bluuebunny/crossref_metadata_2025_split huggingface dataset:
Propagating activity in neocortex, mediated by gap-junctions and modulated by extracellular potassium
Authors: Papasavvas Christoforos A. , Parrish R. Ryley , Trevelyan Andrew J. 
Published: June 2019

AbstractParvalbumin-expressing interneurons in cortical networks are coupled by gap-junctions, forming a syncytium that supports propagating epileptiform discharges, induced by 4-aminopyridine. It remains unclear, however, whether these propagating events occur under more natural states, without pharmacological blockade. In particular, we investigated whether propagation also happens when extracellular K+ rises, as is known to occur following intense network activity, such as during seizures. We examined how increasing [K+]o affects the likelihood of propagating activity away from a site of focal (200-400µm) optogenetic activation of PV-interneurons. Activity was recorded using a linear 16-electrode array placed along layer V of primary visual cortex. At baseline levels of [K+]o (3.5mM), induced activity was recorded only within the illuminated area. However, when [K+]o was increased above a threshold level (50th percentile= 8.0mM; interquartile range= 7.5-9.5mM), time-locked, fast-spiking unit activity, indicative of parvalbumin-expressing interneuron firing, was also recorded outside the illuminated area, propagating at 59.1 mm/s. Blockade of glutamatergic synaptic transmission reduced the efficacy of propagation, but could be restored by further increasing [K+]o. Propagation was further reduced, and in most cases prevented altogether, by pharmacological blockade of gap-junctions, achieved by any of three different drugs, quinine, mefloquine or carbenoxolone. Wash-out of quinine rapidly re-established the pattern of propagating activity. Computer simulations show qualitative differences between propagating discharges in high [K+]o and 4-aminopyridine, arising from differences in the electrotonic effects of these two manipulations. These interneuronal syncytial interactions are likely to affect the complex electrographic dynamics of seizures, once [K+]o is raised above this threshold level.Significance statementWe demonstrate the spatially extended propagation of activity through a gap-junction mediated syncytium of parvalbumin-expressing interneurons, in conditions that are known to exist at times within the brain. Previous work has only shown gap-junction coordination very locally, through directly connected cells, or induced at a distance by pharmacological means. We show that cell-class specific spread is facilitated by raised extracellular K+. This is highly pertinent to what happens at the onset of, and during, seizures, when extracellular K+ can rise rapidly to levels well in excess of the measured threshold for propagation. Our data suggests that interneuronal coupling will be enhanced at this time, and this has clear implications for the behaviour of these cells as seizures progress.
PQLC2 signals lysosomal cationic amino acid abundance to the C9orf72 complex
Authors: Amick Joseph , Tharkeshwar Arun Kumar , Talaia Gabriel , Ferguson Shawn M. 
Published: June 2019

AbstractThe C9orf72 protein is required for normal lysosome function. In support of such functions, C9orf72 forms a heterotrimeric complex with SMCR8 and WDR41 that is recruited to lysosomes when amino acids are scarce. These properties raise questions about the identity of the lysosomal binding partner of the C9orf72 complex and the amino acid sensing mechanism that regulates C9orf72 complex abundance on lysosomes. We now demonstrate that an interaction with the lysosomal cationic amino acid transporter PQLC2 mediates C9orf72 complex recruitment to lysosomes. This is achieved through an interaction between PQLC2 and WDR41. The interaction between PQLC2 and the C9orf72 complex is negatively regulated by arginine, lysine and histidine, amino acids that PQLC2 transports across the membrane of lysosomes. These results define a new role for PQLC2 in the regulated recruitment of the C9orf72 complex to lysosomes and reveal a novel mechanism that allows cells to sense and respond to changes in the availability of cationic amino acids within lysosomes.
Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
Authors: Kavagutti Vinicius S. , Andrei Adrian-Ştefan , Mehrshad Maliheh , Salcher Michaela M. , Ghai Rohit 
Published: June 2019

AbstractThe persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain obscure. Here, using ultra-deep metagenomic sequencing from freshwater habitats we recovered complete genomes of >2000 phages, including small “miniphages” and large “megaphages” infecting iconic prokaryotic lineages. We also show that many phages encode genes that likely enhance survival of infected microbes during strong eukaryotic grazing pressure. For instance, we describe genes that afford protection to their host from reactive oxygen species (ROS) in the environment and from the oxidative burst in protist phagolysosomes (phage-mediated ROS defense) or those that directly effect targeted killing of the predators upon ingestion of a phage-infected microbe (Trojan horse). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.
Seven-year-olds recall non-adjacent dependencies after overnight retention
Authors: Schaadt Gesa , Paul Mariella , Muralikrishnan R. , Männel Claudia , Friederici Angela D. 
Published: June 2019

AbstractBecoming a successful speaker depends on acquiring and learning grammatical dependencies between neighboring and non-neighboring linguistic elements (non-adjacent dependencies; NADs). Previous studies have demonstrated children’s and adults’ ability to distinguish NADs from NAD violations right after familiarization. However, demonstrating NAD recall after retention is crucial to demonstrate a lasting effect of NAD learning. We tested 7-year-olds’ NAD learning in a natural, non-native language on one day and NAD recall on the next day by means of event-related potentials (ERPs). Our results revealed ERPs with a more positive amplitude to NAD violations than correct NADs after familiarization on day one, but ERPs with a more negative amplitude to NAD violations on day two. This change from more positive to more negative ERPs to NAD violations possibly indicates that children’s representations of NADs changed during an overnight retention period, potentially associated with children’s NAD learning. Indeed, our descriptive analyses showed that both ERP patterns (i.e., day one: positive, day two: negative) were related to stronger behavioral improvement (i.e., more correct answers on day two compared to day one) in a grammaticality judgment task from day one to day two. We suggest these findings to indicate that children successfully built associative representations of NADs on day one and then strengthened these associations during overnight retention, revealing NAD recall on day two. The present results suggest that 7-year-olds readily track NADs in a natural, non-native language and are able to recall NADs after a retention period involving sleep, providing evidence of a lasting effect of NAD learning.Highlights7-year-olds’ non-adjacent dependency learning in a foreign language testedChildren gave grammaticality judgments while electroencephalography was recordedBrain responses revealed children’s learning of non-adjacent dependenciesBrain responses after overnight retention showed different polarityChildren’s recall of dependencies after sleep associated with representation change
The phylogenetic range of bacterial and viral pathogens of vertebrates
Authors: Shaw Liam P. , Wang Alethea D. , Dylus David , Meier Magda , Pogacnik Grega , Dessimoz Christophe , Balloux Francois 
Published: June 2019

AbstractMany major human pathogens are multi-host pathogens, able to infect other vertebrate species. Describing the general patterns of host-pathogen associations across pathogen taxa is therefore important to understand risk factors for human disease emergence. However, there is a lack of comprehensive curated databases for this purpose, with most previous efforts focusing on viruses. Here, we report the largest manually compiled host-pathogen association database, covering 2,595 bacteria and viruses infecting 2,656 vertebrate hosts. We also build a tree for host species using nine mitochondrial genes, giving a quantitative measure of the phylogenetic similarity of hosts. We find that the majority of bacteria and viruses are specialists infecting only a single host species, with bacteria having a significantly higher proportion of specialists compared to viruses. Conversely, multi-host viruses have a more restricted host range than multi-host bacteria. We perform multiple analyses of factors associated with pathogen richness per host species and the pathogen traits associated with greater host range and zoonotic potential. We show that factors previously identified as important for zoonotic potential in viruses—such as phylogenetic range, research effort, and being vector-borne—are also predictive in bacteria. We find that the fraction of pathogens shared between two hosts decreases with the phylogenetic distance between them. Our results suggest that host phylogenetic similarity is the primary factor for host-switching in pathogens.
PTY 2 As DPP-IV Inhibitor Prevents Intestinal Cell’s Apoptosis
Authors: Srivastava Shivani , Pandey Harsh , Singh Surya K , Tripathi Yamini Bhusan 
Published: June 2019

ABSTRACTEnhanced DPP-IV expression is found to get enhanced in various intestinal diseases. PTY-2 has already been known to have DPP-IV inhibitory potential. This inhibition has not yet been studied at mRNA level. Increased incretin secretion due to DPP-IV inhibition could lead to suppression of stress & intestinal cells apoptosis. Through histological analysis, we have found morphological damage of intestine after STZ injection (65 mg/kg bw) to male Charles foster rats. mRNA expressions were analyzed by PCR and apoptosis of cells was checked through tunnel assay & Bcl 2 expression. The number and length of villi get reduced in STZ induced diabetic control, but these damages have been getting reversed after the PTY-2 treatment for 10 days. The expression of SOD was found to get reduced while that of DPP-IV was enhanced in diabetic control group along with significant intestinal cell apoptosis. PTY-2 treatment reduces the stress by upregulating the expression of SOD and through downregulation of DPP-IV mRNA expression. These recoveries by PTY-2 leads to suppression of intestinal cells apoptosis. These short studies explain the protective action of PTY-2 against STZ induced intestinal damage. Hence, PTY-2 could be taken as an herbal treatment against intestinal disorders in case of chronic diabetes.
Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin
Authors: Lee Juhye M. , Eguia Rachel , Zost Seth J. , Choudhary Saket , Wilson Patrick C. , Bedford Trevor , Stevens-Ayers Terry , Boeckh Michael , Hurt Aeron , Lakdawala Seema S. , Hensley Scott E. , Bloom Jesse D. 
Published: June 2019

AbstractA longstanding question is how influenza evolves to escape human immunity, which is polyclonal and can target many distinct epitopes on the virus. Here we map how all amino-acid mutations to influenza’s major surface protein affect viral neutralization by polyclonal human sera. The serum of some individuals is so focused that it selects single mutations that reduce viral neutralization by over an order of magnitude. However, different viral mutations escape the sera of different individuals. This individual-to-individual variation in viral escape mutations isnotpresent among ferrets, which are frequently used as a model in influenza studies. Our results show how different single mutations help influenza escape the immunity of different members of the human population, a phenomenon that could shape viral evolution and disease susceptibility.
Inhibition of Histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing
Authors: Liu Bin , Chen Siwei , Rose Anouk La , Chen Deng , Cao Fangyuan , Kiemel Dominik , Aïssi Manon , Dekker FJ , Haisma HJ 
Published: June 2019

AbstractDespite the rapid development of CRISPR/Cas9-mediated gene editing technology, the gene editing potential of CRISPR/Cas9 is hampered by low efficiency, especially for clinical applications. One of the major challenges is that chromatin compaction inevitably limits the Cas9 protein access to the target DNA. However, chromatin compaction is precisely regulated by histone acetylation and deacetylation. To overcome these challenges, we have comprehensively assessed the impacts of histone modifiers such as HDAC (1-9) inhibitors and HAT (p300/CBP, Tip60 and MOZ) inhibitors, on CRISPR/Cas9 mediated gene editing efficiency. Our findings demonstrate that attenuation of HDAC1, HDAC2 activity, but not other HDACs, enhances CRISPR/Cas9-mediated gene knockout frequencies by NHEJ as well as gene knock-in by HDR. Conversely, inhibition of HDAC3 decreases gene editing frequencies. Furthermore, our study showed that attenuation of HDAC1, HDAC2 activity leads to an open chromatin state, facilitates Cas9 access and binding to the targeted DNA and increases the gene editing frequencies. This approach can be applied to other nucleases, such as ZFN and TALEN.
Tetrodotoxin-sensitive sodium channels mediate action potential firing and excitability in menthol-sensitive Vglut3-lineage sensory neurons
Authors: Griffith Theanne N. , Docter Trevor A. , Lumpkin Ellen A. 
Published: June 2019

AbstractSmall-diameter vesicular glutamate transporter 3-lineage (Vglut3lineage) dorsal root ganglion (DRG) neurons play an important role in mechanosensation and thermal hypersensitivity; however, little is known about their intrinsic electrical properties. We therefore set out to investigate mechanisms of excitability within this population. Calcium microfluorimetry analysis of male and female mouse DRG neurons demonstrated that the cooling compound menthol selectively activates a subset of Vglut3lineage neurons. Whole-cell recordings showed that small-diameter Vglut3lineage DRG neurons fire menthol-evoked action potentials and exhibited robust, transient receptor potential melastatin 8 (TRPM8)-dependent discharges at room temperature. This heightened excitability was confirmed by current-clamp and action potential phase-plot analyses, which showed menthol-sensitive Vglut3lineage neurons to have more depolarized membrane potentials, lower firing thresholds, and higher evoked firing frequencies compared with menthol-insensitive Vglut3lineage neurons. A biophysical analysis revealed voltage-gated sodium channel (NaV) currents in menthol-sensitive Vglut3lineage neurons were resistant to entry into slow inactivation compared with menthol-insensitive neurons. Multiplex in situ hybridization showed similar distributions of tetrodotoxin (TTX)-sensitive NaVs transcripts between TRPM8-positive and -negative Vglut3lineage neurons; however, NaV1.8 transcripts, which encode TTX-resistant channels, were more prevalent in TRPM8-negative neurons. Conversely, pharmacological analyses identified distinct functional contributions of NaV subunits, with NaV1.1 driving firing in menthol-sensitive neurons, whereas other small-diameter Vglut3lineage neurons rely primarily on TTX-resistant NaV channels. Additionally, when NaV1.1 channels were blocked, the remaining NaV currents readily entered into slow inactivation in menthol-sensitive Vglut3lineage neurons. Thus, these data demonstrate that TTX-sensitive NaVs drive action potential firing in menthol-sensitive sensory neurons and contribute to their heightened excitability.Significance StatementSomatosensensory neurons encode various sensory modalities including thermoreception, mechanoreception, nociception and itch. This report identifies a previously unknown requirement for tetrodotoxin-sensitive sodium channels in action potential firing in a discrete subpopulation of small-diameter sensory neurons that are activated by the cooling agent menthol. Together, our results provide a mechanistic understanding of factors that control intrinsic excitability in functionally distinct subsets of peripheral neurons. Furthermore, as menthol has been used for centuries as an analgesic and anti-pruritic, these findings support the viability of NaV1.1 as a therapeutic target for sensory disorders.
Carbohydrate and PepO control bimodality in competence development byStreptococcus mutans
Authors: Underhill Simon A.M. , Shields Robert C. , Burne Robert A. , Hagen Stephen J. 
Published: June 2019

AbstractInStreptococcus mutans, the alternative sigma factor ComX controls entry into genetic competence. Competence signaling peptide (CSP) induces bimodal expression ofcomX, with only a fraction of cells in the population becoming transformable. Curiously, bimodalcomXactivation in response to CSP is affected by peptides in the growth medium and by carbohydrate source. CSP elicits bimodal expression ofcomXin media rich in small peptides, but in defined media lacking small peptides CSP induces no response incomX. In addition, growth on certain sugars other than glucose increases the proportion of the population that activatescomXin response to CSP, relative to growth on glucose. By investigating the connection between media and bimodalcomXexpression, we find evidence for two mechanisms that modulate transcriptional positive feedback in the ComRS system, which is the origin ofcomXbimodality. We find that the endopeptidase PepO suppresses the ComRS feedback loop, most likely by degrading the intracellular XIP/ComS signal. Deletion ofpepOeliminates bimodality incomX, leading to a unimodalcomXresponse to CSP in defined and complex media. We also find that CSP upregulatescomRin a carbohydrate source-dependent fashion, providing an additional stimulus to the ComRS feedback system. Our data provide mechanistic insight into how CSP regulates the bistable competence circuit and explain the puzzle of growth medium-dependence inS. mutanscompetence regulation.
DREAM Interrupted: Severing LIN-35-MuvB association in Caenorhabditis elegans impairs DREAM function but not its chromatin localization
Authors: Goetsch Paul D. , Strome Susan 
Published: June 2019

AbstractThe mammalian pocket protein family, which includes the Retinoblastoma protein (pRb) and Rb-like pocket proteins p107 and p130, regulates entry into and exit from the cell cycle by repressing cell cycle gene expression. Although pRb plays a dominant role in mammalian systems, p107 and p130 are the ancestral pocket proteins. The Rb-like pocket proteins interact with the highly conserved 5-subunit MuvB complex and an E2F-DP transcription factor heterodimer, forming the DREAM (for Dp, Rb-like, E2F, and MuvB) complex. DREAM complex assembly on chromatin culminates in repression of target genes mediated by the MuvB subcomplex. Here, we examined how the Rb-like pocket protein contributes to DREAM formation and function by disrupting the interaction between the sole Caenorhabditis elegans pocket protein LIN-35 and the MuvB subunit LIN-52 using CRISPR/Cas9 targeted mutagenesis. A triple alanine substitution of LIN-52’s LxCxE motif severed LIN-35-MuvB association and caused classical DREAM mutant phenotypes, including synthetic multiple vulvae, high-temperature arrest, and ectopic expression of germline genes in the soma. However, RNA-seq revealed limited upregulation of DREAM target genes when LIN-35-MuvB association was severed, as compared to gene upregulation following LIN-35 loss. Based on chromatin immunoprecipitation, disrupting LIN-35-MuvB association did not affect the chromatin localization of E2F-DP, LIN-35, or MuvB components. In a previous study we showed that in worms lacking LIN-35, E2F-DP and MuvB chromatin occupancy was reduced genome-wide. With LIN-35 present but unable to associate with MuvB, our present study suggests that the E2F-DP-LIN-35 interaction promotes E2F-DP’s chromatin localization, which we hypothesize supports MuvB chromatin occupancy indirectly through DNA. Altogether, this study highlights how the pocket protein’s association with MuvB supports DREAM function but is not required for DREAM’s chromatin occupancy.
Single-cell profiling guided combinatorial immunotherapy for fast-evolving CDK4/6 inhibitor resistant HER2-positive breast cancer
Authors: Wang Qingfei , Guldner Ian H. , Golomb Samantha M. , Sun Longhua , Harris Jack , Lu Xin , Zhang Siyuan 
Published: June 2019

AbstractDevelopment of acquired resistance to targeted cancer therapy is one of the most significant clinical challenges. Acquiring resistance under drug selection pressure is a result of evolutionary adaptation to a complex and dynamic tumor microenvironment (TME). New therapy regimens combining CDK4/6 inhibitor are under active investigation in clinical trials to treat HER2+ breast cancer patients. In parallel with clinical trial settings, in this study, we sought to prospectively model the tumor evolution in response to a targeted therapy regimen in vivo and identify a clinically actionable strategy to combat potential acquired resistance. Notably, despite a promising initial response, acquired resistance emerged rapidly to the anti-Her2/Neu antibody plus CDK4/6 inhibitor Palbociclib combination treatment. By leveraging high-throughput single-cell analyses of the evolving tumors over the course of treatments, we revealed a distinct immunosuppressive immature myeloid cell (IMC) population infiltrated in the resistant TME. Guided by single-cell transcriptome analysis, we demonstrated a combinatorial immunotherapy of IMC-targeting tyrosine kinase inhibitor cabozantinib and immune checkpoint blockades enhanced anti-tumor immunity, and overcame the resistance. Further, sequential combinatorial immunotherapy enabled a sustained control of the rapidly evolving CDK4/6 inhibitor-resistant tumors. Our study demonstrates a translational framework for treating rapidly evolving tumors through preclinical modeling and single-cell analyses. Our findings provide a rationale for an immediate clinical proposition of combinatorial immunotherapy for HER2+ breast cancer as a strategy to mitigate the emergence of resistance.