bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organizational properties of a functional mammalian cis-regulome
Authors: Chaudhri Virendra K. , Dienger-Stambaugh Krista , Wu Zhiguo , Shrestha Mahesh , Singh Harinder 
Published: February 2019

AbstractMammalian genomic states are distinguished by their chromatin and transcription profiles. Most genomic analyses rely on chromatin profiling to infer cis-regulomes controlling distinctive cellular states. By coupling FAIRE-seq with STARR-seq and integrating Hi-C we assemble a functional cis-regulome for activated murine B-cells. Within 55,130 accessible chromatin regions we delineate 9,989 active enhancers communicating with 7,530 promoters. The cis-regulome is dominated by long range enhancer-promoter interactions (>100kb) and complex combinatorics, implying rapid evolvability. Genes with multiple enhancers display higher rates of transcription and multi-genic enhancers manifest graded levels of H3K4me1 and H3K27ac in poised and activated states, respectively. Motif analysis of pathway-specific enhancers reveals diverse transcription factor (TF) codes controlling discrete processes. The cis-regulome strikingly enriches for combinatorial DNA binding regions of lineage determining TFs. Their genomic binding patterns reveal that onset of chromatin accessibility is associated with binding of simpler combinations whereas enhancer function requires greater complexity.
Iron activates microglia and directly stimulates indoleamine-2,3-dioxygenase activity in the N171-82Q mouse model of Huntington’s disease
Authors: Donley David W. , Realing Marley , Gigley Jason P. , Fox Jonathan H. 
Published: February 2019

AbstractHuntington’s disease (HD) is a neurodegenerative disorder caused by a dominant CAG-repeat expansion in the huntingtin gene. Morphologic activation of microglia is a key marker of neuroinflammation that is present before clinical onset in HD patients. The kynurenine pathway of tryptophan degradation is restricted in part to microglia and is activated in HD, where it contributes to disease progression. Indoleamine-2,3-dioxygenase (IDO) is a microglial enzyme that catalyzes the first step in this pathway. HD brain microglial cells also accumulate iron; however, the role of iron in promoting microglial activation and the kynurenine pathway is unclear. Based on analyses of morphological characteristics of microglia, we showed that HD mice demonstrate an activated microglial morphology compared with controls. Neonatal iron supplementation resulted in additional microglial morphology changes compared with HD controls. Increased microglial activation in iron-supplemented HD mice was indicated by increased soma volume and decreased process length. In our assessment of whether iron can affect the kynurenine pathway, iron directly enhanced the activity of human recombinant IDO1 with an EC50 of 1.24 nM. We also detected elevated microglial cytoplasmic labile iron in N171-82Q HD mice, an increase that is consistent with the cellular location of IDO. We further demonstrated that neonatal iron supplementation, a model for studying the role of iron in neurodegeneration, activates IDO directly in the mouse brain and promotes neurodegeneration in HD mice. Kynurenine pathway metabolites were also modified in HD and by iron supplementation in wild-type mice. These findings indicate that iron dysregulation contributes to the activation of microglia and the kynurenine pathway in a mouse model of HD.
Mutant huntingtin protein alters the response of microglial cells to inflammatory stimuli
Authors: Donley David W. , Nelson Ryan , Gigley Jason P. , Fox Jonathan H. 
Published: February 2019

AbstractHuntington’s disease (HD) is a progressive neurodegenerative disease that affects the striatum and cerebral cortex. It is caused by a dominant CAG trinucleotide expansion in exon 1 of theHTTgene. Mutant huntingtin protein (mHtt) is expressed in neurons and immune cells. HD patients demonstrate altered blood cytokine profiles and altered responses of peripheral immune cells to inflammatory stimuli. However, the effects of mHtt on microglial immune responses are not fully understood. Herein we discuss the current understanding of how mHtt alters microglial inflammatory responses. Using lentivirus, we expressed the N171 N-terminal fragment of wild-type or mhtt containing 18 and 82 glutamine repeats in cultured EOC-20 microglial cells. We then measured responses to lipopolysaccharide or interleukin-6. Mutant huntingtin-expressing microglial cells produced less interleukin-6 and nitric oxide in response to lipopolysaccharide stimulation than wild-type huntingtin-expressing cells. However, mHtt-expressing microglia stimulated with interleukin-6 produced more nitric oxide than wild-type cells. Mutant huntingtin-expressing cells had higher basal NF-κB and further elevations of NF-κB after interleukin-6 but not lipopolysaccharide stimulation. Thus we demonstrate the potential of mHtt to dampen responses to lipopolysaccharide but potentiate responses to interleukin-6. This work adds to the emerging understanding that mHtt alters not only baseline status of cells but may also result in altered immune responses dependent on the nature of the inflammatory stimuli. We also present our perspective that in human HD the extent of inflammation may depend, in part, on altered responses to varied inflammatory stimuli including environmental factors such as infection.
Introgressive and horizontal acquisition of Wolbachia byDrosophila yakuba-clade hosts and horizontal transfer of incompatibility loci between distantly related Wolbachia
Authors: Cooper Brandon S. , Vanderpool Dan , Conner William R. , Matute Daniel R. , Turelli Michael 
Published: February 2019

ABSTRACTMaternally transmitted Wolbachia infect about half of insect species, yet the predominant mode(s) of Wolbachia acquisition remains uncertain. Species-specific associations could be old, with Wolbachia and hosts co-diversifying (i.e., cladogenic acquisition), or relatively young and acquired by horizontal transfer or introgression. The threeDrosophila yakuba-clade hosts ((D. santomea, D. yakuba),D. teissieri) diverged about three million years ago and currently hybridize on Bioko and São Tomé, west African islands. Each species is polymorphic for nearly identical Wolbachia that cause weak cytoplasmic incompatibility (CI)–reduced egg hatch when uninfected females mate with infected males.D. yakuba-clade Wolbachia are closely related towMel, globally polymorphic inD. melanogaster. We use draft Wolbachia and mitochondrial genomes to demonstrate thatD. yakuba-clade Wolbachia and mitochondrial phylogenies tend to follow host nuclear phylogenies; however, roughly half ofD. santomeaindividuals, sampled both inside and outside of the São Tomé hybrid zone, have introgressedD. yakubamitochondria. Both mitochondria and Wolbachia possess far more recent common ancestors than the bulk of the host nuclear genomes, precluding cladogenic Wolbachia acquisition. General concordance of Wolbachia and mitochondrial phylogenies suggests that horizontal transmission is rare, but varying relative rates of molecular divergence complicate time-based statistical tests. Loci that cause CI inwMel are disrupted inD. yakuba-clade Wolbachia; however, a second set of loci predicted to cause CI are located in the same WO prophage region. These alternative CI loci seem to have been acquired horizontally from distantly related Wolbachia, with transfer mediated by flanking Wolbachia-specific ISWpi1 transposons.
Amino Sugars Modify Antagonistic Interactions between Commensal Oral Streptococci andStreptococcus mutans
Authors: Chen Lulu , Chakraborty Brinta , Zou Jing , Burne Robert A. , Zeng Lin 
Published: February 2019

ABSTRACTN-acetylglucosamine (GlcNAc) and glucosamine (GlcN) enhance the competitiveness of the laboratory strain DL1 ofStreptococcus gordoniiagainst the caries pathogenStreptococcus mutans. Here we examine how amino sugars affect the interaction of five low-passage clinical isolates of abundant commensal streptococci withS. mutansutilizing a dual-species biofilm model. Compared to glucose, growth on GlcN or GlcNAc significantly reduced the viability ofS. mutansin co-cultures with most commensals, shifting the proportions of species. Consistent with these results, production of H2O2was increased in most commensals when growing on amino sugars, and inhibition ofS. mutansbyStreptococcus cristatus, Streptococcus oralis,orS. gordoniiwas enhanced by amino sugars on agar plates. All commensals exceptS. oralishad higher arginine deiminase activities when grown on GlcN, and in some cases GlcNAc. Inex vivobiofilms formed using pooled cell-containing saliva (CCS), the proportions ofS. mutanswere drastically diminished when GlcNAc was the primary carbohydrate. Increased production of H2O2could account in large part for the inhibitory effects of CCS biofilms. Surprisingly, amino sugars appeared to improve mutacin production byS. mutanson agar plates, suggesting that the commensals have mechanisms to actively subvert antagonism byS. mutansin co-cultures. Collectively, these findings demonstrate that amino sugars can enhance the beneficial properties of low-passage commensal oral streptococci and highlight their potential for moderating the cariogenicity of oral biofilms.SIGNIFICANCEDental caries is driven by dysbiosis of oral biofilms in which dominance by acid-producing and acid-tolerant bacteria results in loss of tooth mineral. Our previous work demonstrated the beneficial effects of amino sugars, GlcNAc and GlcN, in promoting the antagonistic properties of a health-associated oral bacterium,Streptococcus gordonii,in competition with the major caries pathogenStreptococcus mutans.Here we investigated 5 low-passage clinical isolates of the most common streptococcal species to establish how amino sugars may influence the ecology and virulence of oral biofilms. Using multiplein vitromodels, including a human saliva-derived microcosm biofilm, experiments showed significant enhancement by at least one amino sugar in the ability of most of these bacteria to suppress the caries pathogen. Therefore, our findings demonstrated the mechanism of action by which amino sugars may affect human oral biofilms to promote health.
Characterization of pyruvate dehydrogenase complex E1 alpha and beta subunits ofMycoplasma synoviae
Authors: Bao Shijun , Ding Xiaoqin , Yu Shengqing , Ding Chan 
Published: February 2019

ABSTRACTMycoplasma synoviae(MS) is an important pathogen, causing enormous economic losses to the poultry industry worldwide every year. Therefore, the studies on MS will lay the foundation for diagnosis, prevention and treatment of MS infection. In this study, primers designed based on the sequences of pyruvate dehydrogenase complex (PDC) E1 alpha and beta subunit genes (pdhAandpdhB, respectively) of MS WVU1853 strain in GenBank were used to amplify thepdhAandpdhBgenes of MS WVU1853 strain through PCR. Then the prokaryotic expression vectors pET-pdhA and pET-pdhB were constructed and were expressed inEscherichia coliBL21(DE3) cells. Subsequently, the recombinant proteins rMSPDHA and rMSPDHB were purified and anti-rMSPDHA and anti-rMSPDHB sera were prepared by immunizing rabbits, respectively. Finally, the subcellular localization of PDHA and PDHB in MS, binding activity of rMSPDHA and rMSPDHB to chicken plasminogen (Plg) and human fibronectin (Fn), complement-dependent mycoplasmacidal assays, and adherence and adherence inhibition assays were accomplished. The results showed that PDHA and PDHB were distributed both on the surface membrane and within soluble cytosolic fractions of MS cells. The rMSPDHA and rMSPDHB presented binding activity with chicken Plg and human Fn. The rabbit anti-rMSPDHA and anti-rMSPDHB sera had distinct mycoplasmacidal efficacy in the presence of guinea pig complement, and the adherence of MS to DF-1 cells pretreated with Plg was effectively inhibited by treatment with anti-rMSPDHA or anti-rMSPDHB sera. Hence, the study indicates that the surface-associated MSPDHA and MSPDHB are the adhesion-related factors of MS that contributes to bind to Plg/Fn and adhesion to DF-1 cells.
Data-driven spatial filtering for improved measurement of cortical tracking of multiple representations of speech
Authors: Lesenfants D , Vanthornhout J , Verschueren E , Francart T 
Published: February 2019

AbstractObjectiveMeasurement of the cortical tracking of continuous natural speech from electroencephalography (EEG) recordings using a forward model is becoming an important tool in auditory neuroscience. However, it requires a manual channel selection based on visual inspection or prior knowledge to obtain a summary measure of cortical tracking. In this study, we present a method to on the one hand remove non-stimulus-related activity from the EEG signals to be predicted, and on the other hand automatically select the channels of interest. We also aim to show that the EEG prediction from phonology-related speech features is possible in Dutch.ApproachEighteen participants listened to a Flemish story, while their EEG was recorded. Subject-specific and grand-average temporal responses functions were determined between the EEG activity in different frequency bands and several stimulus features: the envelope, spectrogram, phonemes, phonetic features or a combination. The temporal response functions were then used to predict EEG from the stimulus, and the predicted was compared with the recorded EEG, yielding a measure of cortical tracking of stimulus features. A spatial filter was calculated based on the generalized eigenvalue decomposition (GEVD), and the effect on EEG prediction accuracy was determined.Main resultsA model including both low- and high-level speech representations was able to better predict the brain responses to the speech than a model only including low-level features. The inclusion of a GEVD-based spatial filter in the model increased the prediction accuracy of cortical responses to each speech feature at both single-subject (270% improvement) and group-level (310 %).SignificanceWe showed that the inclusion of acoustical and phonetic speech information and the addition of a data-driven spatial filter allow improved modelling of the relationship between the speech and its brain response and offer an automatic channel selection.HighlightsAutomatic channel selection for evaluating the cortical tracking of continuous natural speechData-driven spatial filtering for removing non-stimulus-related activity from the EEG signalsImproved prediction of brain responses to speech by combining acoustical and phonetic speech information in DutchDisclosureThe authors report no disclosures relevant to the manuscript.
Direct Evidence for Glucose Consumption Acceleration by Carbonates in Cultured Cells
Authors: Sorimachi Kenji 
Published: February 2019

AbstractEstablished Py-3Y1-S2 rat fibroblast cells were used to evaluate whether NaHCO3or Na2CO3influences glucose metabolismin vitro, because factors that contribute to metabolic pathways are much simpler to evaluate in cultured cells than in whole animal bodies. The effects of the carbonates on glucose consumption decreased at high concentrations, >5 mg/ml for Na2CO3and >7 mg/ml for NaHCO3, because of the increased pH of the culture medium. The effects of the carbonates on glucose consumption were additive with those of vanadium and concanavalin A. Streptozotocin, alloxan, and nicotinamide, which induce diabetes in animals, reduced glucose consumption by Py-3Y1-S2 cells, and the inhibitory effects of these reagents were abolished by both Na2CO3and NaHCO3. Finally, the carbonates increased lactate production from glucose in the cells, followed by acceleration of lactate secretion into the culture medium. The present study clarified that NaHCO3and Na2CO3directly regulate glucose metabolism.
Rapid sperm capture: High-throughput flagellar waveform analysis
Authors: Gallagher M.T. , Cupples G. , Ooi E.H. , Kirkman-Brown J.C. , Smith D.J. 
Published: February 2019

SummaryFlagella are critical across all eukaryotic life, and the human sperm flagellum is crucial to natural fertility. Existing automated sperm diagnostics (CASA) rely on tracking the sperm head and extrapolating measures. We describe fully-automated tracking and analysis of flagellar movement for large cell numbers. The analysis is demonstrated on freely-motile cells in low and high viscosity fluids, and validated on published data of tethered cells undergoing pharmacological hyperactivation. Direct analysis of the flagellar beat reveals that the CASA measure ‘beat cross frequency’, does not measure beat frequency. A new measurement, track centroid speed, is validated as an accurate differentiator of progressive motility. Coupled with fluid mechanics codes, waveform data enables extraction of experimentally intractable quantities such as energy dissipation, disturbance of the surrounding medium and viscous stresses. We provide a powerful and accessible research tool, enabling connection of the cell’s mechanical activity to its motility and effect on its environment.
Functional diversification of hybridoma produced antibodies by CRISPR/HDR genomic engineering
Authors: der Schoot Johan M.S. van , Fennemann Felix L. , Valente Michael , Dolen Yusuf , Hagemans Iris M. , Becker Anouk M.D. , Le Gall Camille M. , Dalen Duco van , Cevirgel Alper , van Bruggen J. Armando C. , Engelfriet M , Caval Tomislav , Bentlage Arthur E.H. , Fransen Marieke F. , Nederend Maaike , Leusen Jeanette H.W. , Heck Albert J.R. , Vidarsson Gestur , Figdor Carl G. , Verdoes Martijn , Scheeren Ferenc A. 
Published: February 2019

AbstractHybridoma technology is instrumental for the development of novel antibody therapeutics and diagnostics. Recent preclinical and clinical studies highlight the importance of antibody isotype for therapeutic efficacy. However, since the sequence encoding the constant domains is fixed, tuning antibody function in hybridomas has been restricted. Here, we demonstrate a versatile CRISPR/HDR platform to rapidly engineer the constant immunoglobulin domains to obtain recombinant hybridomas which secrete antibodies in the preferred format, species and isotype. Using this platform, we obtained recombinant hybridomas secreting Fab’ fragments, isotype switched chimeric antibodies, and Fc-silent mutants. These antibody products are stable, retain their antigen specificity, and display their intrinsic Fc-effector functions in vitro and in vivo. Furthermore, we can site-specifically attach cargo to these antibody products via chemo-enzymatic modification. We believe this versatile platform facilitates antibody engineering for the entire scientific community, empowering preclinical antibody research.One Sentence SummaryWe demonstrate a universal CRISPR/HDR based platform for rapid genetic engineering of hybridomas to obtain functionally diverse antibody isotype panels in the species and format of choice.
Identification of CP77 as the third orthopoxvirus SAMD9L inhibitor with a unique specificity for a rodent SAMD9L
Authors: Zhang Fushun , Meng Xiangzhi , Townsend Michael B , Satheshkumar Panayampalli Subbian , Xiang Yan 
Published: February 2019

ABSTRACTOrthopoxviruses (OPXVs) have a broad host range in mammalian cells, but Chinese hamster ovary (CHO) cells are non-permissive for vaccinia virus (VACV). Here, we revealed a species-specific difference in host restriction factor SAMD9L as the cause for the restriction and identified orthopoxvirus CP77 as a unique inhibitor capable of antagonizing Chinese hamster SAMD9L (chSAMD9L). Two known VACV inhibitors of SAMD9 and SAMD9L (SAMD9&L), K1 and C7, can bind human and mouse SAMD9&L, but neither can bind chSAMD9L. CRISPR-Cas9 knockout of chSAMD9L from CHO cells removed the restriction for VACV, while ectopic expression of chSAMD9L imposed the restriction for VACV in a human cell line, demonstrating that chSAMD9L is a potent restriction factor for VACV. Contrary to K1 and C7, cowpox virus CP77 can bind chSAMD9L and rescue VACV replication in cells expressing chSAMD9L, indicating that CP77 is yet another SAMD9L inhibitor but has a unique specificity for chSAMD9L. Binding studies showed that the N-terminal 382 amino acids of CP77 were sufficient for binding chSAMD9L and that both K1 and CP77 target a common internal region of SAMD9L. Growth studies with nearly all OPXV species showed that the ability of OPXVs in antagonizing chSAMD9L correlates with CP77 gene status and that a functional CP77 ortholog was maintained in many OPXVs, including monkeypox virus. Our data suggest that species-specific difference in rodent SAMD9L poses a barrier for cross-species OPXV infection and that OPXVs have evolved three SAMD9L inhibitors with different specificities to overcome this barrier.IMPORTANCESeveral OPXV species, including monkeypox virus and cowpox virus, cause zoonotic infection in humans. They are believed to use wild rodents as the reservoir or intermediate hosts, but the host or viral factors that are important for OPXV host range in rodents are unknown. Here, we showed that the abortive replication of several OPXV species in a Chinese hamster cell line was caused by a species-specific difference in the host antiviral factor SAMD9L, indicating that SAMD9L divergence in different rodent species poses a barrier for cross-species OPXV infection. While the Chinese hamster SAMD9L could not be inhibited by two previously identified OPXV inhibitors of human and mouse SAMD9L, it can be inhibited by cowpox virus CP77, indicating that OPXVs encode three SAMD9L inhibitors with different specificity. Our data suggest that OPXV host range in broad rodent species depends on three SAMD9L inhibitors with different specificities.
Diversity of photosynthetic picoeukaryotes in eutrophic shallow lakes as assessed by combining flow cytometry cell-sorting and high throughput sequencing
Authors: Metz Sebastián , dos Santos Adriana Lopes , Berman Manuel Castro , Bigeard Estelle , Licursi Magdalena , Not Fabrice , Lara Enrique , Unrein Fernando 
Published: February 2019

ABSTRACTPhotosynthetic picoeukaryotes (PPE) are key components of primary production in marine and freshwater ecosystems. In contrast with those of marine environments, freshwater PPE groups have received little attention. In this work, we used flow cytometry cell sorting, microscopy and metabarcoding to investigate the composition of small photosynthetic eukaryote communities from six eutrophic shallow lakes in South America, Argentina. We compared the total molecular diversity obtained from PPE sorted populations as well as from filtered total plankton samples (FTP). Most reads obtained from sorted populations belonged to the classes: Trebouxiophyceae, Chlorophyceae and Bacillariophyceae. We retrieved sequences from non-photosynthetic groups, such as Chytridiomycetes and Ichthyosporea which contain a number of described parasites, indicating that these organisms were probably in association with the autotrophic cells sorted. Dominant groups among sorted PPEs were poorly represented in FTP and their richness was on average lower than in the sorted samples. A significant number of operational taxonomic units (OTUs) were exclusively found in sorting samples, emphasizing that sequences from FTP underestimate the diversity of PPE. Moreover, 22% of the OTUs found among the dominant groups had a low similarity (<95%) with reported sequences in public databases, demonstrating a high potential for novel diversity in these lakes.