bluuebunny/crossref_metadata_2025_split huggingface dataset:
Knockout of zebrafish desmin genes does not cause skeletal muscle degeneration but alters calcium flux
Authors: Kurekci Gulsum Kayman , Mangit Ecem Kural , Koyunlar Cansu , Unsal Seyda , Saglam Berk , Ergin Bora , Gizer Merve , Uyanik Ismail , Düz Niloufar Boustanabadimaralan , Korkusuz Petek , Talim Beril , Purali Nuhan , Hughes Simon M. , Dincer Pervin R. 
Published: October 2020

AbstractDesmin is a muscle-specific intermediate filament protein that has fundamental role in muscle structure and force transmission. Whereas human desmin protein is encoded by a single gene, two desmin paralogs (desmaanddesmb) exist in zebrafish.Desmaanddesmbshow differential spatiotemporal expression during zebrafish embryonic and larval development, being similarly expressed in skeletal muscle until hatching, after which expression ofdesmbshifts to gut smooth muscle. We generated knockout (KO) mutant lines carrying loss-of-function mutations for each gene by using CRISPR/Cas9. Mutants are viable and fertile, and lack obvious skeletal muscle, heart or intestinal defects. In contrast to morphants, knockout of each gene did not cause any overt muscular phenotype, but did alter calcium flux in myofibres. These results point to a possible compensation mechanism in these mutant lines generated by targeting nonsense mutations to the first coding exon.
Multivariate genomic analysis of 1.5 million people identifies genes related to addiction, antisocial behavior, and health
Authors: Linnér Richard Karlsson , Mallard Travis T. , Barr Peter B. , Sanchez-Roige Sandra , Madole James W. , Driver Morgan N. , Poore Holly E. , Grotzinger Andrew D. , Tielbeek Jorim J. , Johnson Emma C. , Liu Mengzhen , Zhou Hang , Kember Rachel L. , Pasman Joëlle A. , Verweij Karin J.H. , Liu Dajiang J. , Vrieze Scott ,   COGA Collaborators, Kranzler Henry R. , Gelernter Joel , Harris Kathleen Mullan , Tucker-Drob Elliot M. , Waldman Irwin , Palmer Abraham A. , Harden K. Paige , Koellinger Philipp D. , Dick Danielle M. 
Published: October 2020

AbstractBehaviors and disorders related to self-regulation, such as substance use, antisocial conduct, and ADHD, are collectively referred to asexternalizingand have a shared genetic liability. We applied a multivariate approach that leverages genetic correlations among externalizing traits for genome-wide association analyses. By pooling data from ~1.5 million people, our approach is statistically more powerful than single-trait analyses and identifies more than 500 genetic loci. The identified loci were enriched for genes expressed in the brain and related to nervous system development. A polygenic score constructed from our results captures variation in a broad range of behavioral and medical outcomes that were not part of our genome-wide analyses, including traits that until now lacked well-performing polygenic scores, such as opioid use disorder, suicide, HIV infections, criminal convictions, and unemployment. Our findings are consistent with the idea that persistent difficulties in self-regulation can be conceptualized as a neurodevelopmental condition.
A pan-cancer metabolic atlas of the tumor microenvironment
Authors: Rohatgi Neha , Ghoshdastider Umesh , Baruah Probhonjon , Skanderup Anders Jacobsen 
Published: October 2020

AbstractTumors are heterogeneous cellular environments with entwined metabolic dependencies. Here, we used a tumor transcriptome deconvolution approach to profile the metabolic states of cancer and non-cancer (stromal) cells in bulk tumors of 20 solid tumor types. We identified metabolic genes and processes recurrently altered in cancer cells across tumor types, including pan-cancer upregulation of deoxythymidine triphosphate (dTTP) production. In contrast, the tryptophan catabolism rate limiting enzymes,IDO1andTDO2, were highly overexpressed in stroma, suggesting that kynurenine-mediated suppression of antitumor immunity is predominantly constrained by the stroma. Oxidative phosphorylation was unexpectedly the most upregulated metabolic process in cancer cells compared to both stromal cells and a large atlas of cancer cell lines, suggesting that the Warburg effect may be less pronounced in cancer cellsin vivo. Overall, our analysis highlights fundamental differences in metabolic states of cancer and stromal cells inside tumors and establishes a pan-cancer resource to interrogate tumor metabolism.
Mapping calcium dynamics in a developing tubular structure
Authors: Hoyer Jorgen , Saba Morsal , Dondorp Daniel , Kolar Kushal , Esposito Riccardo , Chatzigeorgiou Marios 
Published: October 2020

AbstractCalcium is a ubiquitous and versatile second messenger that plays a central role in the development and function of a wide range of cell types, tissues and organs. Despite significant recent progress in the understanding of calcium (Ca2+) signalling in organs such as the developing and adult brain, we have relatively little knowledge of the contribution of Ca2+to the development of tubes, structures widely present in multicellular organisms. Here we image Ca2+dynamics in the developing notochord ofCiona intestinalis. We show that notochord cells exhibit distinct Ca2+dynamics during specific morphogenetic events such as cell intercalation, cell elongation and tubulogenesis. We used an optogenetically controlled Ca2+actuator to show that sequestration of Ca2+results in defective notochord cell intercalation, and pharmacological inhibition to reveal that stretch-activated ion channels (SACs), inositol triphosphate receptor (IP3R) signalling, Store Operated Calcium Entry (SOCE), Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) and gap junctions are required for regulating notochord Ca2+activity during tubulogenesis. Cytoskeletal rearrangements drive the cell shape changes that accompany tubulogenesis. In line with this, we show that Ca2+signalling modulates reorganization of the cytoskeletal network across the morphogenetic events leading up to and during tubulogenesis of the notochord. We additionally demonstrate that perturbation of the actin cytoskeleton drastically remodels Ca2+dynamics, suggesting a feedback mechanism between actin dynamics and Ca2+signalling during notochord development. This work provides a framework to quantitatively define how Ca2+signalling regulates tubulogenesis using the notochord as model organ, a defining structure of all chordates.
A Simultaneous EEG-fMRI Study of Thalamic Load-Dependent Working Memory Delay Period Activity
Authors: Gomes Bernard A. , Plaska Chelsea Reichert , Ortega Jefferson , Ellmore Timothy M. 
Published: October 2020

AbstractWorking memory (WM) is an essential component of executive functions which depend on maintaining task-related information online for brief periods in both the presence and absence of interfering stimuli. Active maintenance occurs during the WM delay period, the time between stimulus encoding and subsequent retrieval. Previous studies have extensively documented prefrontal (PFC) and posterior parietal (PPC) cortex activity during the WM delay period, but the role of subcortical structures including the thalamus remains to be fully elucidated, especially in humans. Using simultaneous EEG-fMRI, we investigated the role of the thalamus during the WM delay period following low and high memory load encoding. During the delay, participants passively viewed scrambled images containing similar color and spatial frequency to serve as a perceptual baseline. Using individual fMRI-weighted source analyses centered around delay period onset, the effects of increased and decreased memory load on maintenance were observed bilaterally in thalamus with higher source activity evoked during low compared to high load maintenance. The main finding that thalamic activation was attenuated during high compared to low load maintenance suggesting a sensory filtering role for thalamus during consolidation of stimuli in WM where the highest evoked activity occurs when fewer stimuli need to be maintained in the presence of interfering perceptual stimuli during the delay. The results support the idea that the thalamus plays a role in short-term memory maintenance by regulating processing of interfering stimuli.
Visualization and Modeling of Inhibition of IL-1β and TNF-α mRNA Transcription at the Single-Cell Level
Authors: Kalb Daniel , Vo Huy D. , Adikari Samantha , Hong-Geller Elizabeth , Munsky Brian , Werner James 
Published: October 2020

AbstractIL-1β and TNF-α are canonical immune response mediators that play key regulatory roles in a wide range of inflammatory responses to both chronic and acute conditions. Here we employ an automated microscopy platform for the analysis of messenger RNA (mRNA) expression of IL-1β and TNF-α at the single-cell level. The amount of IL-1β and TNF-α mRNA expressed in a human monocytic leukemia cell line (THP-1) is visualized and counted using single-molecule fluorescent in-situ hybridization (smFISH) following exposure of the cells to lipopolysaccharide (LPS), an outer-membrane component of Gram-negative bacteria. We show that the small molecule inhibitors MG132 (a 26S proteasome inhibitor used to block NF-κB signaling) and U0126 (a MAPK Kinase inhibitor used to block CCAAT-enhancer-binding proteins C/EBP) successfully block IL-1β and TNF-α mRNA expression. Based upon this single-cell mRNA expression data, we screened 36 different mathematical models of gene expression, and found two similar models that capture the effects by which the drugs U0126 and MG132 affect the rates at which the genes transition into highly activated states. When their parameters were informed by the action of each drug independently, both models were able to predict the effects of the combined drug treatment. From our data and models, we postulate that IL-1β is activated by both NF-κB and C/EBP, while TNF-α is predominantly activated by NF-κB. Our combined single-cell experimental modeling efforts shows the interconnection between these two genes and demonstrates how the single-cell responses, including the distribution shapes, mean expression, and kinetics of gene expression, change with inhibition.
Simplified artificial blood feeding and oral infection method for mosquitoes
Authors: Pereira Thiago Nunes , Carvalho Fabiano Duarte , da Silva Lidia Henrique , de Mendonça Silvana Faria , Moreira Luciano Andrade 
Published: October 2020

ABSTRACTMosquitoes such asAedes aegypti, Aedes albopictus and Culex quinquefasciatusare vectors of many pathogens that greatly affect humankind. The maintenance of these mosquitoes in laboratory permit different studies that can help understanding their biology, as well as the vector-pathogen interaction. In addition to sugar meals, the blood feeding is essential for maintenance of the reproductive cycle in several vectors. The main blood sources for many mosquito colonies are direct feeding on live animal or the use of human/animal blood through artificial feeders. However, this latter process has some disadvantages, as artificial feeders can be very laborious for assembly and decontamination. Based on these observations, a simplified technique for feeding and artificial infection was developed with cotton-pads soaked (CS) and blood or blood and viral supernatant to simulate an artificial infection. The efficiency of the CS technique was investigated through the number of mosquitoes fed/infected, when compared to their respective control group. The CS technique, with blood at room temperature, promoted a feeding rate of 61.4% forAe. albopictus, 70.8% forCx. quinquefasciatusand 17% forAe. aegypti. The control group (Hemotec-feeding) presented 47.9%, 16.5% and 59.1% of feeding success, respectively. To improve the CS technique forAe. aegyptimosquitoes, the procedure was then performed with blood at 38°C, which was possible to observe a feeding rate of 47.3%, in comparison to 53.2% for the control group (Hemotec). When using the CS technique for artificial infection with Mayaro virus, more than 80% of infection was observed forAe. aegyptiand 100% forAe. albopictus. In the traditional infection technique (glass feeder), the infection rate was 90% (Ae. aegypti) and 96.6%(Ae. albopictus). ForCx. quinquefasciatus, the infection was positive only with the CS technique, resulting in 1 (5%) mosquito infected with Mayaro virus. Our results suggest that this simplified technique of low-cost feeding and easy assembly, offers good results for feeding (maintenance of colonies) and artificial infection of different species of mosquitoes.
Larval diet affects adult reproduction but not survival regardless of injury and infection stress inDrosophila melanogaster
Authors: Savola Eevi , Vale Pedro , Walling Craig 
Published: October 2020

ABSTRACTEarly-life conditions have profound effects on many life-history traits. In particular, early-life diet affects both juvenile development, and adult survival and reproduction. Early-life diet also has consequences for the ability of adults to withstand stressors such as starvation, temperature and desiccation. However, it is less well known how early-life diet influences the ability of adults to respond to infection. Here we test whether varying the larval diet of femaleDrosophila melanogaster(through altering protein to carbohydrate ratio, P:C) influences the long-term response to injury and infection with the bacterial pathogenPseudomonas entomophila. Given previous work manipulating adult dietary P:C, we predicted that adults from larvae raised on higher P:C diets would be more likely to survive infection and have increased reproduction, but shorter lifespans and an increased rate of ageing. For larval development, we predicted that low P:C would lead to a longer development time and lower viability. We found that early-life and lifetime egg production were highest at intermediate to high larval P:C diets, but there was no effect of larval P:C on adult survival. Larval diet had no effect on survival or reproduction post-infection. Larval development was quickest on intermediate P:C and egg-to-pupae and egg-to-adult viability were higher on higher P:C. Overall, despite larval P:C affecting several traits measured in this study, we saw no evidence that larval P:C altered the consequence of infection or injury for adult survival and early-life and lifetime reproduction. Taken together, these data suggest that larval diets appear to have a limited impact on adult response to infection.
Single cell transcriptome sequencing on the Nanopore platform with ScNapBar
Authors: Wang Qi , Bönigk Sven , Böhm Volker , Gehring Niels , Altmüller Janine , Dieterich Christoph 
Published: October 2020

AbstractThe current ecosystem of single cell RNA-seq platforms is rapidly expanding, but robust solutions for single cell and single molecule full-length RNA sequencing are virtually absent. A high-throughput solution that covers all aspects is necessary to study the complex life of mRNA on the single cell level. The Nanopore platform offers long read sequencing and can be integrated with the popular single cell sequencing method on the 10x Chromium platform. However, the high error-rate of Nanopore reads poses a challenge in downstream processing (e.g. for cell barcode assignment). We propose a solution to this particular problem by using a hybrid sequencing approach on Nanopore and Illumina platforms. Our software ScNapBar enables cell barcode assignment with high accuracy, especially if sequencing saturation is low. ScNapBar uses unique molecular identifier (UMI) or Naïve Bayes probabilistic approaches in the barcode assignment, depending on the available Illumina sequencing depth. We have benchmarked the two approaches on simulated and real Nanopore datasets. We further applied ScNapBar to pools of cells with an active or a silenced non-sense mediated RNA decay pathway. Our Nanopore read assignment distinguishes the respective cell populations and reveals characteristic nonsense-mediated mRNA decay events depending on cell status.
Evolutionary recent dual obligatory symbiosis among adelgids indicates a transition between fungus and insect associated lifestyles
Authors: Szabó Gitta , Schulz Frederik , Manzano-Marín Alejandro , Toenshoff Elena Rebecca , Horn Matthias 
Published: October 2020

ABSTRACTAdelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of theAdelges laricis/tardusspecies complex containing betaproteobacterial (‘CandidatusVallotia tarda’) and gammaproteobacterial (‘CandidatusProfftia tarda’) symbionts. Genomic characteristics and metabolic pathway reconstructions revealed thatVallotiaandProfftiaare evolutionary young endosymbionts, which complement each other’s role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts ofRhizopusfungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.
De NovoLipid Labeling for Comprehensive Analysis of Subcellular Distribution and Trafficking in Live Cells
Authors: Zhang Jun , Nie Jia , Sun Haoran , Andersen John-Paul , Shi Yuguang 
Published: October 2020

AbstractLipids exert dynamic biological functions which are determined both by their fatty acyl compositions and precise spatiotemporal distributions inside the cell. There are more than 1000 lipid species in a typical mammalian cell. However, it remains a daunting task to investigate any of these features in live cells for each of the more than 1000 lipid species. Here we resolved this issue by developing ade novolipid labeling method for major lipid species, including glycerolipids, glycerophospholipids, and cholesterol esters by using a single fluorescent probe. The method not only allowed us to probe the precise subcellular distribution and trafficking of individual lipid species in live cells, but also uncovered some unexpected biological functions of previously reported lipid metabolic enzymes that were not possible by conventional biochemical methods. We envision that this method will become an indispensable tool for the functional analysis of individual lipid species and numerous lipid metabolic enzymes and transporters in live cells.
High-Resolution Phylogenetic and Population Genetic Analysis of Microbial Communities with RoC-ITS
Authors: Rusch Douglas B. , Huang Jie , Hemmerich Chris , Hahn Matthew W. 
Published: October 2020

AbstractMicrobial communities are inter-connected systems of incredible complexity and dynamism that play crucial roles in health, energy, and the environment. To better understand microbial communities and how they respond to change, it is important to know which microbes are present and their relative abundances at the greatest taxonomic resolution possible. Here, we describe a novel protocol (RoC-ITS) that uses the single-molecule Nanopore sequencing platform to assay the composition of microbial communities in unprecedented detail. This methodology produces long-read sequences including multiple copies of the same complete 16S ribosomal gene and its neighboring internally transcribed spacer (ITS) using rolling-circle amplification. The ribosomal 16S gene provides phylogenetic information down to the species-level, while the much less conserved ITS region contains strain-level information. When linked together, this combination of markers allows for the identification of individual ribosomal units within a specific organism, the assessment of their relative stoichiometry, and the ability to monitor subtle shifts in microbial community composition with a single generic assay. We applied RoC-ITS to a mock microbial community that was also sequenced using the Illumina platform, demonstrating its accuracy in quantifying the relative abundance and identity of each species.
Resolving transcriptional states and predicting lineages in the annelidCapitella teletausing single-cell RNAseq
Authors: Sur Abhinav , Meyer Néva P. 
Published: October 2020

AbstractEvolution and diversification of cell types has contributed to animal evolution. However, gene regulatory mechanisms underlying cell fate acquisition during development remains largely uncharacterized in spiralians. Here we use a whole-organism, single-cell transcriptomic approach to map larval cell types in the annelidCapitella teletaat 24- and 48-hours post gastrulation (stages 4 and 5). We identified eight unique cell clusters (undifferentiated precursors, ectoderm, muscle, ciliary-band, gut, neurons, neurosecretory cells and protonephridia), thus helping to identify previously uncharacterized molecular signatures such as novel neurosecretory cell markers. Analysis of coregulatory programs in individual clusters revealed gene interactions that can be used for comparisons of cell types across taxa. We examined the neural and neurosecretory clusters more deeply and characterized a differentiation trajectory starting from dividing precursors to neurons using Monocle3 and velocyto. Pseudotime analysis along this trajectory identified temporally-distinct cell states undergoing progressive gene expression changes over time. Our data revealed two potentially distinct neural differentiation trajectories including an early trajectory for brain neurosecretory cells. This work provides a valuable resource for future functional investigations to better understanding neurogenesis and the transitions from neural precursors to neurons in an annelid.
Modeling airway dysfunction in asthma using synthetic mucus biomaterials
Authors: Song Daniel , Iverson Ethan , Kaler Logan , Bader Shahed , Scull Margaret A. , Duncan Gregg A. 
Published: October 2020

AbstractAs asthma worsens, occlusion of airways with mucus significantly contributes to airflow obstruction and reduced lung function. Recent evidence from clinical studies has shown mucus obtained from adults and children with asthma possesses altered mucin composition. However, how these changes alter the functional properties of the mucus gel is not yet fully understood. To study this, we have engineered a synthetic mucus biomaterial to closely mimic the properties of native mucus in health and disease. We demonstrate this model possesses comparable biophysical and transport properties to native mucusex vivocollected from human subjects andin vitroisolated from human airway epithelial (HAE) tissue cultures. We found by systematically varying mucin composition that mucus gel viscoelasticity is enhanced when predominantly composed of mucin 5AC (MUC5AC), as is observed in asthma. As a result, asthma-like synthetic mucus gels are more slowly transported on the surface of HAE tissue cultures and at a similar rate to native mucus produced by HAE cultures stimulated with the type 2 cytokine IL-13, known to contribute to airway inflammation and MUC5AC hypersecretion in asthma. We also discovered the barrier function of asthma-like synthetic mucus towards influenza A virus was impaired as evidenced by the increased frequency of infection in MUC5AC-rich hydrogel coated HAE cultures. Together, this work establishes a biomaterial-based approach to understand airway dysfunction in asthma and related muco-obstructive lung diseases.Graphical Abstract