bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enigma at the nanoscale: can the NPC act as an intrinsic reporter for isotropic expansion microscopy?
Authors: Pesce Luca , Cozzolino Marco , Lanzanò Luca , Diaspro Alberto , Bianchini Paolo 
Published: October 2018

AbstractExpansion microscopy is a super-resolution method that allows expanding uniformly biological samples, by increasing the relative distances among fluorescent molecules labeling specific components. The main “enigma” regarding this approach is given by the isotropic behavior at the nanoscale. The present study aims to determine the robustness of such a technique, quantifying the expansion parameters i.e. scale factor, isotropy, uniformity. Our focus is on the nuclear pore complex (NPC), as well-known nanoscale component endowed of a preserved and symmetrical structure localized on the nuclear envelope. Here, we show that Nup153 is a good reporter to quantitatively address the isotropy of the expansion process. The quantitative analysis carried out on NPCs, at different spatial scales, allows concluding that expansion microscopy can be used at the nanoscale with a uniform accuracy in the range of 20 nm. In addition, it is an excellent method for structural studies of macromolecular complexes.
Fibrocyte accumulation in bronchi: a cellular hallmark of COPD
Authors: Dupin Isabelle , Thumerel Matthieu , Maurat Elise , Coste Florence , Begueret Hugues , Trian Thomas , Montaudon Michel , Marthan Roger , Girodet Pierre-Olivier , Berger Patrick 
Published: October 2018

AbstractBackgroundThe remodeling mechanism and cellular players causing persistent airflow limitation in chronic obstructive pulmonary disease (COPD) remain largely elusive. We have recently demonstrated that circulating fibrocytes, a rare population of fibroblast-like cells produced by the bone marrow stroma, are increased in COPD patients during an exacerbation. It remains, however, unclear, whether fibrocytes are present in bronchial tissue of COPD patients.ObjectiveWe aimed to quantify fibrocytes density in bronchial specimens from both control subjects and COPD patients, and to define associations with clinical, functional and computed tomography relevant parameters.Methods17 COPD patients and 25 control subjects with normal lung function testing and no chronic symptoms, all of them requiring thoracic surgery, were recruited. LFT and CT-scan were performed before surgery. Using co-immunostaining and image analysis, we identify CD45+ FSP1+ cells as tissue fibrocytes and quantify their density in distal and proximal bronchial specimens from the whole series.ResultsHere, we demonstrate that fibrocytes are increased in both distal and proximal tissue specimens of COPD patients, compared to those of controls. The density of fibrocytes is negatively correlated with lung function parameters, such as FEV1 and FEV1/FVC, and positively with bronchial wall thickness assessed by CT scan. High density of distal bronchial fibrocytes predicts presence of COPD with a sensitivity of 83% and a specificity of 70%.ConclusionsOur results thus suggest that recruitment of fibrocytes in the bronchi may participate to lung function decline during COPD progression.Clinical ImplicationsHigh density of tissue fibrocytes is associated with a deteriorated lung function and an increase in airway wall thickness. A low density tissue fibrocytes virtually eliminates the presence of COPD.Capsule summaryBlood fibrocytes assessed during exacerbation is a predictor of mortality in COPD. This study shows an increase of bronchial fibrocytes, that is associated with lower lung function, increased bronchial thickness and air trapping in COPD.
Transcriptome analysis of the human tibial nerve identifies sexually dimorphic expression of genes involved in pain, inflammation and neuro-immunity
Authors: Ray Pradipta , Khan Jawad , Wangzhou Andi , Tavares-Ferreira Diana , Akopian Armen N. , Dussor Gregory , Price Theodore J. 
Published: October 2018

AbstractSex differences in gene expression are important contributors to normal physiology and mechanisms of disease. This is increasingly apparent in understanding and potentially treating chronic pain where molecular mechanisms driving sex differences in neuronal plasticity are giving new insight into why certain chronic pain disorders preferentially affect women versus men. Large transcriptomic resources are increasingly available and can be used to mine for sex differences and molecular insight using donor cohorts. We analyzed more than 250 human tibial nerve (hTN) transcriptomes from the GTex Consortium project to gain insight into sex-dependent gene expression in the peripheral nervous system (PNS). We discover 149 genes with sex differential expression. Many of the genes upregulated in men are associated with inflammation, and appear to be primarily expressed by glia or immune cells. In women, we find the differentially upregulated transcription factor SP4 that drives a regulatory program, and may impact sex differences in PNS physiology. Many of these 149 DE genes have some previous association with chronic pain but few of them have been explored thoroughly. Additionally, using clinical data in the GTex database, we identify a subset of differentially expressed (DE) genes in diseases associated with chronic pain, arthritis and type II diabetes. Our work identifies sexually dimorphic gene expression in the human PNS with implications for discovery of sex-specific pain mechanisms.
Cyclical environments drive variation in life history strategies: a general theory of cyclical phenology
Authors: Park John S. 
Published: October 2018

ABSTRACTCycles, such as seasons or tides, characterize many systems in nature. Overwhelming evidence shows that climate change-driven alterations to environmental cycles—such as longer seasons— are associated with phenological shifts around the world, suggesting a deep link between environmental cycles and life cycles. However, general mechanisms of life history evolution in cyclical environments are still not well understood. Here I build a demographic framework and ask how life history strategies optimize fitness when the environment perturbs a structured population cyclically, and how strategies should change as cyclicality changes. I show that cycle periodicity alters optimality predictions of classic life history theory because repeated cycles have rippling selective consequences over time and generations. Notably, fitness landscapes that relate environmental cyclicality and life history optimality vary dramatically depending on which trade-offs govern a given species. The model tuned with known life history trade-offs in a marine intertidal copepod T. californicus successfully predicted the shape of life history variation across natural populations spanning a gradient of tidal periodicities. This framework shows how environmental cycles can drive life history variation—without complex assumptions of individual responses to cues such as temperature—thus expanding the range of life history diversity explained by theory and providing a basis for adaptive phenology.
Pervasive and Dynamic Transcription Initiation inSaccharomyces cerevisiae
Authors: Lu Zhaolian , Lin Zhenguo 
Published: October 2018

AbstractTranscription initiation is finely regulated to ensure the proper expression and function of these genes. The regulated transcription initiation in response to various environmental cues in the model organismSaccharomyces cerevisiaehas not been systematically investigated. In this study, we generated quantitative maps of transcription start site (TSS) at a single-nucleotide resolution forS. cerevisiaegrown in nine different conditions using no-amplification non-tagging Cap analysis of gene expression (nAnT-iCAGE) sequencing. Based on 337 million uniquely mapped CAGE tags, we mapped ~1 million well-supported TSSs, suggesting highly pervasive transcription initiation in the compact genome of yeast. The comprehensive TSS maps allowed us to identify core promoters for ~96% verified protein-coding genes and to revise the predicted translation start codon for 183 genes. We found that 56% of yeast genes have at least two core promoters and alternative usage of different core promoters in a gene is widespread in response to changing environments. More importantly, most core promoter shifts are coupled with differential gene expression, indicating that core promoter shift might play an important role in controlling transcriptional activity of yeast genes. Based on their dynamic activities, we divided yeast core promoters as constitutive core promoters (55%) and inducible core promoters (45%). The two classes of core promoters exhibit distinctive patterns in transcriptional abundance, chromatin structure, promoter shape, and sequence context. In summary, the quantitative TSS maps generated by this study improved the annotation of yeast genome, and revealed a highly pervasive and dynamic nature of transcription initiation in yeast.
Subthalamic nucleus mediates the modulation on cocaine self-administration induced by ultrasonic 3 vocalizations playback in rats
Authors: Christian Montanari , Elodie Giorla , Yann Pelloux , Christelle Baunez 
Published: October 2018

AbstractDrug intake is known to be under the influence of social context. We have recently shown that presence of a peer influences drug intake in both rats and humans. Whether or not social acoustic communications between the peers play a role during cocaine or sucrose self-administration (SA) was investigated here, using playback of ultrasonic vocalizations (USV) at 50- and 22-kHz, conveying respectively positive and negative internal affective states in adult rats. To assess the neurobiological substrate of a potential USV influence on drug and food intake, we tested the effects of subthalamic nucleus (STN) lesions, given its role in emotional and motivational processes. In sham-control rats, playback of USV associated with positive affective states induced long-term decreased cocaine consumption, while USV associated with negative affective states induced short-term increase. Interestingly, no effect of USV playback was observed on sucrose intake, whatever the frequency. STN lesions abolished the influence of USV on cocaine intake, highlighting the influence of STN in emotional processes induced by USV emitted by a peer. These results show how acoustic social communication is important to regulate drug intake in rats and how STN modulation could interfere with addiction processes.
Choice between 1- and 2-furrow cytokinesis inCaenorhabditis elegansembryos with tripolar spindles
Authors: Kondo Tomo , Kimura Akatsuki 
Published: October 2018

AbstractExcess numbers of centrosomes often lead to multipolar spindles, and thus probably to multipolar mitosis and aneuploidy. InCaenorhabditis elegans, approximately 70% of the paternalemb-27APC6mutant embryonic cells contained more than 2 centrosomes and formed multipolar spindles. However, only 30% of the cells with tripolar spindles formed 2 cytokinetic furrows. The rest formed 1 furrow, like normal cells. To investigate the mechanism how the cells avoided to form 2 cytokinetic furrows even with a tripolar spindle, we conducted live-cell imaging inemb-27APC6mutant cells. We found that the chromatids were aligned only on 2 of the 3 sides of the tripolar spindle, and the angle of the tripolar spindle relative to the long axis of the cell correlated with the number of cytokinetic furrow. Our numerical modeling showed that the combination of cell shape, cortical pulling forces, and heterogeneity of centrosome size determines whether cells with tripolar spindle form 1 or 2 cytokinetic furrows.
ddcP, pstB, and excess D-lactate impact synergism between vancomycin and chlorhexidine against Enterococcus faecium 1,231,410
Authors: Bhardwaj Pooja , Islam Moutusee Z. , Kim Christi , Nguyen Uyen Thy , Palmer Kelli L. 
Published: October 2018

AbstractVancomycin-resistant enterococci (VRE) are important nosocomial pathogens that cause life-threatening infections. To control hospital-associated infections, skin antisepsis and bathing utilizing chlorhexidine is recommended for VRE patients in acute care hospitals. Previously, we reported that exposure to inhibitory chlorhexidine levels induced the expression of vancomycin resistance genes in VanA-type Enterococcus faecium. However, vancomycin susceptibility actually increased for VanA-type E. faecium in the presence of chlorhexidine. Hence, a synergistic effect of the two antimicrobials was observed. In this study, we used multiple approaches to investigate the mechanism of synergism between chlorhexidine and vancomycin in the VanA-type VRE strain E. faecium 1,231,410. We generated clean deletions of 7 of 11 pbp, transpeptidase, and carboxypeptidase genes in this strain (ponA, pbpF, pbpZ, pbpA, ddcP, ldtfm, and vanY). Deletion of ddcP, encoding a membrane-bound carboxypeptidase, altered the synergism phenotype. Furthermore, using in vitro evolution, we isolated a spontaneous synergy escaper mutant and utilized whole genome sequencing to determine that a mutation in pstB, encoding an ATPase of phosphate-specific transporters, also altered synergism. Finally, addition of excess D-lactate, but not D-alanine, enhanced synergism. Overall, our work identified factors that alter chlorhexidine-induced vancomycin resensitization in a model VanA-type VRE strain.
Werner helicase control of human papillomavirus 16 E1-E2 DNA replication is regulated by SIRT1 deacetylation
Authors: Das Dipon , Bristol Molly L , Smith Nathan W , Wang Xu , Pichierri Pietro , Morgan Iain M 
Published: October 2018

AbstractHuman papillomaviruses (HPV) are double stranded DNA viruses causative in a host of human diseases including several cancers. Following infection two viral proteins, E1 and E2, activate viral replication in association with cellular factors, and stimulate the DNA damage response (DDR) during the replication process. E1-E2 uses homologous replication (HR) to facilitate DNA replication, but an understanding of host factors involved in this process remains incomplete. Previously we demonstrated that the class III deacetylase SIRT1, which can regulate HR, is recruited to E1-E2 replicating DNA and regulates the level of replication. Here we demonstrate that SIRT1 promotes the fidelity of E1-E2 replication and that the absence of SIRT1 results in reduced recruitment of the DNA repair protein Werner helicase (WRN) to E1-E2 replicating DNA. CRISPR/Cas9 editing demonstrates that WRN, like SIRT1, regulates the quantity and fidelity of E1-E2 replication. This is the first report of WRN regulation of E1-E2 DNA replication, or a role for WRN in the HPV life cycle. In the absence of SIRT1 there is an increased acetylation and stability of WRN, but a reduced ability to interact with E1-E2 replicating DNA. We present a model in which E1-E2 replication turns on the DDR stimulating SIRT1 deacetylation of WRN. This deacetylation promotes WRN interaction with E1-E2 replicating DNA to control the quantity and fidelity of replication. As well as offering a crucial insight into HPV replication control, this system offers a unique model for investigating the link between SIRT1 and WRN in controlling replication in mammalian cells.ImportanceHPV16 is the major viral human carcinogen, responsible for between 3 and 4% of all cancers worldwide. Following infection this virus activates the DNA damage response (DDR) to promote its life cycle, and recruits DDR proteins to its replicating DNA in order to facilitate homologous recombination during replication. This promotes the production of viable viral progeny. Our understanding of how HPV16 replication interacts with the DDR remains incomplete. Here we demonstrate that the cellular deacetylase SIRT1, which is a part of the E1-E2 replication complex, regulates recruitment of the DNA repair protein WRN to the replicating DNA. We demonstrate that WRN regulates the level and fidelity of E1-E2 replication. Overall the results suggest a mechanism where SIRT1 deacetylation of WRN promotes its interaction with E1-E2 replicating DNA to control the levels and fidelity of that replication.
Latent developmental potential to form limb-like skeletal structures in zebrafish
Authors: Hawkins M. Brent , Henke Katrin , Harris Matthew P. 
Published: October 2018

AbstractThe evolution of fins into limbs was a key transition in vertebrate history. A hallmark of this transition is the addition of multiple long bones to the proximal-distal axis of paired appendages. Whereas limb skeletons are often elaborate and diverse, teleost pectoral fins retain a simple endoskeleton. Fins and limbs share many core developmental processes, but how these programs were reshaped to produce limbs from fins during evolution remains enigmatic. Here we identify zebrafish mutants that form supernumerary long bones along the proximal-distal axis of pectoral fins with limb-like patterning. These new skeletal elements are integrated into the fin, as they are connected to the musculature, form joints, and articulate with neighboring bones. This phenotype is caused by activating mutations in previously unrecognized regulators of appendage development,vav2andwaslb, which we show function in a common pathway. We find that this pathway functions in appendage development across vertebrates, and loss ofWaslin developing limbs results in patterning defects identical to those seen inHoxallknockout mice. Concordantly, formation of supernumerary fin long bones requires the function ofhoxallparalogs, indicating developmental homology with the forearm and the existence of a latent functional Hox code patterning the fin endoskeleton. Our findings reveal an inherent limb-like patterning ability in fins that can be activated by simple genetic perturbation, resulting in the elaboration of the endoskeleton.
Cellular polarity asymmetrically functionalizes pathogen recognition receptor-mediated intrinsic immune response in human intestinal epithelium cells
Authors: Stanifer Megan L. , Muenchau Stephanie , Mukenhirn Markus , Pervolaraki Kalliopi , Kanaya Takashi , Albrecht Dorothee , Odendall Charlotte , Hielscher Thomas , Haucke Volker , Kagan Jonathan , Bartfeld Sina , Ohno Hiroshi , Boulant Steeve 
Published: October 2018

SummaryIntestinal epithelial cells (IECs) act as a physical barrier separating the commensal-containing intestinal tract from the sterile interior. These cells have found a complex balance allowing them to be prepared for pathogen attacks while still tolerating the presence of bacteria/viral stimuli present in the lumen of the gut. Using primary human IECs, we probed the mechanisms, which allow for such a tolerance. We discovered that viral infection emanating from the basolateral side of IECs elicited a stronger intrinsic immune response as compared to lumenal apical infection. We determined that this asymmetric immune response was driven by the clathrin-sorting adapter AP-1B which mediates the polarized sorting of Toll-like receptor 3 (TLR3) toward the basolateral side of IECs. Mice and human IECs lacking AP-1B showed an exacerbated immune response following apical stimulation. Together these results suggest a model where the cellular polarity program plays an integral role in the ability of IECs to partially tolerate apical commensals while remaining fully responsive against invasive basolateral pathogens.
Re-purposing Ac/Ds transgenic system for CRISPR/dCas9 modulation of enhancers and non-coding RNAs in zebrafish
Authors: Chong-Morrison Vanessa , Simões Filipa C. , Senanayake Upeka , Carroll Dervla S. , Riley Paul R. , Sauka-Spengler Tatjana 
Published: October 2018

AbstractDue to its genetic amenability coupled with recent advances in genome editing, the zebrafish serves as an excellent model to examine the function of both coding and non-coding elements. Recently, the non-coding genome has gained prominence due to its critical role in development and disease. Here, we have re-purposed the Ac/Ds maize transposition system to reliably screen and efficiently characterise zebrafish enhancers, with or without germline propagation. We further utilised the system to stably express guide RNAs in microinjected embryos enabling tissue-specific CRISPR/dCas9-interference (CRISPRi) knockdown of lncRNA and enhancer activity without disrupting the underlying genetic sequence. Our study highlights the utility of Ac/Ds transposition for transient epigenome modulation of non-coding elements in zebrafish.Summary statementWe adapted the Ac/Ds transposition system, which enables continuous expression of guide RNAs for CRISPR/dCas9 perturbation, to examine the function of non-coding RNAs and enhancer elements in zebrafish.
Imaging Sterols and Oxysterols in Mouse Brain Reveals Distinct Spatial Cholesterol Metabolism
Authors: Yutuc Eylan , Angelini Roberto , Baumert Mark , Mast Natalia , Pikuleva Irina , Newton Jillian , Clench Malcolm R. , Skibinski David O.F. , Howell Owain W. , Wang Yuqin , Griffiths William J. 
Published: October 2018

AbstractDysregulated cholesterol metabolism is implicated in a number of neurological disorders. Many sterols, including cholesterol and its precursors and metabolites, are biologically active and important for proper brain function. However, spatial cholesterol metabolism in brain and the resulting sterol distributions are poorly defined. To better understand cholesterol metabolismin situacross the complex functional regions of brain, we have developed on-tissue enzyme-assisted derivatisation in combination with micro-liquid-extraction for surface analysis and liquid chromatography - mass spectrometry to image sterols in tissue slices (10 µm) of mouse brain. The method provides sterolomic analysis at 400 µm spot diameter with a limit of quantification of 0.01 ng/mm2. It overcomes the limitations of previous mass spectrometry imaging techniques in analysis of low abundance and difficult to ionise sterol molecules, allowing isomer differentiation and structure identification. Here we demonstrate the spatial distribution and quantification of multiple sterols involved in cholesterol metabolic pathways in wild type andcholesterol 24S-hydroxylaseknock-out mouse brain. The technology described provides a powerful tool for future studies of spatial cholesterol metabolism in healthy and diseased tissues.SignificanceThe brain is a remarkably complex organ and cholesterol homeostasis underpins brain function. It is known that cholesterol is not evenly distributed across different brain regions, however, the precise map of cholesterol metabolism in the brain remains unclear. If cholesterol metabolism is to be correlated with brain function it is essential to generate such a map. Here we describe an advanced mass spectrometry imaging platform to reveal spatial cholesterol metabolismin situat 400 µm resolution on 10 µm tissue slices from mouse brain. We mapped, not only cholesterol, but also other biologically active sterols arising from cholesterol turnover in both wild type and mice lacking cholesterol 24-hydroxylase (Cyp46a1), the major cholesterol metabolising enzyme.
The hippocampus is necessary for the sleep-dependent consolidation of a task that does not require the hippocampus for initial learning
Authors: Schapiro Anna C. , Reid Allison G. , Morgan Alexandra , Manoach Dara S. , Verfaellie Mieke , Stickgold Robert 
Published: October 2018

AbstractDuring sleep, the hippocampus plays an active role in consolidating memories that depend on it for initial encoding. There are hints in the literature that the hippocampus may have a broader influence, contributing to the consolidation of memories that may not initially require the area. We tested this possibility by evaluating learning and consolidation of the motor sequence task (MST) in hippocampal amnesics and demographically matched control participants. While the groups showed similar initial learning, only controls exhibited evidence of sleep-dependent consolidation. These results demonstrate that the hippocampus can be required for normal consolidation of a task without being required for its acquisition, suggesting that the area plays a broader role in coordinating sleep-dependent memory consolidation than has previously been assumed.