bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dopamine signaling in wake promoting clock neurons is not required for the normal regulation of sleep inDrosophila
Authors: Fernandez-Chiappe Florencia , Hermann-Luibl Christiane , Peteranderl Alina , Reinhard Nils , Hieke Marie , Selcho Mareike , Shafer Orie T. , Muraro Nara I. , Helfrich-Förster Charlotte 
Published: May 2020

AbstractDopamine is a wakefulness promoting neuromodulator in mammals and fruit flies. InD. melanogaster, the network of clock neurons that drives sleep/activity cycles comprises both wake and sleep promoting cell types, indicating that the sleep-wake circuitry is intimately linked to the circadian clock. The large and small ventrolateral neurons (l-LNvs and s-LNvs) have been identified as wake-promoting neurons within the clock neuron network. The l-LNvs are innervated by dopaminergic neurons, and earlier work proposed that dopamine signaling raises cAMP levels in the l-LNvs and thus induces excitatory electrical activity (action potential firing), which results in wakefulness and inhibits sleep. Here, we test this hypothesis by combining cAMP imaging and patch-clamp recordings in isolated brains. We find that dopamine application indeed increases cAMP levels and depolarizes the l-LNvs, but surprisingly, it does not result in increased firing rates. Down-regulation of the excitatory dopamine receptor, Dop1R1 in the l-and s-LNvs, but not of Dop1R2, abolished the depolarization of l-LNvs in response to dopamine. This indicates that dopamine signals via Dop1R1 to the l-LNvs. Down-regulation of Dop1R1 or Dop1R2 receptors in the l- and s-LNvs does not affect sleep. Unexpectedly, we find a moderate decrease of daytime sleep with down-regulation of Dop1R1 and of nighttime sleep with down-regulation of Dop1R2. Since the l-LNvs do not utilize Dop1R2 receptors and the s-LNvs respond also to dopamine, we conclude that the s-LNvs are responsible for the observed decrease in nighttime sleep. In summary, dopamine signaling in the wake-promoting LNvs is not required for daytime arousal, but likely promotes nighttime sleep via the s-LNvs.Significance statementIn insect and mammalian brains, sleep promoting networks are intimately linked to the circadian clock, and the mechanisms underlying sleep and circadian timekeeping are evolutionarily ancient and highly conserved. Here we show that dopamine, one important sleep modulator in flies and mammals, plays surprisingly complex roles in the regulation of sleep by clock containing neurons. Dopamine inhibits neurons in a central brain sleep center to promote sleep and excites wake-promoting circadian clock neurons. It is therefore predicted to promote wakefulness through both of these networks. Nevertheless, our results reveal that dopamine acting on wake promoting clock neurons promotes sleep, revealing a previously unappreciated complexity in the dopaminergic control of sleep.
Methodological priorities in assessing wild edible plant knowledge and use – a case study among the Baka in Cameroon
Authors: Gallois Sandrine , Heger Thomas , Henry Amanda G. , van Andel Tinde 
Published: May 2020

AbstractFreelisting and dietary recalls are frequently used methods in ethnobotany to assess wild edible plant (WEP) knowledge and use. Though theseex-situinterviewing methods are practical to perform and may yield large datasets in a short time, they are known to be limited by the informant’s memory and cognitive bias. Alternatively, the much more laborious walk-in-the-woods method may be used, in which informants point out edible plantsin-situ. Few studies, however, examine quantitatively how these different methods influence results. In this study, we assessed how these methods capture the diversity of wild edible plant knowledge and use among the Baka, a group of forager-horticulturalists from southeastern Cameroon. We show that within a single population, and when data on consumption frequency are collected simultaneously, the walk-in-the-woods method results in more detailed information of WEP knowledge and use than do freelisting or dietary recalls. Ourin-situmethod yielded 91 species of WEP, much more than theex-situmethods of freelisting (34 spp.) and dietary recalls (12 spp.). Our results imply that previous studies based only onex situsurveys may have underestimated the importance of WEP for local communities. We propose that future studies on WEP knowledge and use frequency should rely on mixed methods, taking anin-situmethod as the starting point of their approach.
Non-denaturing bisulfite treatment and single-molecule real-time sequencing reveals d-loop footprints, their length, position and distribution
Authors: Shah Shanaya Shital , Hartono Stella , Chédin Frédéric , Heyer Wolf-Dietrich 
Published: May 2020

ABSTRACTDisplacement loops (D-loops) are signature intermediates formed during homologous recombination. Numerous factors regulate D-loop formation and disruption, thereby influencing crucial aspects of DNA repair, including donor choice and the possibility of a crossover outcome. While D-loop detection methods exist, it is currently unfeasible to assess the relationship between D-loop editors and D-loop characteristics such as length and position. Here, we developed a novel in vitro assay to characterize the length and position of individual D-loop with base-pair resolution and deep coverage, while also revealing their distribution in a population. Non-denaturing bisulfite treatment modifies the cytosines on the displaced strand of the D-loop to uracil, leaving a permanent signature for the displaced strand. Subsequent single-molecule real-time sequencing uncovers the cytosine conversion patch as a D-loop footprint, revealing D-loop characteristics at unprecedented resolution. The D-loop Mapping Assay is widely applicable with different substrates and donor types and can be used to study factors that influence D-loop properties.
Rapid divergence of the copulation proteins in theDrosophila dunnigroup is associated with hybrid post-mating-prezygotic incompatibilities
Authors: Hill Tom , Rosales-Stephens Hazel-Lynn , Unckless Robert L. 
Published: May 2020

AbstractProteins involved in post-copulatory interactions between males and females are among the fastest evolving genes in many species and this has been attributed to reproductive conflict. Likely as a result, these proteins are frequently involved in cases of post-mating-prezygotic isolation between species. TheDrosophila dunnisubgroup consists of a dozen recently diverged species found across the Caribbean islands with varying levels of hybrid incompatibility. We sought to examine how post-mating-prezygotic factors are involved in isolation among members of this species group. We performed experimental crosses between species in thedunnigroup and find evidence of hybrid inviability. We also find an insemination reaction-like response preventing egg laying and leading to reduced female survival post-mating. To identify that genes may be involved in these incompatibilities, we sequenced and assembled the genomes of four species in thedunnisubgroup and looked for signals of rapid evolution between species. Despite low levels of divergence, we found evidence of rapid evolution and divergence of some reproductive proteins, specifically the seminal fluid proteins. This suggests post-mating-prezygotic isolation as a barrier for gene flow between even the most closely related species in this group and seminal fluid proteins as a possible culprit.
A large accessory genome, high recombination rates, and selection of secondary metabolite genes help maintain global distribution and broad host range of the fungal plant pathogenClaviceps purpurea
Authors: Wyka Stephen A. , Mondo Stephen J. , Liu Miao , Nalam Vamsi , Broders Kirk D. 
Published: May 2020

AbstractPangenome analyses are increasingly being utilized to study the evolution of eukaryotic organisms, which is often governed by variable gene content. While pangenomes can provide insight into polymorphic gene content, inferences about the ecological and adaptive potential of such organisms also need to be accompanied by additional supportive genomic analyses. In this study we constructed a pangenome ofClaviceps purpureafrom 24 genomes and examined the positive selection and recombination landscape of an economically important fungal organism for pharmacology and agricultural research. Together, these analyses revealed thatC. purpureahas a relatively large accessory genome (∼ 38%) that is likely maintained by high recombination rates (ρ = 0.044) and transposon mediated gene duplication. However, due to observations of relatively low transposable element (TE) content (8.8%) and a lack of variability in genome sizes, prolific TE expansion is likely controlled by these high recombination rates, which may additionally be influencing the overall trend of purifying selection across the genome. Despite this trend, we observed a strong positive selection pressure on secondary metabolite genes, particularly within the ergoline biosynthetic cluster where we also revealed that thelpsA1andlpsA2genes were the result of a recombination event. These results indicate that secondary metabolites are primary factors affecting the diversification of the species into new ecological niches and help maintain its global distribution and broad host range. These results showcase the use of selection and recombination landscapes to identify mechanisms contributing to pangenome structure and primary factors influencing the evolution of an organism.Author SummaryThe use of genomic data to better understand the lifestyle of a pathogen and its relationship with its host has expanded our ability to investigate the evolutionary history of these organisms. This in turn has allowed us to decipher and understand the ambiguity surrounding the true nature of the fungal plant pathogenClaviceps purpurea. By combining three different types of broad genomic analyses we identified primary factors affecting the evolution and adaptive potential of this pathogen; particularly a large accessory genome, high recombination rates, and positive selection of genes associated with stress tolerance. These factors likely contribute to the pathogen’s global distribution and broad host range. Furthermore, these findings will influence the direction of future research into optimal control methods.
Chronic high dietary sucrose induces sexually dimorphic metabolic adaptations in liver and adipose tissue
Authors: Stephenson Erin J , Stayton Amanda S , Sethuraman Aarti , Rao Prahlad K , Gomes Charles Klazer , Mulcahy Molly C , McAllan Liam , Puchowicz Michelle A , Pierre Joseph F , Bridges Dave , Han Joan C 
Published: May 2020

SummaryAlmost all effective treatments for non-alcoholic fatty liver disease (NAFLD) involve reduction of adiposity, which suggests the metabolic axis between liver and adipose tissue is essential to NAFLD development. Since excessive dietary sugar intake may be an initiating factor for NAFLD, we have characterized the metabolic effects of liquid sucrose intake at concentrations relevant to typical human consumption in mice. We report that sucrose intake induces sexually dimorphic effects in liver, adipose tissue, and the microbiome; differences concordant with steatosis severity. We show that when steatosis is decoupled from impairments in insulin responsiveness, sex is a moderating factor that influences sucrose-driven lipid storage and the contribution ofde novofatty acid synthesis to the overall hepatic triglyceride pool. Our findings provide physiologic insight into how sex influences the regulation of adipose-liver crosstalk and highlight the importance of extrahepatic metabolism in the pathogenesis of diet-induced steatosis and NAFLD.
Perforin-2 limits pathogen proliferation at the maternal-fetal interface
Authors: Gayle Petoria , McGaughey Vanessa , Hernandez Rosmely , Wylie Marina , Colletti Rachel C. , Nguyen Ka Lam , Arons Marshall , Padula Laura , Strbo Natasa , Schesser Kurt 
Published: May 2020

AbstractPlacental immune responses are highly regulated to strike a balance between protection and tolerance. For relatively mild infections, protection encompasses both the mother and fetus; however, during worsening conditions, protection becomes exclusively reserved for the mother. Previously, we and others have shown that the host factor Perforin-2 plays a central role in protecting mice and cells against infection. Here, we analyzed Perforin-2 activity in the mouse placenta to determine whether Perforin-2 plays a similarly protective role. We show that Perforin-2 is critical for inhibitingListeria monocytogenescolonization of the placenta and fetus and that this protection is due to both maternal and fetal-encoded Perforin-2.Perforin-2mRNA is readily detectable in individual immune cells of the decidua and these levels are further enhanced specifically in decidual macrophages during high-dose infections that result in fetal expulsion. Unexpectedly, inductive Perforin-2 expression in decidual macrophages did not occur during milder infections in which fetal viability remained intact. This pattern of expression significantly differed from that observed in splenic macrophages in which inductive Perforin-2 expression was observed in both high and mild infection conditions. In the placenta, inductive Perforin-2 expression in decidual macrophages was co-incident with their polarization from a M2 to M1 phenotype that normally occurs in the placenta during high-burden infections. Our results suggest that Perforin-2 is part of a host response that is protective either for both the mother and fetus in milder infections or exclusively for the mother during high-dose infections.
Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation
Authors: Evano Brendan , Gill Diljeet , Hernando-Herraez Irene , Comai Glenda , Stubbs Thomas M. , Commere Pierre-Henri , Reik Wolf , Tajbakhsh Shahragim 
Published: May 2020

ABSTRACTAdult skeletal muscles are maintained during homeostasis and regenerated upon injury by muscle stem cells (MuSCs). A heterogeneity in self-renewal, differentiation and regeneration properties has been reported for MuSCs based on their anatomical location. Although MuSCs derived from extraocular muscles (EOM) have a higher regenerative capacity than those derived from limb muscles, the molecular determinants that govern these differences remain undefined. Here we show that EOM and limb MuSCs have distinct DNA methylation signatures associated with enhancers of location-specific genes, and that the EOM transcriptome is reprogrammed following transplantation into a limb muscle environment. Notably, EOM MuSCs expressed host-site specific positionalHoxcodes after engraftment and self-renewal within the host muscle. However, about 10% of EOM-specific genes showed engraftment-resistant expression, pointing to cell-intrinsic molecular determinants of the higher engraftment potential of EOM MuSCs. Our results underscore the molecular diversity of distinct MuSC populations and molecularly define their plasticity in response to microenvironmental cues. These findings provide insights into strategies designed to improve the functional capacity of MuSCs in the context of regenerative medicine.
TET1 dioxygenase is required for FOXA2-associated chromatin remodeling in pancreatic beta-cell differentiation
Authors: Li Jianfang , Wu Xinwei , Lee Minjung , Ke Jie , Lan Qingping , Li Jia , Huang Yun , Sun De-Qiang , Xie Ruiyu 
Published: May 2020

AbstractExisting knowledge of the role of epigenetic modifiers in pancreas development has exponentially increased. However, the function of TET dioxygenases in pancreatic endocrine specification remains obscure. We set out to tackle this issue using a human embryonic stem cell (hESC) differentiation system, in whichTET1/TET2/TET3triple knock-out cells display severe defects in pancreatic β-cell specification. Integrative whole-genome analysis identifies unique cell-type-specific hypermethylated regions (hyper-DMRs) displaying reduced chromatin activity and remarkable enrichment of FOXA2, a pioneer transcription factor essential for pancreatic endoderm specification. Intriguingly, TET depletion leads to significant changes in FOXA2 binding at pancreatic progenitor stage, in which gene loci with decreased FOXA2 binding features low levels of active chromatin modifications and enriches for bHLH motifs. Transduction of full-lengthTET1but not the TET1-catalytic-domain inTET-deficient cells effectively rescues β-cell differentiation accompanied by restoringPAX4hypomethylation. Taking these findings together with the defective generation of functional β-cells upon TET1-inactivation, our study unveils an essential role of TET1-dependent demethylation in establishing β-cell identity. Moreover, we discover a physical interaction between TET1 and FOXA2 in endodermal lineage intermediates, which provides a new mechanistic clue regarding the complex crosstalk between TET dioxygenases and pioneer transcription factors in epigenetic regulation during pancreas specification.
Development and clinical application of a rapid and sensitive loop-mediated isothermal amplification test for SARS-CoV-2 infection
Authors: Hu Xuejiao , Deng Qianyun , Li Junmin , Chen Jierong , Wang Zixia , Zhang Xiqin , Fang Zhixin , Li Haijian , Zhao Yunhu , Yu Pan , Li Wenmin , Wang Xiaoming , Li Shan , Zhang Lei , Hou Tieying 
Published: May 2020

ABSTRACTBackgroundThe SARS-CoV-2 outbreak urgently requires sensitive and convenient COVID-19 diagnostics for the containment and timely treatment of patients. We aimed to develop and validate a novel reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to detect SARS-CoV-2 in qualified laboratories and point-of-care settings.MethodsPatients with suspected COVID-19 and close contacts were recruited from two hospitals between Jan 26 and April 8, 2020. Respiratory samples were collected and tested using the RT-LAMP assays, and the results were compared with those obtained by RT-qPCR. Samples yielding inconsistent results between these two methods were subjected to next-generation sequencing for confirmation. The RT-LAMP assay was also tested on an asymptomatic COVID-19 carrier and patients with other respiratory viral infections.ResultsSamples were collected from a cohort of 129 cases (329 nasopharyngeal swabs) and an independent cohort of 76 patients (152 nasopharyngeal swabs and sputum samples). The RT-LAMP assay was validated to be accurate (overall sensitivity and specificity: 88.89% and 99.00%; positive and negative predictive values: 94.74% and 97.78%, respectively) and diagnostically useful (positive and negative likelihood ratios: 88.89 and 0.11, respectively). RT-LAMP showed an increased sensitivity (88.89% vs 81.48%) and high consistency (kappa 0.92) compared with RT-qPCR for SARS-CoV-2 screening while requiring only constant temperature heating and visual inspection. The time required for RT-LAMP was less than 1 h from sample preparation to result. In addition, RT-LAMP was feasible for use with asymptomatic patients and did not cross-react with other respiratory pathogens.ConclusionThe developed RT-LAMP assay offers rapid, sensitive and straightforward detection of SARS-CoV-2 infection and could aid the expansion of COVID-19 testing in the public domain and hospitals.
Neurons need no adaptation to optimally code arbitrarily complex stimuli
Authors: Forkosh Oren 
Published: May 2020

ABSTRACTNeural networks seem to be able to handle almost any task they face. This feat involves coping efficiently with different data types, at multiple scales, and with varying statistical properties. Here, we show that this so-called optimal coding can occur at the single-neuron level and does not require adaptation. Differentiator neurons, i.e., neurons that spike whenever there is an increase in the input stimuli, are capable of capturing arbitrary statistics and scale of practically any stimulus they encounter. We show this optimality both analytically and using simulations, which demonstrate how an ideal neuron can handle drastically different probability distributions. While the mechanism we present is an oversimplification of “real” neurons and does not necessarily capture all neuron types, this is also its strength since it can function alongside other neuronal goals such as data manipulation and learning. Depicting the simplicity of neural response to complex stimuli, this result may also indicate a straightforward way to improve current artificial neural networks.
Repeat length increases disease penetrance and severity in C9orf72 ALS/FTD BAC transgenic mice
Authors: Pattamatta Amrutha , Nguyen Lien , Olafson Hailey , Scotti Marina , Laboissonniere Lauren A. , Richardson Jared , Berglund J. Andrew , Zu Tao , Wang Eric.T. , Ranum Laura P.W. 
Published: May 2020

AbstractC9orf72 ALS/FTD patients show remarkable clinical heterogeneity, but the complex biology of the repeat expansion mutation has limited our understanding of the disease. BAC transgenic mice were used to better understand the molecular mechanisms and repeat length effects of C9orf72 ALS/FTD. Genetic analyses of these mice demonstrate that the BAC transgene and not integration site effects cause ALS/FTD phenotypes. Transcriptomic changes in cell proliferation, inflammation and neuronal pathways are found late in disease and alternative splicing changes provide early molecular markers that worsen with disease progression. Isogenic sublines of mice with 800, 500 or 50 G4C2 repeats generated from the single-copy C9-500 line show longer repeats result in earlier onset, increased disease penetrance, and increased levels of RNA foci and RAN aggregates. These data demonstrate G4C2 repeat length is an important driver of disease and identify alternative splicing changes as early biomarkers of C9orf72 ALS/FTD.
Integration of multiple imaging platforms to uncover cardiac defects in adult zebrafish
Authors: Bensimon-Brito Anabela , Boezio Giulia L. M. , Cardeira-da-Silva João , Wietelmann Astrid , Helker Christian S. M. , Ramadass Radhan , Piesker Janett , Nauerth Arno , Mueller Clemens , Stainier Didier Y. R. 
Published: May 2020

AbstractMammalian models have been instrumental to investigate adult heart function and human disease. However, electrophysiological differences with human hearts and high costs emphasize the need for additional models. The zebrafish is a well-established genetic model to study cardiac development and function; however, analysis of cardiac phenotypes in adult specimens is particularly challenging as they are opaque. Here, we optimized and combined multiple imaging techniques including echocardiography, magnetic resonance imaging and micro-computed tomography to identify and analyze cardiac phenotypes in adult zebrafish. Usingalk5a/tgfbr1amutants as a case study, we observed morphological and functional cardiac defects, which were undetected with conventional approaches. Correlation analysis of multiple parameters revealed an association between hemodynamic defects and structural alterations of the heart, as observed clinically. Thus, we report a comprehensive and sensitive platform to identify otherwise indiscernible cardiac phenotypes in adult zebrafish, a model with clear advantages to study cardiac function and disease.