bluuebunny/crossref_metadata_2025_split huggingface dataset:
MiRNAs profiling and degradome sequencing between the CMS-line N816S and its maintainer line Ning5m during anther development in pepper (Capsicum annuumL.)
Authors: Zhang Hongyuan , Huang Shuping , Tan Jie , Chen Xia , Zhang Min 
Published: February 2020

AbstractUtilization of cytoplasmic male sterility (CMS) is significant for agriculture. MiRNAs are a class of endogenously non-coding small RNAs (21-24 nt) that play key roles in the regulation of various growth and developmental processes in plants. The knowledge miRNA-guided CMS regulation is rather limited in pepper. To better understand the miRNAs involvement and regulatory mechanism of CMS, miRNA libraries from anther of CMS-line N816S and its maintainer line Ning5m were generated by miRNAome sequencing in pepper. A total of 76 differentially expressed miRNAs were detected, of which 18 miRNAs were further confirmed by quantitative real-time PCR (qRT-PCR). In addition, miRNA targets were identified by degradome sequencing. The result showed that 1292 targets that were potentially cleaved by 321 miRNAs (250 conserved miRNAs and 71 novel miRNAs). Gene Ontology (GO) and KEGG pathway analysis indicated that 35 differentially expressed miRNAs might play roles in the regulation of CMS sterility, by cleaving 77 target transcripts, such asMYBs, SPLs, andAFRs, of which targeted by miR156, miR167, miRNA858 family. Nineteen miRNA-cleaved targets were selectively examined by qRT-PCR, and the results showed that there were mostly negative correlations between miRNAs and their targets on the expression level. These findings provide a valuable information to understand miRNAs mechanism during anther development and CMS occurrence in pepper.
Haplotype Threading: Accurate Polyploid Phasing from Long Reads
Authors: Schrinner Sven D. , Mari Rebecca Serra , Ebler Jana , Rautiainen Mikko , Seillier Lancelot , Reimer Julia J. , Usadel Björn , Marschall Tobias , Klau Gunnar W. 
Published: February 2020

AbstractResolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. As a highly complex computational problem, polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.We present WhatsHap polyphase, a novel two-stage approach that addresses these challenges by (i) clustering reads using a position-dependent scoring function and (ii) threading the haplotypes through the clusters by dynamic programming. We demonstrate on a simulated data set that this results in accurate haplotypes with switch error rates that are around three times lower than those obtainable by the current state-of-the-art and even around seven times lower in regions of collapsing haplotypes. Using a real data set comprising long and short read tetraploid potato sequencing data we show that WhatsHap polyphaseis able to phase the majority of the potato genes after error correction, which enables the assembly of local genomic regions of interest at haplotype level. Our algorithm is implemented as part of the widely used open source tool WhatsHap and ready to be included in production settings.
Mindfulness meditation experience is associated with increased ability to monitor covert somatosensory attention
Authors: Whitmarsh Stephen , Jensen Ole , Barendregt Henk 
Published: February 2020

AbstractThe distinguishing practice of mindfulness meditation is the intentional regulation of attention towards the present moment. Mindfulness meditation therefore emphasizes metacognitive functions, in particular the ability to monitor the attentional focus on a moment-by-moment basis. In this study we set out to test whether mindfulness meditation experience is associated with an increased ability to monitor moment-by-moment fluctuation in the attentional state. In response to auditory cues, participants maintained somatosensory attention to either their left or right hand. At random moments, trials were terminated by a probe sound to which participants reported their level of attention at that moment. MEG was recorded during the attention interval preceding probe onset. Using a beamformer approach, alpha activity in contralateral primary somatosensory regions was quantified. Alpha activity for self-reported high versus low attention trials was compared both within and between groups of either highly experienced experienced mindfulness meditators, novice meditators or meditation-naive participants (controls). As predicted, generally contralateral alpha power was associated with self-reported attention. Novice meditators (< 1000 h of meditation) showed temporal profiles similar to controls, displaying a correspondence between self-report and alpha power preceding probe onset. Expert meditators (≫ 1000 h) showed a strikingly different pattern, however. Their self-reported attentional state corresponded with alpha power during a more extended time interval preceding those of controls and novice meditators. In addition, self-reported low attention trials showed a distinctive alpha suppression preceding probe onset, suggesting that the ability for moment-by-moment monitoring of the attentional state permitted greater attentional control.
In cell architecture of the nuclear pore complex and snapshots of its turnover
Authors: Allegretti Matteo , Zimmerli Christian E. , Rantos Vasileios , Wilfling Florian , Ronchi Paolo , Fung Herman K.H. , Lee Chia-Wei , Hagen Wim , Turonova Beata , Karius Kai , Zhang Xiaojie , Müller Christoph , Schwab Yannick , Mahamid Julia , Pfander Boris , Kosinski Jan , Beck Martin 
Published: February 2020

SummaryNuclear pore complexes (NPCs) mediate exchange across the nuclear envelope. They consist of hundreds of proteins called nucleoporins (Nups) that assemble in multiple copies to fuse the inner and outer nuclear membranes. Elucidating the molecular function and architecture of NPCs imposes a formidable challenge and requires the convergence ofin vitroandin situapproaches. How exactly NPC architecture accommodates processes such as mRNA export or NPC assembly and turnover inside of cells remains poorly understood. Here we combine integratedin situstructural biology, correlative light and electron microscopy with yeast genetics to structurally analyze NPCs within the native context ofSaccharomyces cerevisiaecells under conditions of starvation and exponential growth. We find an unanticipatedin situlayout of nucleoporins with respect to overall dimensions and conformation of the NPC scaffold that could not have been predicted from previousin vitroanalysis. Particularly striking is the configuration of the Nup159 complex, which appears critical to spatially accommodate not only mRNA export but also NPC turnover by selective autophagy. We capture structural snapshots of NPC turnover, revealing that it occurs through nuclear envelope herniae and NPC-containing nuclear vesicles. Our study provides the basis for understanding the various membrane remodeling events that happen at the interface of the nuclear envelope with the autophagy apparatus and emphasizes the need of investigating macromolecular complexes in their cellular context.
Unravelling the developmental and functional significance of an ancient Argonaute duplication
Authors: Fridrich Arie , Modepalli Vengamanaidu , Lewandowska Magda , Aharoni Reuven , Moran Yehu 
Published: February 2020

AbstractmicroRNAs (miRNAs), base-pair to messenger RNA targets and guide Argonaute proteins to mediate their silencing. This target regulation is considered crucial for animal physiology and development. However, this notion is based exclusively on studies in bilaterians, which comprise almost all lab model animals. To fill this glaring phylogenetic gap, we characterized the functions of two Argonaute paralogs in the sea anemoneNematostella vectensisof the phylum Cnidaria, which is separated from bilaterians by ∼600 million years. Using genetic manipulation, Argonaute-immunoprecipitations and high-throughput sequencing we provide experimental evidence for the developmental importance of miRNAs in a non-bilaterian animal. Additionally, we uncover unexpected differential distribution of distinct miRNAs between the two Argonautes and the ability of one of them to load additional types of small RNAs. This enables us to postulate a novel model for evolution of miRNA precursors in sea anemones and their relatives, revealing alternative trajectories for metazoan miRNA evolution.
RNA structure prediction using positive and negative evolutionary information
Authors: Rivas Elena 
Published: February 2020

AbstractKnowing the structure of conserved structural RNAs is important to elucidate their function and mechanism of action. However, predicting a conserved RNA structure remains unreliable, even when using a combination of thermodynamic stability and evolutionary covariation information. Here we present a method to predict a conserved RNA structure that combines the following three features. First, it uses significant covariation due to RNA structure and removes spurious covariation due to phylogeny. Second, it uses negative evolutionary information: basepairs that have variation but no significant covariation are prevented from occurring. Lastly, it uses a battery of probabilistic folding algorithms that incorporate all positive covariation into one structure. The method, named CaCoFold (Cascade variation/covariation Constrained Folding algorithm), predicts a nested structure guided by a maximal subset of positive basepairs, and recursively incorporates all remaining positive basepairs into alternative helices. The alternative helices can be compatible with the nested structure such as pseudoknots, or overlapping such as competing structures, base triplets, or other 3D non-antiparallel interactions. We present evidence that CaCoFold predictions are consistent with structures modeled from crystallography.Author SummaryThe availability of deeper comparative sequence alignments and recent advances in statistical analysis of RNA sequence covariation have made it possible to identify a reliable set of conserved base pairs, as well as a reliable set of non-basepairs (positions that vary without covarying). Predicting an overall consensus secondary structure consistent with a set of individual inferred pairs and non-pairs remains a problem. Current RNA structure prediction algorithms that predict nested secondary structures cannot use the full set of inferred covarying pairs, because covariation analysis also identifies important non-nested pairing interactions such as pseudoknots, base triples, and alternative structures. Moreover, although algorithms for incorporating negative constraints exist, negative information from covariation analysis (inferred non-pairs) has not been systematically exploited.Here I introduce an efficient approximate RNA structure prediction algorithm that incorporates all inferred pairs and excludes all non-pairs. Using this, and an improved visualization tool, I show that the method correctly identifies many non-nested structures in agreement with known crystal structures, and improves many curated consensus secondary structure annotations in RNA sequence alignment databases.
TRPV1 expressed throughout the arterial circulation enables inflammatory vasoconstriction
Authors: Phan Thieu X. , Ton Hoai T. , Gulyás Hajnalka , Pórszász Róbert , Tóth Attila , Russo Rebekah , Kay Matthew W. , Sahibzada Niaz , Ahern Gerard P. 
Published: February 2020

AbstractThe capsaicin receptor, TRPV1, is a key ion channel involved in inflammatory pain signaling. Although mainly studied in sensory nerves, there are reports of TRPV1 expression in isolated segments of the vasculature, but whether the channel localizes to vascular endothelium or smooth muscle is controversial and the distribution and functional roles of TRPV1 in arteries remain unknown. We mapped functional TRPV1 expression throughout the mouse arterial circulation. Analysis of reporter mouse lines TRPV1PLAP-nlacZand TRPV1-Cre:tdTomato combined with Ca2+imaging revealed specific localization of TRPV1 to smooth muscle of terminal arterioles in the heart, fat and skeletal muscle. Capsaicin evoked inward currents and raised intracellular Ca2+levels in arterial smooth muscle cells, constricted arteriolesex vivoandin vivoand increased systemic blood pressure in mice and rats. Further, capsaicin markedly and dose-dependently reduced coronary flow. Pharmacologic and/or genetic disruption of TRPV1 abolished all these effects of capsaicin as well as vasoconstriction triggered by lysophosphatidic acid, a bioactive lipid generated by platelets and atherogenic plaques. Notably, ablation of sensory nerves did not affect the responses to capsaicin revealing a vascular smooth muscle-restricted signaling mechanism. Moreover, unlike in sensory nerves, TRPV1 function in arteries was resistant to activity-induced desensitization. Thus, TRPV1 activation in vascular myocytes of resistance arterioles enables a persistent depolarizing current, leading to constriction of coronary, skeletal muscle, and adipose arterioles and a sustained increase in systemic blood pressure.
Bidirectional synaptic plasticity rapidly modifies hippocampal representations
Authors: Milstein Aaron D. , Li Yiding , Bittner Katie C. , Grienberger Christine , Soltesz Ivan , Magee Jeffrey C. , Romani Sandro 
Published: February 2020

SummaryLearning requires neural adaptations thought to be mediated by activity-dependent synaptic plasticity. A relatively non-standard form of synaptic plasticity driven by dendritic plateau potentials has been reported to underlie place field formation in hippocampal CA1 neurons. Here we found that this behavioral timescale synaptic plasticity (BTSP) can also reshape existing place fields via bidirectional synaptic weight changes that depend on the temporal proximity of plateau potentials to pre-existing place fields. When evoked near an existing place field, plateau potentials induced less synaptic potentiation and more depression, suggesting BTSP might depend inversely on postsynaptic activation. However, manipulations of place cell membrane potential and computational modeling indicated that this anti-correlation actually results from a dependence on current synaptic weight such that weak inputs potentiate and strong inputs depress. A network model implementing this bidirectional synaptic learning rule suggested that BTSP enables population activity, rather than pairwise neuronal correlations, to drive neural adaptations to experience.
Cooperative policing behavior regulates reproductive division of labor in a termite
Authors: Sun Qian , Hampton Jordan D. , Haynes Kenneth F. , Merchant Austin , Zhou Xuguo 
Published: February 2020

AbstractReproductive conflicts are common in insect societies where helping castes retain reproductive potential. One of the mechanisms regulating the conflicts is policing, a coercive behavior that reduces direct reproduction by other individuals. In eusocial Hymenoptera (ants, bees, and wasps), workers or the queen act aggressively toward fertile workers, or destroy their eggs. In many termite species (order Blattodea), upon the death of primary queen and king, workers or nymphs can differentiate into neotenic reproductives and inherit the breeding position. During this process, competition among neotenics is inevitable, but how this conflict is resolved remains unclear. Here, we report a policing behavior that regulates reproductive division of labor in the eastern subterranean termite,Reticulitermes flavipes. Our results demonstrate that the policing behavior is a cooperative effort performed sequentially by successful neotenics and workers. A neotenic reproductive initiates the attack of the fellow neotenic by biting and displays alarm behavior. Workers are then recruited to cannibalize the injured neotenic. Furthermore, the initiation of policing is age-dependent, with older reproductives attacking younger ones, thereby inheriting the reproductive position. This study provides empirical evidence of policing behavior in termites, which represents a convergent trait shared between eusocial Hymenoptera and Blattodea.
Ribosome Profiling in Archaea Reveals Leaderless Translation, Novel Translational Initiation Sites, and Ribosome Pausing at Single Codon Resolution
Authors: Gelsinger Diego Rivera , Dallon Emma , Reddy Rahul , Mohammad Fuad , Buskirk Allen R. , DiRuggiero Jocelyne 
Published: February 2020

ABSTRACTHigh-throughput methods, such as ribosome profiling, have revealed the complexity of translation regulation in Bacteria and Eukarya with large-scale effects on cellular functions. In contrast, the translational landscape in Archaea remains mostly unexplored. Here, we developed ribosome profiling in a model archaeon,Haloferax volcanii, elucidating, for the first time, the translational landscape of a representative of the third domain of life. We determined the ribosome footprint ofH. volcaniito be comparable in size to that of the Eukarya. We linked footprint lengths to initiating and elongating states of the ribosome on leadered transcripts, operons, and on leaderless transcripts, the latter representing 70% ofH. volcaniitranscriptome. We manipulated ribosome activity with translation inhibitors to reveal ribosome pausing at specific codons. Lastly, we found that the drug harringtonine arrested ribosomes at initiation sites in this archaeon. This drug treatment allowed us to confirm known translation initiation sites and also reveal putative novel initiation sites in intergenic regions and within genes. Ribosome profiling revealed an uncharacterized complexity of translation in this archaeon with bacteria-like, eukarya-like, and potentially novel translation mechanisms. These mechanisms are likely to be functionally essential and to contribute to an expanded proteome with regulatory roles in gene expression.
A neural circuit for flexible control of persistent behavioral states
Authors: Ji Ni , Madan Gurrein K. , Fabre Guadalupe I. , Dayan Alyssa , Baker Casey M. , Nwabudike Ijeoma , Flavell Steven W. 
Published: February 2020

ABSTRACTTo adapt to their environments, animals must generate behaviors that are closely aligned to a rapidly changing sensory world. However, behavioral states such as foraging or courtship typically persist over long time scales to ensure proper execution. It remains unclear how neural circuits generate persistent behavioral states while maintaining the flexibility to select among alternative states when the sensory context changes. Here, we elucidate the functional architecture of a neural circuit controlling the choice between roaming and dwelling states, which underlie exploration and exploitation during foraging inC. elegans. By imaging ensemble-level neural activity in freely-moving animals, we identify stable, circuit-wide activity patterns corresponding to each behavioral state. Combining circuit-wide imaging with genetic analysis, we find that mutual inhibition between two antagonistic neuromodulatory systems underlies the persistence and mutual exclusivity of the opposing network states. Through machine learning analysis and circuit perturbations, we identify a sensory processing neuron that can transmit information about food odors to both the roaming and dwelling circuits and bias the animal towards different states in different sensory contexts, giving rise to context-appropriate state transitions. Our findings reveal a potentially general circuit architecture that enables flexible, sensory-driven control of persistent behavioral states.
Physiological and head motion signatures in static and time-varying functional connectivity and their subject discriminability
Authors: Xifra-Porxas Alba , Kassinopoulos Michalis , Mitsis Georgios D. 
Published: February 2020

AbstractHuman brain connectivity yields significant potential as a noninvasive biomarker. Several studies have used fMRI-based connectivity fingerprinting to characterize individual patterns of brain activity. However, it is not clear whether these patterns mainly reflect neural activity or the effect of physiological and motion processes. To answer this question, we capitalize on a large data sample from the Human Connectome Project and rigorously investigate the contribution of the aforementioned processes on functional connectivity (FC) and time-varying FC, as well as their contribution to subject identifiability. We find that head motion, as well as heart rate and breathing fluctuations, induce artifactual connectivity within distinct resting-state networks and that they correlate with recurrent patterns in time-varying FC. Even though the spatiotemporal signatures of these processes yield above-chance levels in subject identifiability, removing their effects at the preprocessing stage improves identifiability, suggesting a neural component underpinning the inter-individual differences in connectivity.
Altered Temporal Variability of Local and Large-scale Resting-state Brain Functional Connectivity Patterns in Schizophrenia and Bipolar Disorder
Authors: Long Yicheng , Liu Zhening , Chan Calais Kin-yuen , Wu Guowei , Xue Zhimin , Pan Yunzhi , Chen Xudong , Huang Xiaojun , Pu Weidan 
Published: February 2020

AbstractSchizophrenia and bipolar disorder share some common clinical features and are both characterized by aberrant resting-state functional connectivity (FC). However, little is known about the common and specific aberrant features of the dynamic FC patterns in these two disorders. In this study, we explored the differences in dynamic FC among schizophrenia patients (n= 66), type I bipolar disorder patients (n= 53) and healthy controls (n= 66), by comparing temporal variabilities of FC patterns involved in specific brain regions and large-scale brain networks. Compared with healthy controls, both patient groups showed significantly increased regional FC variabilities in subcortical areas including the thalamus and basal ganglia, as well as increased inter-network FC variability between the thalamus and sensorimotor areas. Specifically, more widespread changes were found in the schizophrenia group, involving increased FC variabilities in sensorimotor, visual, attention, limbic and subcortical areas at both regional and network levels, as well as decreased regional FC variabilities in the default-mode areas. The observed alterations shared by schizophrenia and bipolar disorder may help to explain their overlapped clinical features; meanwhile, the schizophrenia-specific abnormalities in a wider range may support that schizophrenia is associated with more severe functional brain deficits than bipolar disorder.