bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy of de novo assembly of DNA sequences from double-digest libraries varies substantially among software
Authors: LaCava Melanie E. F. , Aikens Ellen O. , Megna Libby C. , Randolph Gregg , Hubbard Charley , Buerkle C. Alex 
Published: July 2019

AbstractAdvances in DNA sequencing have made it feasible to gather genomic data for non-model organisms and large sets of individuals, often using methods for sequencing subsets of the genome. Several of these methods sequence DNA associated with endonuclease restriction sites (various RAD and GBS methods). For use in taxa without a reference genome, these methods rely on de novo assembly of fragments in the sequencing library. Many of the software options available for this application were originally developed for other assembly types and we do not know their accuracy for reduced representation libraries. To address this important knowledge gap, we simulated data from the Arabidopsis thaliana and Homo sapiens genomes and compared de novo assemblies by six software programs that are commonly used or promising for this purpose (ABySS, CD-HIT, Stacks, Stacks2, Velvet and VSEARCH). We simulated different mutation rates and types of mutations, and then applied the six assemblers to the simulated datasets, varying assembly parameters. We found substantial variation in software performance across simulations and parameter settings. ABySS failed to recover any true genome fragments, and Velvet and VSEARCH performed poorly for most simulations. Stacks and Stacks2 produced accurate assemblies of simulations containing SNPs, but the addition of insertion and deletion mutations decreased their performance. CD-HIT was the only assembler that consistently recovered a high proportion of true genome fragments. Here, we demonstrate the substantial difference in the accuracy of assemblies from different software programs and the importance of comparing assemblies that result from different parameter settings.
Genetic Bases Of Aposematic Traits: Insights from the Skin Transcriptional Profiles of Oophaga Poison Frogs
Authors: Posso-Terranova Andrés , Andres José 
Published: July 2019

AbstractAposematic organisms advertise their defensive toxins to predators using a variety of warning signals, including bright coloration. While most Neotropical poison frogs (Dendrobatidae) rely on crypsis to avoid predators, Oophaga poison frogs from South America advertise their chemical defenses, a complex mix of diet-derived alkaloids, by using conspicuous hues. The present study aimed to characterize the skin transcriptomic profiles of the South American clade of Oophaga poison frogs (O. anchicayensis, O. solanensis, O. lehmanni and O. sylvatica). Our analyses showed very similar transcriptomic profiles for these closely related species in terms of functional annotation and relative abundance of gene ontology terms expressed. Analyses of expression profiles of Oophaga and available skin transcriptomes of cryptic anurans allowed us to propose possible mechanisms for the active sequestration of alkaloid-based chemical defenses and to highlight some genes that may be potentially involved in resistance mechanisms to avoid self-intoxication and skin coloration. In doing so, we provide an important molecular resource for the study of warning signals that will facilitate the assembly and annotation of future poison frog genomes.
Advanced Glycation End-Products Suppress Mitochondrial Function and Proliferative Capacity of Achilles Tendon-Derived Fibroblasts
Authors: Patel Shivam H. , Yue Feng , Saw Shannon K. , Foguth Rachel , Cannon Jason R. , Shannahan Jonathan H. , Kuang Shihuan , Sabbaghi Arman , Carroll Chad C. 
Published: July 2019

AbstractDebilitating cases of tendon pain and degeneration affect the majority of diabetic individuals. The high rate of tendon degeneration persists even when glucose levels are well controlled, suggesting that other mechanisms may drive tendon degeneration in diabetic patients. The purpose of this study was to investigate the impact of advanced glycation end-products on tendon fibroblasts to further our mechanistic understanding of the development and progression of diabetic tendinopathy. We proposed that advanced glycation end-products would induce limitations to mitochondrial function and proliferative capacity in tendon-derived fibroblasts, restricting their ability to maintain biosynthesis of tendon extracellular matrix. Using an in-vitro cell culture system, rat Achilles tendon fibroblasts were treated with glycolaldehyde-derived advanced glycation end-products (0, 50, 100, and 200μg/ml) for 48 hours in normal glucose (5.5mM) and high glucose (25mM) conditions. We demonstrate that tendon fibroblasts treated with advanced glycation end-products display reduced ATP production, electron transport efficiency, and proliferative capacity. These impairments were coupled with alterations in mitochondrial DNA content and expression of genes associated with extracellular matrix remodeling, mitochondrial energy metabolism, and apoptosis. Our findings suggest that advanced glycation end-products disrupt tendon fibroblast homeostasis and may be involved in the development and progression of diabetic tendinopathy.
Remodeling of theC. elegansNon-coding RNA Transcriptome by Heat Shock
Authors: Schreiner William P. , Pagliuso Delaney C. , Garrigues Jacob M. , Chen Jerry S. , Aalto Antti P. , Pasquinelli Amy E. 
Published: July 2019

ABSTRACTElevated temperatures activate a Heat Shock Response (HSR) to protect cells from the pathological effects of protein mis-folding, cellular mis-organization, organelle dysfunction and altered membrane fluidity. This response includes activation of the conserved transcription factor Heat Shock Factor 1 (HSF-1), which binds Heat Shock Elements (HSEs) in the promoters of genes induced by heat shock (HS). The up-regulation of protein-coding genes (PCGs), such as Heat Shock Proteins (HSPs) and cytoskeletal regulators, is critical for cellular survival during elevated temperatures. While the transcriptional response of PCGs to heat shock has been comprehensively analyzed in a variety of organisms, the effect of this stress on the expression of non-coding RNAs (ncRNAs) has not been systematically examined. Here we show that inCaenorhabditis elegansHS induces up- and down-regulation of specific ncRNAs from multiple classes, including miRNA, piRNA, lincRNA, pseudogene, and repeat elements. Moreover, some ncRNA genes appear to be direct targets of the HSR, as they contain HSF-1 bound HSEs in their promoters and their expression is regulated by this factor during HS. These results demonstrate that multiple ncRNA genes respond to HS, some as direct HSF-1 targets, providing new candidates that may contribute to organismal survival during this stress.
Lignin-based resistance toCuscuta campestrisparasitism in Heinz resistant tomato cultivars
Authors: Jhu Min-Yao , Farhi Moran , Wang Li , Philbrook Richard N. , Belcher Michael S. , Nakayama Hokuto , Zumstein Kristina S. , Rowland Steven D. , Ron Mily , Shih Patrick M. , Sinha Neelima R. 
Published: July 2019

AbstractCuscutaspecies (dodders) are agriculturally destructive parasitic angiosperms. These parasitic plants use haustoria as physiological bridges to extract nutrients and water from hosts.Cuscuta campestrishas a broad host range and wide geographical distribution. While some wild tomato relatives are resistant, cultivated tomatoes are generally susceptible toC. campestrisinfestations. However, some specific Heinz tomato hybrid cultivars exhibit resistance to dodders in the field, but their defense mechanism was unknown. Here, we discovered that the stem cortex in these resistant lines responds with local lignification uponC. campestrisattachment, preventing parasite entry into the host.LIF1(Lignin Induction Factor 1, anAP2-like transcription factor),SlMYB55, andCuRLR1(Cuscuta R-gene for Lignin-based Resistance 1, aCC-NBS-LRR) are identified as crucial factors conferring host resistance by regulating lignification.SlWRKY16is upregulated uponC. campestrisinfestation and acts as a negative regulator ofLIF1function. Intriguingly,CuRLR1may play a role in signaling or function as a receptor for receivingCuscutasignals or effectors to regulate lignification-based resistance. In summary, these four regulators control the lignin-based resistance response, preventingC. campestrisfrom parasitizing these resistant tomatoes. This discovery provides a foundation for investigating multilayer resistance againstCuscutaspecies and has potential for application in other essential crops attacked by parasitic plants.One-sentence summaryFour key regulators confer lignin accumulation in the tomato stem cortex to blockC. campestrishost penetration upon infection.
Assessment of a split homing based gene drive for efficient knockout of multiple genes
Authors: Kandul Nikolay P. , Liu Junru , Buchman Anna , Gantz Valentino M. , Bier Ethan , Akbari Omar S. 
Published: July 2019

AbstractHoming based gene drives (HGD) possess the potential to spread linked cargo genes into natural populations and are poised to revolutionize population control of animals. Given that host-encoded genes have been identified that are important for pathogen transmission, targeting these genes using guide RNAs as cargo genes linked to drives may provide a robust method to prevent transmission. However, effectiveness of the inclusion of additional guide RNAs that target separate host encoded genes has not been thoroughly explored. To test this approach, here we generated a split-HGD in Drosophila melanogaster that encoded a drive linked effector consisting of a second gRNA engineered to target a separate host encoded gene, which we term a gRNA-mediated effector (GME). This design enabled us to assess homing and knockout efficiencies of two target genes simultaneously, and also explore the timing and tissue specificity of Cas9 expression on cleavage/homing rates. We demonstrate that inclusion of a GME can result in high efficiency of disruption of its target gene during super-Mendelian propagation of split-HGD. However, maternal deposition and embryonic expression of Cas9 resulted in the generation of drive resistant alleles which can accumulate and limit the spread of such a drive. Alternative design principles are discussed that could mitigate the accumulation of resistance alleles while incorporating a GME.
Motor Output Matters: Evidence of a Continuous Relationship Between Stop/No-go P300 Amplitude and Response Force on Failed Inhibitions at the Trial-Level
Authors: Nguyen An T. , Albrecht Matthew A. , Lipp Ottmar V. , Marinovic Welber 
Published: July 2019

AbstractMotor actions can be suppressed with varying degrees of success, but this variability is not captured in many experiments where responses are represented in binary (response vs. no-response). Although the Stop/No-go P300 (an enhanced frontocentral positivity in the event-related potential (ERP) peaking around 300 ms after a Stop/No-go stimulus, compared to Go trials) has been implicated as a measure of inhibitory-control, it is unclear how the range of motor outputs relates to the P300. We examined the nature of this association in two experiments using an Anticipatory Timing and a Go/No-go Task. Force, response onset time, and the P300 were measured.In both experiments, our results showed that trial-by-trial P300 amplitude on Failed Inhibitions were continuously related to Force, where higher response forces (reflecting a greater degree of error) were associated with smaller P300 amplitudes. Compared to Successful Inhibitions, P300 amplitude was reduced and ERP onset latencies were delayed on Failed Inhibitions. Although the binary categorisation of inhibition-success (Successful vs. Failed) accounted for more variance in the data compared to force, it misses a reliable linear relationship that can be captured by continuous measures of motor output. Overall, the results provide strong evidence that the engagement of inhibitory-control varies on a continuum from trial-to-trial and that this engagement is reflected by the P300. We present an activation-to-threshold model of inhibitory-control to explain our results, which offers a new conceptual framework for describing the implementation of inhibitory-control in highly prepared motor responses. Our results also highlight the importance of studying the spectrum of motor outputs and the need for future models of inhibitory-control to account for motor output.
Identification and evolution of avian endogenous foamy viruses
Authors: Chen Yicong , Wei Xiaoman , Zhang Guojie , Holmes Edward C. , Cui Jie 
Published: July 2019

AbstractA history of long-term co-divergence means that foamy viruses (familyRetroviridae) provide an ideal framework to understanding virus-host evolution over extended time periods. Endogenous foamy viruses (EndFVs) are rare, and to date have only been described in a limited number of mammals, amphibians, reptiles and fish genomes. By screening 414 avian genomes we identified EndFVs in two bird species: the Maguari Stork (Ciconia maguari) and the Oriental Stork (C. boyciana). Analyses of phylogenetic relationships, genome structures and flanking sequences revealed a single origin of EndFVs inCiconiaspecies. In addition, the marked incongruence between the virus and host phylogenies suggested that this integration event occurred independently in birds. In sum, by providing evidence that birds can be infected with foamy viruses, we fill the last major gap in the taxonomic distribution of foamy viruses and their animal hosts.
CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps
Authors: Hait Tom Aharon , Elkon Ran , Shamir Ron 
Published: July 2019

ABSTRACTSpatiotemporal gene expression patterns are governed to a large extent by the activity of enhancer elements, which engage in physical contacts with their target genes. Identification of enhancer-promoter (EP) links that are functional only in a specific subset of cell types is a key challenge in understanding gene regulation. We introduce CT-FOCS, a statistical inference method that uses linear mixed effect models to infer EP links that show marked activity only in a single or a small subset of cell types out of a large panel of probed cell types. Analyzing 808 samples from FANTOM5, covering 472 cell lines, primary cells, and tissues, CT-FOCS inferred such EP links more accurately than recent state-of-the-art methods. Furthermore, we show that strictly cell type-specific EP links are very uncommon in the human genome.
SILAC-based quantitative proteomic analysis ofDrosophilagastrula stage embryos mutant for fibroblast growth factor signaling
Authors: Beati Hamze , Langlands Alistair , ’ten Have Sara , Müller H.-Arno J. 
Published: July 2019

AbstractThe application of quantitative proteomics in model organisms has been successful in determining changes in the proteome under distinct physiological conditions. Quantitative mass spectrometry-based proteomic analyses in combination with genetics provide powerful tools in developmental cell signaling research.Drosophila melanogasteris one of the most widely used genetic models for studying development and disease. Here we combined quantitative proteomics with genetic selection to determine global changes in the proteome upon depletion of the Heartless (Htl) Fibroblast-Growth Factor (FGF) receptor signaling inDrosophilaembryos at early gastrulation stages. We present a robust, single generation SILAC (stable isotope labeling with amino acids in cell culture) protocol for labeling proteins in early embryos and for selection of homozygously mutant embryos at pre-gastrula stages using an independent genetic marker. Our analyses detected quantitative changes in the global proteome ofhtlmutant embryos during gastrulation. We identified distinct classes of down-regulated and up-regulated proteins and network analyses indicates functionally related groups of proteins in each class. These data suggest that FGF signaling in the early embryo affects global changes in the abundance of metabolic, nucleoplasmic, cytoskeletal and endomembrane transport proteins.
Platelet Thrombus Formation in eHUS is Prevented by Anti-MBL2
Authors: Kushak R. I. , Boyle D.C , Rosales I.A. , Ingelfinger J.R. , Stahl G.L , Ozaki M , Colvin R.B. , Grabowski E.F. 
Published: July 2019

AbstractEpidemic Hemolytic Uremic Syndrome (eHUS) caused by Shiga toxin-producing bacteria is characterized by thrombocytopenia, microangiopathic hemolytic anemia, and acute kidney injury that cause acute renal failure in up to 65% of affected patients. We hypothesized that the mannose-binding lectin (MBL) pathway of complement activation plays an important role in human eHUS, as we previously demonstrated that injection of Shiga Toxin-2 (Stx-2) led to fibrin deposition in mouse glomeruli that was blocked by co-injection of the anti-MBL-2 antibody 3F8. However, the markers of platelet thrombosis in affected mouse glomeruli were not delineated. To investigate the effect of 3F8 on markers of platelet thrombosis, we used kidney sections from our mouse model (MBL-2+/+ Mbl-A/C−/−;MBL2 KI mouse). Mice in the control group received PBS, while mice in a second group received Stx-2, and those in a third group received 3F8 and Stx-2. Using double immunofluorescence (IF) followed by digital image analysis, kidney sections were stained for fibrin(ogen) and CD41 (marker for platelets), von-Willebrand factor (marker for endothelial cells and platelets), and podocin (marker for podocytes). Electron microscopy (EM) was performed on ultrathin sections from mice and human with HUS. Injection of Stx-2 resulted in an increase of both fibrin and platelets in glomeruli, while administration of 3F8 with Stx-2 reduced both platelet and fibrin to control levels. EM studies confirmed that CD41-positive objects observed by IF were platelets. The increases in platelet number and fibrin levels by injection of Stx-2 are consistent with the generation of platelet-fibrin thrombi that were prevented by 3F8.
Short-term synaptic plasticity makes neurons sensitive to the distribution of presynaptic population firing rates
Authors: Tauffer Luiz , Kumar Arvind 
Published: July 2019

AbstractThe ability to discriminate spikes that encode a particular stimulus from spikes produced by background activity is essential for reliable information processing in the brain. We describe how synaptic short-term plasticity (STP) modulates the output of presynaptic populations as a function of the distribution of the spiking activity and find a strong relationship between STP features and sparseness of the population code, which could solve the discrimination problem. Furthermore, we show that feedforward excitation followed by inhibition (FF-EI), combined with target-dependent STP, promote substantial increase in the signal gain even for considerable deviations from the optimal conditions, granting robustness to this mechanism. A simulated neuron driven by a spiking FF-EI network is reliably modulated as predicted by a rate analysis and inherits the ability to differentiate sparse signals from dense background activity changes of the same magnitude, even at very low signal-to-noise conditions. We propose that the STP-based distribution discrimination is likely a latent function in several regions such as the cerebellum and the hippocampus.
The biosynthetic gene cluster of the C-nucleoside antibiotic pyrazomycin with a rare pyrazole moiety
Authors: Zhao Guiyun , Yao Shunyu , Rothchild Kristina W , Liu Tengfei , Liu Yu , Lian Jiazhang , He Hai-Yan , Ryan Katherine S , Du Yi-Ling 
Published: July 2019

AbstractPyrazomycin is a rare C-nucleoside antibiotic with a naturally occurring pyrazole ring, whose biosynthetic origin has remained obscure for decades. In this study, we report the identification of the gene cluster responsible for pyrazomycin biosynthesis in Streptomyces candidus NRRL 3601, revealing that StrR-family regulator PyrR is the cluster-situated transcriptional activator governing pyrazomycin biosynthesis. Furthermore, our results from in vivo reconstitution and stable-isotope feeding experiments support that PyrN is a new nitrogen-nitrogen bond forming enzyme linking the ε-NH2 nitrogen of l-N6-OH-lysine and α-NH2 nitrogen of l-glutamate. This study lays the foundation for further genetic and biochemical characterization of pyrazomycin pathway enzymes constructing the characteristic pyrazole ring.
P granules protect RNA interference genes from silencing by piRNAs
Authors: Ouyang John Paul T. , Folkmann Andrew , Bernard Lauren , Lee Chih-Yung , Seroussi Uri , Charlesworth Amanda G. , Claycomb Julie M. , Seydoux Geraldine 
Published: July 2019

SUMMARYP granules are perinuclear condensates in C. elegans germ cells proposed to serve as hubs for self/non-self RNA discrimination by Argonautes. We report that a mutant (meg-3 meg-4) that does not assemble P granules in primordial germ cells loses competence for RNA-interference over several generations and accumulates silencing small RNAs against hundreds of endogenous genes, including the RNA-interference genes rde-11 and sid-1. In wild-type, rde-11 and sid-1 transcripts are heavily targeted by piRNAs, accumulate in P granules, but maintain expression. In the primordial germ cells of meg-3 meg-4 mutants, rde-11 and sid-1 transcripts disperse in the cytoplasm with the small RNA biogenesis machinery, become hyper-targeted by secondary sRNAs, and are eventually silenced. Silencing requires the PIWI-class Argonaute PRG-1 and the nuclear Argonaute HRDE-1 that maintains trans-generational silencing of piRNA targets. These observations support a “safe harbor” model for P granules in protecting germline transcripts from piRNA-initiated silencing.
A novel mass assay to measure phosphatidylinositol-5-phosphate from cells and tissues
Authors: Ghosh Avishek , Sharma Sanjeev , Shinde Dhananjay , Ramya Visvanathan , Raghu Padinjat 
Published: July 2019

AbstractPhosphatidylinositol-5-phosphate (PI5P) is a low abundance lipid proposed to have functions in cell migration, DNA damage responses, receptor trafficking and insulin signalling in metazoans. However, studies of PI5P function are limited by the lack of scalable techniques to quantify its level from cells and tissues in multicellular organisms. Currently, PI5P measurement requires the use of radionuclide labelling approaches that are not easily applicable in tissues or in vivo samples. In this study, we describe a simple and reliable, non-radioactive mass assay to measure total PI5P levels from cells and tissues of Drosophila, a genetically tractable multicellular model. We use 18O-ATP to label PI5P from tissue extracts while converting it into PI(4,5)P2 using an in vitro kinase reaction. The product of this reaction can be selectively detected and quantified with high sensitivity using a liquid chromatography-tandem mass spectrometry platform. Further, using this method, we capture and quantify the unique acyl chain composition of PI5P from Drosophila cells and tissues. Finally, we demonstrate the use of this technique to quantify elevations in PI5P levels, from both Drosophila larval tissues and cultured cells depleted of phosphatidylinositol 5 phosphate 4-kinase (PIP4K), that metabolizes PI5P into PI(4,5)P2 thus regulating its levels. Thus, we demonstrate the potential of our method to quantify PI5P levels with high sensitivity levels from cells and tissues of multicellular organisms thus accelerating understanding of PI5P functions in vivo.