalian glucose homeostasis, calorie restriction signaling and aging.
A Galaxy-based training resource for single-cell RNA-seq quality control and analyses
Authors: Etherington Graham J , Soranzo Nicola , Mohammed Suhaib , Haerty Wilfried , Davey Robert P , Di Palma Federica 
Published: August 2019

AbstractBackgroundIt is not a trivial step to move from single-cell RNA-seq (scRNA-seq) data production to data analysis. There is a lack of intuitive training materials and easy-to-use analysis tools, and researchers can find it difficult to master the basics of scRNA-seq quality control and analysis.ResultsWe have developed a range of easy-to-use scripts, together with their corresponding Galaxy wrappers, that make scRNA-seq training and analysis accessible to researchers previously daunted by the prospect of scRNA-seq analysis. The simple command-line tools and the point-and-click nature of Galaxy makes it easy to assess, visualise, and quality control scRNA-seq data.ConclusionWe have developed a suite of scRNA-seq tools that can be used for both training and more in-depth analyses.
Cornichon Homolog-3 (CNIH3) Modulates Spatial Memory in Female Mice
Authors: Frye Hannah E. , Williams Sidney B. , Trousdale Christopher R. , Nelson Elliot C. , Dougherty Joseph D. , Morón Jose A. 
Published: August 2019

ABSTRACTCornichon homolog-3 (CNIH3) is an AMPA receptor (AMPAR) auxiliary protein that traffics AMPARs to the postsynaptic membrane and potentiates AMPAR signaling. AMPARs are key components of hippocampal synaptic plasticity and memory formation, however the role of CNIH3 in memory has yet to be elucidated. To study the role of CNIH3 on mouse behavior, we bred and characterized a line of Cnih3-/- mice from C57BL/6 Cnih3tm1a(KOMP)Wtsi mice obtained from the Knockout Mouse Project (KOMP). In agreement with previous studies of CNIH3 in the brain, we observed concentrated expression of Cnih3 in the dorsal hippocampus, a region associated with spatial learning and memory. Therefore, we tested Cnih3+/+, Cnih3+/-, and Cnih3-/- mice in the Barnes maze paradigm to measure spatial memory. We observed no change in spatial memory in male Cnih3+/- and Cnih3-/- mice compared to male Cnih3+/+ controls, however, Cnih3-/- female mice made significantly more primary errors, had a higher primary latency, and took less efficient routes to the target in the maze compared to Cnih3+/+ female mice. Next, to investigate an enhancement of spatial memory by Cnih3 overexpression, specifically in the dorsal hippocampus, we developed an AAV5 viral construct to express wild-type Cnih3 in excitatory neurons. Female mice overexpressing Cnih3 made significantly fewer errors, had a lower primary latency to the target, and took more efficient routes to the maze target compared to YFP expressing control females. No change in spatial memory was observed in male Cnih3 overexpression mice. This study, the first to identify sex-specific effects of the AMPAR auxiliary protein CNIH3 on spatial memory, provides the groundwork for future studies investigating the role of CNIH3 on sexually dimorphic AMPAR-dependent behavior and hippocampal synaptic plasticity.
Evolutionary increases in catecholamine signaling may underlie the emergence of adaptive traits and behaviors in the blind cavefish, Astyanax mexicanus
Authors: Gallman Kathryn , Rivera Daihana , Soares Daphne 
Published: August 2019

AbstractEvolutionary changes in catecholamine neurotransmitters such as dopamine and noradrenaline can lead to habitat specific behaviors. We used tyrosine hydroxylase, a conserved precursor to the biosynthesis of dopamine and noradrenaline, to compare catecholaminergic neurons in the brain of a species undergoing allopatric speciation. The teleost fish Astyanax mexicanus is extant in two readily available forms, an ancestral river dwelling form (surface) and various derived blind cave forms (cavefish). Adaptation to nutrient poor cave life without predation has led to marked differences in the behavior of this species. The cavefish has lost defensive responses, such as stimulus aversion, found in the ancestral surface fish and instead displays enhanced food seeking behaviors. This is reflected by an increase in catecholamine immunoreactivity in the cavefish brain in regions associated with non-visual sensory perception, motor control pathways, attention, and endocrine release. These neuroanatomical regions include the olfactory system, the basal telencephalon, the preoptic nuclei, the posterior tuberculum, caudal hypothalamus, and isthmus. These results indicate that the evolutionary shift from aversive defensive responses to attractive exploratory behaviors was driven by increases in the size and/or quantity of catecholaminergic neurons in the cavefish brain.
Maximizing Ecosystem Services Provided to the New Oil Crop Brassica carinata Through Landscape and Arthropod Diversity
Authors: Stiles Shane , Lundgren Jon , Fenster Charles , Nottebrock Henning 
Published: August 2019

ABSTRACTPrairies, once spanning the Upper Midwest, have now largely been replaced by agriculture. The lack of resources available to pollinators in agricultural fields and practices commonly employed has led to a decline in insect diversity. To enhance sustainable practices, we must better understand how ecosystem services such as pest control and pollination services provided by a diverse insect and pollinator community scale to current farming practices as related to crop yield and how landscape features may positively contribute to insect and pollinator diversity. We examined how landscape heterogeneity relates to insect and pollinator diversity, as well as how insect and pollinator diversity relates to crop yield across common farming practices. We planted 35 single acre sites of Brassica carinata, a generalist flower possibly capable of supporting a diverse insect community. We randomly assigned each site with a combination of three common farming practices: tilling (yes/no), added honey bee hives (yes/no), and treatment with systemic neonicotinoids (yes/no). Insect and pollinator diversity and the surrounding landscape at multiple spatial scales were calculated. We observed a significant positive relationship between insect (and pollinator) diversity with yield in the absence of any farming practice. All farming practices will increase yield. However, farming practices alter the relationship between yield and diversity. The addition of seed treatment or tillage negates the relationship between insect (and pollinator) diversity with yield. Seed treatment alone results in a flat relationship between diversity and yield for all insects and a negative relationship for pollinators. Increased landscape heterogeneity results in a positive relationship between insect diversity at the 1000 m scale and pollinator diversity at the 3000 m scale, suggesting large-scale heterogeneity contributes to overall insect diversity. Our results show that increasing large-scale landscape heterogeneity increases diversity serving as a substitute for common farming practices such as application of pesticides, tilling, or bee hives. Increased heterogeneity could save farmers from the input cost of treatment or tillage, by way of increased insect diversity, while still providing similar yields.
Dynamic 3D chromosomal landscapes in acute leukemia
Authors: Kloetgen Andreas , Thandapani Palaniraja , Ntziachristos Panagiotis , Ghebrechristos Yohana , Nomikou Sofia , Lazaris Charalampos , Chen Xufeng , Hu Hai , Bakogianni Sofia , Wang Jingjing , Fu Yi , Boccalatte Francesco , Zhong Hua , Paietta Elisabeth , Trimarchi Thomas , Zhu Yixing , van Vlierberghe Pieter , Inghirami Giorgio G , Lionnet Timothee , Aifantis Iannis , Tsirigos Aristotelis 
Published: August 2019

ABSTRACTThree-dimensional (3D) chromatin architectural changes can alter the integrity of topologically associated domains (TADs) and rewire specific enhancer-promoter interactions impacting gene expression. Recently, such alterations have been implicated in human disease, highlighting the need for a deeper understanding of their role. Here, we investigate the reorganization of chromatin architecture in T cell acute lymphoblastic leukemia (T-ALL) using primary human leukemia specimens and its dynamic responses to pharmacological agents. Systematic integration of matched in situ Hi-C, RNA-Seq and CTCF ChIP-Seq datasets revealed widespread changes in intra-TAD chromatin interactions and TAD boundary insulation in T-ALL. Our studies identify and focus on a TAD “fusion” event being associated with loss of CTCF-mediated insulation, enabling direct interactions between the MYC promoter and a distal super-enhancer. Moreover, our data show that small molecule inhibitors targeting either oncogenic signal transduction or epigenetic regulation reduce specific 3D interactions associated with transformation. Overall, our study highlights the impact, complexity and dynamic nature of 3D chromatin architecture in human acute leukemia.One Sentence Summary3D chromatin alterations in T cell leukemia are accompanied by changes in insulation and oncogene expression and can be partially restored by targeted drug treatments.
Computational mapping of the differentially expressed gene-lncRNA pairs present at the root nodule developmental stages of Arachis hypogaea
Authors: Rizvi Ahsan Z. , Dhusia Kalyani 
Published: August 2019

AbstractRNA-sequencing (RNA-seq) data analysis of the different stages of root nodules formation in peanut Arachis hypogaea investigate the genetic features. Genes related to the root nodules formations in this plant are extensively studied [1] [2] [3] [4] [5], but less information is present for their relations with long noncoding RNAs (lncRNAs). Bioinformatics techniques are utilised here to identify the novel lncRNAs present in the publically available RNA-seq data reported [6] for the different stages of root nodules formation in this plant. Highly correlated, significant, and Differentially Expressed (DE) gene-lncRNA pairs are also detected to understand the epigenetic control of lncRNA. These pairs are further differentiated between cis and trans antisense lncRNAs and lincRNAs based on their functions and positions from the genes. Obtained results are the catalogue for the highly correlated and significant DE gene-lncRNA pairs related to root nodules formation in A. hypogaea.
Eye movements during visuomotor adaptation represent only part of the explicit learning
Authors: Bromberg Zohar , Donchin Opher , Haar Shlomi 
Published: August 2019

AbstractVisuomotor rotations are learned through a combination of explicit strategy and implicit recalibration. However, measuring the relative contribution of each remains a challenge and the possibility of multiple explicit and implicit components complicates the issue. Recent interest has focused on the possibility that eye movements reflect explicit strategy. Here we compared eye movements during adaptation to two accepted measures of explicit learning - verbal report and the exclusion test. We found that while reporting, all subjects showed a match between all three measures. However, when subjects did not report their intention, the eye movements of some subjects suggested less explicit adaptation than what was measured in an exclusion test. Interestingly, subjects whose eye movements did match their exclusion could be clustered into two subgroups: fully implicit learners showing no evidence of explicit adaptation and explicit learners with little implicit adaptation. Subjects showing a mix of both explicit and implicit adaptation were also those where eye movements showed less explicit adaptation than did exclusion. Thus, our results support the idea of multiple components of explicit learning as only part of the explicit learning is reflected in the eye movements. Individual subjects may use explicit components that are reflected in the eyes or those that are not or some mixture of the two. Analysis of reaction times suggests that the explicit components reflected in the eye-movements involve longer reaction times. This component, according to recent literature, may be related to mental rotation.Significance StatementVisuomotor adaptation involves both explicit and implicit components: aware re-aiming and unaware error correction. Recent studies suggest that eye movements could be used to capture the explicit component, a method that would have significant advantages over other approaches. We show that eye movements capture only one component of explicit adaptation. This component scales with reaction time while the component unrelated to eye movements does not. Our finding has obvious practical implications for the use of eye movements as a proxy for explicit learning. However, our results also corroborate recent findings suggesting the existence of multiple explicit components, and, specifically, their decomposition into components correlated with reaction time and components that are not.
Metabolic responses in opposite sun-exposed Antarctic cryptoendolithic communities
Authors: Coleine Claudia , Gevi Federica , Fanelli Giuseppina , Onofri Silvano , Timperio Anna Maria , Selbmann Laura 
Published: August 2019

ABSTRACTAntarctic cryptoendolithic communities are self-supporting borderline ecosystems spreading across the extreme conditions of the Antarctic desert and represent the most predominant life-form in the ice-free desert of McMurdo Dry Valleys, accounted as the closest terrestrial Martian analogue. Components of these communities are very adapted extremophiles and extreme-tolerant microorganisms, among the most resistant known to date. Recent advances started to investigate the biodiversity and community composition in these microbial ecosystems but the metabolic activity of the metacommunity has never been investigated to date. In this study, we explored the stress-response, spreading in two different sites of the same location, subjected to increasing environmental pressure due to opposite sun exposure, to verify the effect of sunlight on settlement and adaptation strategies. Results indicated that the metabolic responses are shaped according to external conditions; in the overall 252 altered metabolites (56 and 196 unique for north and south, respectively), distinguished the two differently exposed communities. We also selected 10 metabolites and performed two-stage Receiver Operating Characteristic (ROC) analysis to test them as potential biomarkers. We focused further on melanin and allantoin as protective substances; their concentration was highly different in the community in the shadow or in the sun.
Morphogenesis is transcriptionally coupled to neurogenesis during peripheral olfactory organ development
Authors: Aguillon Raphaël , Madelaine Romain , Guturu Harendra , Link Sandra , Dufourcq Pascale , Lecaudey Virginie , Bejerano Gill , Blader Patrick , Batut Julie 
Published: August 2019

AbstractSense organs acquire their distinctive shapes concomitantly with the differentiation of sensory cells and neurons necessary for their function. While our understanding of the mechanisms controlling morphogenesis and neurogenesis in these structures has grown, how these processes are coordinated remains largely unexplored. Neurogenesis in the zebrafish olfactory epithelium requires the bHLH proneural transcription factor Neurogenin1 (Neurog1). To address whether Neurog1 also controls morphogenesis in this system, we analysed the morphogenetic behaviour of early olfactory neural progenitors inneurog1mutant embryos. Our results indicate that the oriented movements of these progenitors are disrupted in this context. Morphogenesis is similarly affected by mutations in the chemokine receptor gene,cxcr4b, suggesting it is a potential Neurog1 target gene. We find that Neurog1 directly regulatescxcr4bthrough an E-boxes cluster located just upstream of thecxcr4btranscription start site. Our results suggest that proneural transcription factors, such as Neurog1, directly couple distinct aspects of nervous system development.One Sentence SummaryNeurog1 controls olfactory organ morphogenesis viacxcr4b
Meta-transcriptomic comparison of the RNA viromes of the mosquito vectors Culex pipiens and Culex torrentium in northern Europe
Authors: Pettersson John H.-O. , Shi Mang , Eden John-Sebastian , Holmes Edward C. , Hesson Jenny C. 
Published: August 2019

AbstractThere is mounting evidence that mosquitoes harbour an extensive diversity of ‘insect-specific’ RNA viruses in addition to those important to human and animal health. However, because most studies of the mosquito virome have been conducted at lower latitudes there is a major knowledge gap on the genetic diversity, evolutionary history, and spread of RNA viruses sampled from mosquitoes in northern latitudes. Here, we determined and compared the RNA virome of two common northern Culex mosquito species, Cx. pipiens and Cx. torrentium, known vectors of West Nile virus and Sindbis virus, respectively, collected in south-central Sweden. Following bulk RNA-sequencing (meta-transcriptomics) of 12 libraries, comprising 120 specimens of Cx. pipiens and 150 specimens of Cx. torrentium, we identified 40 viruses (representing 14 virus families) of which 28 were novel based on phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) protein. Hence, we found similar levels of virome diversity as in mosquitoes sampled from the more biodiverse lower latitudes. Four libraries, all from Cx. torrentium, had a significantly higher abundance of viral reads, spanning ∼7– 36% of the total amount of reads. Many of these viruses were also related to those sampled on other continents, indicative of widespread global movement and/or long host-virus co-evolution. Importantly, although the two mosquito species investigated have overlapping geographical distributions and share many viruses, approximately one quarter of the viruses were only found at a specific location, such that geography must play an important role in shaping the diversity of RNA viruses in Culex mosquitoes.ImportanceRNA viruses are found in all domains of life and all global habitats. However, the factors that determine virome composition and structure within and between organisms are largely unknown. Herein, we characterised RNA virus diversity in two common mosquito vector species, Culex pipiens and Culex torrentium, sampled from northern Europe. Our analysis revealed extensive viral diversity, including 28 novel viruses, and was comparable to the levels of diversity found in other temperate and tropical regions globally. Importantly, as well as harbouring RNA viruses that are closely related to other mosquito-derived viruses sampled in diverse global locations, we also described a number of viruses that are unique to specific sampling locations in Sweden. Hence, these data showed that geographical factors can play an important role in shaping virome structure even at local scales.
Regulation of Microtubule Disassembly by Spatially Heterogeneous Patterns of Acetylation
Authors: Aparna J S , Padinhateeri Ranjith , Das Dibyendu 
Published: August 2019

AbstractMicrotubules (MTs) are bio-polymers, composed of tubulin proteins, involved in several functions such as cell division, transport of cargoes within cells, maintaining cellular structures etc. Their kinetics are often affected by chemical modifications on the filament known as Post Translational Modifications (PTMs). Acetylation is a PTM which occurs on the luminal surface of the MT lattice and has been observed to reduce the lateral interaction between tubulins on adjacent protofilaments. Depending on the properties of the acetylase enzymeαTAT1 and the structural features of MTs, the patterns of acetylation formed on MTs are observed to be quite diverse. In this study, we present a multi-protofilament model with spatially heterogenous patterns of acetylation, and investigate how the local kinetic differences arising from heterogeneity affect the global kinetics of MT filaments. From the computational study we conclude that a filament with spatially uniform acetylation is least stable against disassembly, while ones with more clustered acetylation patterns may provide better resistance against disassembly. The increase in disassembly times for clustered pattern as compared to uniform pattern can be upto fifty percent for identical amounts of acetylation. Given that acetylated MTs affect several cellular functions as well as diseases such as cancer, our study indicates that spatial patterns of acetylation need to be focussed on, apart from the overall amount of acetylation.Author SummaryMicrotubules (MTs) form a crucial part of the cytoskeletal machinery which regulates several cellular processes. The basic building block of MTs are tubulin proteins. These proteins assemble in lateral and longitudinal directions to form a hollow cylindrical structure of a MT. There are chemical modifications on tubulin, known as Post Translational Modifications (PTMs), which affect the stability and dynamics of MT filaments. We computationally study how one such PTM, namely acetylation, affects the kinetics of disassembly of a MT filament. We propose a model which incorporates spatially heterogeneous patterns of acetylation on MT filament and study how they may regulate the disassembly times and velocities, a factor hitherto unexplored in studies. We conclude that there are significant differences of disassembly velocities and their fluctuations depending on the differnces in spatial patterns of acetylation.