bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracellular DNA promotes efficient extracellular electron transfer by pyocyanin in Pseudomonas aeruginosa biofilms
Authors: Saunders Scott H. , Tse Edmund C.M. , Yates Matthew D. , Otero Fernanda Jiménez , Trammell Scott A. , Stemp Eric D.A. , Barton Jacqueline K. , Tender Leonard M. , Newman Dianne K. 
Published: December 2019

SUMMARYExtracellular electron transfer (EET), the process whereby cells access electron acceptors or donors that reside many cell lengths away, enables metabolic activity by microorganisms, particularly under oxidant-limited conditions that occur in multicellular bacterial biofilms. Although different mechanisms underpin this process in select organisms, a widespread strategy involves extracellular electron shuttles, redox-active metabolites that are secreted and recycled by diverse bacteria. How these shuttles catalyze electron transfer within biofilms without being lost to the environment has been a long-standing question. Here, we show that phenazine electron shuttles mediate efficient EET through interactions with extracellular DNA (eDNA) inPseudomonas aeruginosabiofilms, which are important in nature and disease. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by binding to eDNA. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and phenazines can participate directly in redox reactions through DNA; the biofilm eDNA can also support rapid electron transfer between redox active intercalators. Electrochemical measurements of biofilms indicate that retained PYO supports an efficient redox cycle with rapid EET and slow loss from the biofilm. Together, these results establish that eDNA facilitates phenazine metabolic processes inP. aeruginosabiofilms, suggesting a model for how extracellular electron shuttles achieve retention and efficient EET in biofilms.
Xrn1p Acts at Multiple Steps in the Budding-Yeast RNAi Pathway to Enhance the Efficiency of Silencing
Authors: Getz Matthew A. , Weinberg David E. , Drinnenberg Ines A. , Fink Gerald R. , Bartel David P. 
Published: December 2019

AbstractRNA interference (RNAi) is a gene-silencing pathway that can play roles in viral defense, transposon silencing, heterochromatin formation, and post-transcriptional gene silencing. Although absent fromSaccharomyces cerevisiae, RNAi is present in other budding-yeast species, includingNaumovozyma castellii, which have an unusual Dicer and a conventional Argonaute that are both required for gene silencing. To identify other factors that act in the budding-yeast pathway, we performed an unbiased genetic selection. This selection identified Xrn1p, the cytoplasmic 5′-to-3′ exoribonuclease, as a cofactor of RNAi in budding yeast. Deletion ofXRN1impaired gene silencing inN. castellii, and this impaired silencing was attributable to multiple functions of Xrn1p, including affecting the composition of siRNA species in the cell, influencing the efficiency of siRNA loading into Argonaute, degradation of cleaved passenger strand, and degradation of sliced target RNA.
Out of the Qinghai-Tibetan Plateau and get flourishing - the evolution of Neodon voles (Rodentia: Cricetidae) revealed by systematic sampling and low coverage whole genome sequencing
Authors: Liu Shaoying , Zhou Chengran , Wan Tao , Meng Guanliang , Murphy W. Robert W. , Fan Zhengxin , Tang Mingkun , Liu Yang , Zeng Tao , Chen Shunde , Zhao Yun , Liu Shanlin 
Published: December 2019

AbstractNeodon, genus of a short time evolutionary history, was reported to be diverged from its relatives in early stage of Pleistocene. Only 4 species were well documented in Neodon for a long period of time until last years when a systematic work described and added three new species, adjusted three species used to belong to Lasiopodomys, Phaiomys, Microtus to Neodon and removed one species (Neodon juldaschi) to genus Blanfordimys, leading to a total of eight species recorded in Neodon. To gain a better insight into the phylogeny and ecology of Neodon, we have systematically sampled Neodon species along the whole Hengduan and Himalayan Mountains in the last 20 years. In addition to morphological identification, we generated 1x - 15x whole genome sequencing (WGS) data and achieved the mitochondrial genomes and an average of 5,382 nuclear genes for each morpho-species. Both morphology and phylogeny results supported an extra six new species in Neodon (nominated Neodon shergylaensis sp. nov., N. namchabarwaensis sp. nov., N. liaoruii sp. nov., N. chayuensis sp. nov., N. bomiensis sp. nov., and N. bershulaensis sp. nov.). This is the first study that included Neodon samples covering its entire distribution area in China and this systematic sampling also revealed a long-time underestimation of Neodon’s diversity, and suggested its speciation events linked highly to founder event via dispersal (from Plateau to surrounding mountains). The results also revealed that the Qinghai-Tibetan Plateau is the center of origin of Neodon, and the impetus of speciation include climate change, isolation of rivers and mountains.
Computational characteristics of the striatal dopamine system described by reinforcement learning with fast generalization
Authors: Fujita Yoshihisa , Yagishita Sho , Kasai Haruo , Ishii Shin 
Published: December 2019

AbstractGeneralization enables applying past experience to similar but nonidentical situations. Therefore, it may be essential for adaptive behaviors. Recent neurobiological observation indicates that the striatal dopamine system achieves generalization and subsequent discrimination by updating corticostriatal synaptic connections in differential response to reward and punishment. To analyze how the computational characteristics in this system affect behaviors, we proposed a novel reinforcement learning model with multilayer neural networks in which the synaptic weights of only the last layer are updated according to the prediction error. We set fixed connections between the input and hidden layers so as to maintain the similarity of inputs in the hidden-layer representation. This network enabled fast generalization, and thereby facilitated safe and efficient exploration in reinforcement learning tasks, compared to algorithms which do not show generalization. However, disturbance in the network induced aberrant valuation. In conclusion, the unique computation suggested by corticostriatal plasticity has the advantage of providing safe and quick adaptations to unknown environments, but on the other hand has the potential defect which can induce maladaptive behaviors like delusional symptoms of psychiatric disorders.Author summaryThe brain has an ability to generalize knowledge obtained from reward- and punishment-related learning. Animals that have been trained to associate a stimulus with subsequent reward or punishment respond not only to the same stimulus but also to resembling stimuli. How does generalization affect behaviors in situations where individuals are required to adapt to unknown environments? It may enable efficient learning and promote adaptive behaviors, but inappropriate generalization may disrupt behaviors by associating reward or punishment with irrelevant stimuli. The effect of generalization here should depend on computational characteristics of underlying biological basis in the brain, namely, the striatal dopamine system. In this research, we made a novel computational model based on the characteristics of the striatal dopamine system. Our model enabled fast generalization and showed its advantage of providing safe and quick adaptation to unknown environments. By contrast, disturbance of our model induced abnormal behaviors. The results suggested the advantage and the shortcoming of generalization by the striatal dopamine system.
Synesthesia does not help to recover perceptual dominance following flash suppression
Authors: Arias Diana Jimena , Saint-Amour Dave 
Published: December 2019

AbstractGrapheme-color synesthesia is a perceptual phenomenon that occurs when letters or numbers elicit an abnormal color sensation (e.g., printed black letters are perceived as colored graphemes). Grapheme-color synesthesia is typically reported following explicit presentation of graphemes. Very few studies have investigated color sensations in synesthesia in the absence of visual awareness. To address this issue, we took advantage of the dichoptic flash suppression paradigm to temporarily render a stimulus presented to one eye invisible. Synesthesic alphanumeric and non-synesthetic abstract stimuli were presented to 11 synesthete and 11 matched control participants in achromatic and chromatic experimental conditions. The test stimulus was first displayed to one eye and then masked following the sudden presentation of visual noise in the other eye. The time for an image to be perceived following the onset of the suppressive noise was calculated in each condition. Trials free of flash suppression but mimicking the perceptual suppression of the flash were also tested. Results showed that target detection by synesthetes was significantly better than by controls in the absence of flash suppression. However, no statistically significant difference was found between the groups when the test stimulus was interocularly suppressed, either for synesthetic or non-synesthetic stimuli. This study suggests that synesthesia can be associated with enhanced perception for overt recognition, but does not occur in the absence of visual awareness.
A spatio-temporal mathematical model for the dynamics of paclitaxel in cell monolayers
Authors: Proudfoot Isaac , Vallardi Giulia , Shishikura Yoko , Epemolu Ola , Saurin Adrian T. , Ptashnyk Mariya , Murray Philip J. 
Published: December 2019

AbstractThe authors have withdrawn their manuscript due to the discovery of fundamental issues with the implementation of the ODE/PDE model, whose output was shown in Figure 5 of the original version of this paper, rendering the results and conclusion unreliable. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Boron deficiency-induced root growth inhibition is mediated by brassinosteroid signalling regulation inArabidopsis
Authors: Zhang Cheng , He Mingliang , Wang Sheliang , Chu Liuyang , Wang Chuang , Yang Ningmei , Ding Guangda , Cai Hongmei , Shi Lei , Xu Fangsen 
Published: December 2019

ABSTRACTBrassinosteroid (BR) is a pivotal phytohormone involved in regulating root development. Boron (B) is an essential micronutrient for plant growth and development, and root growth of plants is rapidly inhibited under B deficiency condition, but the mechanisms are still elusive. Here, we demonstrate that BR plays crucial roles in these processes. We identify BR-related processes underlying B deficiency at the physiological, genetic, molecular/cell biological and transcriptome levels, and provide strong evidences that B deficiency can affect BR signalling, thereby altering root growth. RNA-sequencing analysis reveals a high co-regulation between BR-regulated genes and B deficiency-responsive genes. We found that low B negatively regulates BR signalling to control BR signalling-dependent root elongation,bes1-Dexhibits insensitivity to low B stress, andbri1-301mutants fails to respond to B depletion. Exogenous eBL application can rescue the inhibition of root growth under B deficiency condition, and application of BR biosynthesis inhibitor BRZ aggravates root growth inhibition of wild-type under B deficiency condition. B deficiency reduces the nuclear signal of BES1. We further found that B deficiency reduces the accumulation of brassinolide (BL) by reducingBR6ox1andBR6ox2mRNA level to down-regulate BR signalling and modulate root elongation. Altogether, our results uncover a role of BR signalling in root elongation under B deficiency.One-sentence summaryB deficiency reduces the accumulation of brassinolide by reducingBR6ox1andBR6ox2mRNA level to down-regulate BR signalling and modulate root elongation.
Cavefish cope with environmental hypoxia by developing more erythrocytes and overexpression of hypoxia inducible genes
Authors: van der Weele Corine M. , Jeffery William R. 
Published: December 2019

AbstractDark caves lacking primary productivity can expose subterranean animals to hypoxia. We used the surface-dwelling (surface fish) and cave-dwelling (cavefish) morphs of Astyanax mexicanus as a model for understanding the mechanisms of hypoxia tolerance in the cave environment. Primitive hematopoiesis, which is restricted to the posterior lateral mesoderm in other teleosts, also occurs in the anterior lateral mesoderm in Astyanax, potentially pre-adapting surface fish for hypoxic cave colonization. Cavefish have enlarged both hematopoietic domains and develop more erythrocytes than surface fish, which are required for normal development in both morphs. Laboratory induced hypoxia suppresses growth in surface fish but not in cavefish. Both morphs respond to hypoxia by overexpressing Hypoxia-Inducible Factor (HIF) pathway genes, but some hif genes are constitutively upregulated in normoxic cavefish to similar levels as hypoxic surface fish. We conclude that cavefish cope with hypoxia by increasing erythrocyte development and constitutive HIF gene overexpression.SummaryAstyanax mexicanus cavefish cope with hypoxic environments by expanding embryonic hematopoietic domains, increasing the capacity for erythrocyte development, and constitutive overexpression of hypoxia-inducible genes.
Metabolic switching is impaired by aging and facilitated by ketosis independent of glycogen
Authors: Hernandez Abbi R. , Truckenbrod Leah M. , Federico Quinten P. , Campos Keila T. , Moon Brianna M. , Ferekides Nedi , Hoppe Meagan , D’Agostino Dominic , Burke Sara N. 
Published: December 2019

ABSTRACTThe ability to switch between glycolysis and ketosis promotes survival by enabling metabolism through fat oxidation during periods of fasting. Carbohydrate restriction or stress can also elicit metabolic switching. Keto-adapting from glycolysis is delayed in aged rats, but factors mediating this age-related impairment have not been identified. We measured metabolic switching between glycolysis and ketosis, as well as glycogen dynamics, in young and aged rats undergoing time-restricted feeding (TRF) with a standard diet or a low carbohydrate ketogenic diet (KD). TRF alone reversed markers of insulin-related metabolic deficits and accelerated metabolic switching in aged animals. A KD+TRF, however, provided additive benefits on these variables. Remarkably, the ability to keto-adapt was not related to glycogen levels and KD-fed rats showed an enhanced elevation in glucose following epinephrine administration. This study provides new insights into the mechanisms of keto-adaptation demonstrating the utility of dietary interventions to treat metabolic impairments across the lifespan.
Circuit and synaptic organization of forebrain-to-midbrain pathways that promote and suppress vocalization
Authors: Michael Valerie , Goffinet Jack , Pearson John , Wang Fan , Tschida Katherine , Mooney Richard 
Published: December 2019

AbstractAnimals vocalize only in certain behavioral contexts, but the circuits and synapses through which forebrain neurons trigger or suppress vocalization remain unknown. Here we used transsynaptic tracing to identify two populations of inhibitory neurons that lie upstream of neurons in the periaqueductal gray that gate the production of ultrasonic vocalizations in mice (i.e., PAG-USV neurons). Activating PAG-projecting neurons in the preoptic hypothalamus (POAPAGneurons) elicited USV production in the absence of social cues. In contrast, activating PAG-projecting neurons in the central-medial boundary zone of the amygdala (AmgC/M-PAGneurons) transiently suppressed USV production without disrupting non-vocal social behavior. Optogenetics-assisted circuit mapping in brain slices revealed that POAPAGneurons directly inhibit PAG interneurons, which in turn inhibit PAG-USV neurons, whereas AmgC/M-PAGneurons directly inhibit PAG-USV neurons. These experiments identify two major forebrain inputs to the PAG that trigger and suppress vocalization, respectively, while also establishing the synaptic mechanisms through which these neurons exert opposing behavioral effects.
YSL3-mediated copper distribution is required for fertility, grain yield, and size inBrachypodium
Authors: Sheng Huajin , Jiang Yulin , Ishka Maryam Rahmati , Chia Ju-Chen , Dokuchayeva Tatyana , Kavulych Yana , Zavodna Tetiana-Olena , Mendoza Patrick N. , Huang Rong , Smieshka Louisa M. , Woll Arthur R. , Terek Olga I. , Romanyuk Nataliya D. , Zhou Yonghong , Vatamaniuk Olena K. 
Published: December 2019

AbstractAddressing the looming global food security crisis requires the development of high yielding crops. In this regard, the deficiency for the micronutrient copper in agricultural soils decreases grain yield and significantly impacts a globally important crop, wheat. In cereals, grain yield is determined by inflorescence architecture, flower fertility, grain size and weight. Whether copper is involved in these processes and how it is delivered to the reproductive organs is not well understood. We show that copper deficiency alters not only the grain set but also flower development in both wheat and it’s recognized model,Brachypodium distachyon, We then show that a brachypodium yellow-stripe-like 3 (YSL3) transporter localizes to the phloem and mediates copper delivery to flag leaves, anthers and pistils. Failure to deliver copper to these structures in theysl3CRISPR/Cas9 mutant results in delayed flowering, altered inflorescence architecture, reduced floret fertility, grain number, size, and weight. These defects are rescued by copper supplementation and are complemented by theYSL3cDNA. This new knowledge will help to devise sustainable approaches for improving grain yield in regions where soil quality is a major obstacle for crop production.
Cell type specific gene expression profiling reveals a role for the complement component C3A in neutrophil migration to tissue damage
Authors: Houseright Ruth A. , Rosowski Emily E. , Lam Pui Ying , Tauzin Sebastien JM , Mulvaney Oscar , Dewey Colin N. , Bennin David , Huttenlocher Anna 
Published: December 2019

AbstractFollowing acute injury, leukocytes rapidly infiltrate into tissues. For efficient recruitment, leukocytes must sense and respond to signals from both from the damaged tissue and from one another. However, the cell type specific transcriptional changes that influence leukocyte recruitment and wound healing have not been well characterized. In this study, we performed a large-scale translating ribosome affinity purification (TRAP) and RNA sequencing screen in larval zebrafish to identify genes differentially expressed by neutrophils, macrophages, and epithelial cells in the context of wounding. We identified the complement pathway andc3a.1, homologous to the C3A component of human complement, as significantly increased in neutrophils in response to a wound. We report thatc3a.1−/−zebrafish larvae have impaired neutrophil responses to both tail wounds and localized bacterial infections, as well as increased susceptibility to infection due to a neutrophil-intrinsic function of C3A. We further show that C3A enhances migration of human primary neutrophils to IL-8 and thatc3a.1−/−larvae have impaired neutrophil migrationin vivo, and a decrease in neutrophil directed migration speed early after wounding. Together, our findings suggest a role for C3A in mediating efficient neutrophil migration to damaged tissues and support the power of TRAP to identify cell-specific changes in gene expression associated with wound-associated inflammation.
Heme induces innate immune memory
Authors: Jentho Elisa , Novakovic Boris , Ruiz-Moreno Cristian , Kourtzelis Ioannis , Martins Rui , Chavakis Triantafyllos , Soares Miguel Perreira , Kalafati Lydia , Guerra Joel , Roestel Franziska , Bohm Peter , Godmann Maren , Grinenko Tatyana , Eugster Anne , Beretta Martina , Joosten Leo A.B. , Netea Mihai G. , Stunnenberg Hendrik G. , Bauer Michael , Weis Sebastian 
Published: December 2019

ABSTRACTTrained immunity defines long-lasting adaptive responses of innate immunity, mediated by transcriptional and epigenetic modifications of myeloid cells. Here, we report that labile heme, an alarmin released extracellularily upon tissue damage and hemolysis, induces trained immunity in human and murine primary cells and in mice. Heme-trainning in monocytes is associated with epigenetic and transcriptional profiles that overlap to some extent with those seen in β-glucan-training, the prototype agonist of trained immunity. In sharp contrast to β-glucan training however, heme-training relied on activation of the Syk/JNK-pathway. Heme training in mice was associated with long-lasting expansion of myeloid-biased progenitor cells as well as with altered chromatin accessibility in hematopoietic stem and progenitor cells. Finally, heme-induced training was protective against bacterial sepsis in mice.In conclusion, we reveal that heme, abona fidealarmin, induces innate immune memory regulating host response to infection.
Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish
Authors: Powell Daniel L. , Garcia Mateo , Keegan Mackenzie , Reilly Patrick , Du Kang , Díaz-Loyo Alejandra P. , Banerjee Shreya , Blakkan Danielle , Reich David , Andolfatto Peter , Rosenthal Gil , Schartl Manfred , Schumer Molly 
Published: December 2019

AbstractThe establishment of reproductive barriers between populations is the key process that fuels the evolution of new species. A genetic framework for this process was proposed over 80 years ago, which posits “incompatible” interactions between genes that result in reduced survival or reproduction in hybrids. Despite this foundational work, progress has been slow in identifying individual genes that underlie hybrid incompatibilities, with only a handful known to date. Here, we use a combination of approaches to precisely map the genes that drive the development of a melanoma incompatibility in swordtail fish hybrids. We find that one of the genes involved in this incompatibility also causes melanoma in hybrids between distantly related species. Moreover, we show that this melanoma reduces survival in the wild, likely due to progressive degradation of the fin. Together, this work represents only the second case where the genes underlying a vertebrate hybrid incompatibility have been identified and provides the first glimpse into the action of these genes in natural hybrid populations.One sentence summaryUsing a combination of mapping approaches, we identify interacting genes that lead to melanoma in hybrids and characterize their effects in natural hybrid populations.
Sleep-drive reprograms clock neuronal identity through CREB-binding protein induced PDFR expression
Authors: Klose MK , Shaw PJ 
Published: December 2019

AbstractNeuronal circuits can be re-modeled by Hebbian plasticity, synaptic scaling and, under some circumstances, activity-dependent respecification of cell-surface receptors. Although the impact of sleep on Hebbian plasticity and synaptic scaling are well studied, sleep’s role in receptor respecification remains unclear. We demonstrate that high sleep-pressure quickly reprograms theDrosophilawake-promoting large-ventrolateral clock-neurons to express the Pigment Dispersing Factor receptor. The addition of this signaling input into the circuit is associated with increased waking and early mating success. The respecification of Pigment Dispersing Factor receptor in both young and adult large ventrolateral neurons requires two dopamine receptors and activation of the transcriptional regulatornejire(CREB-binding protein). These data identify receptor-respecification as an important mechanism to sculpt circuit function to match sleep levels with demand.