bluuebunny/crossref_metadata_2025_split huggingface dataset:
The temperature-dependent predatory strike of Odonata larvae
Authors: Koehnsen Alexander , Tröger Hannah-Lena , Gorb Stanislav N , Büsse Sebastian 
Published: December 2020

AbstractThe larvae of Odonata are limnic predators capable of catching their prey using a highly modified mouthpart – the labium. Driven by a unique dual catapult mechanism, the apparatus can reach peak accelerations of up to 114.5m/s2. Yet little is known about the kinematics of the predatory strike in an ecological context. Here we show how different ambient temperatures affect the predatory strike and the avoidance reaction of prey items of Odonata larvae. We found that the extension velocity of the labial mask decreases significantly with the ambient temperature both in dragonflies and damselflies. However, temperature has lesser impact on the predatory strike itself than on directly muscle driven movements in both the predator and prey items. This contradicts the previous assumption that catapult mechanisms in insects are unaffected by temperature. Our results indicate that the prehensile labial mask is driven by a series-elastic catapult; a mechanism similar to the temperature dependent jump of frogs, where muscle and spring action are tightly linked. Our study provides novel insights into the predatory strike of Odonata larvae and offers a new ecological perspective on catapult mechanisms in arthropods in general.
Overt visual attention and value computation in complex risky choice
Authors: Fan Xinhao , Elsey Jacob , Wyngaard Aurelien , Yang Youping , Sampson Aaron , Emeric Erik , Glickman Moshe , Usher Marius , Levy Dino , Stuphorn Veit , Niebur Ernst 
Published: December 2020

AbstractTraditional models of decision making under uncertainty explain human behavior in simple situations with a minimal set of alternatives and attributes. Some of them, such as prospect theory, have been proven successful and robust in such simple situations. Yet, less is known about the preference formation during decision making in more complex cases. Furthermore, it is generally accepted that attention plays a role in the decision process but most theories make simplifying assumptions about where attention is deployed. In this study, we replace these assumptions by measuring where humans deploy overt attention,i.e.where they fixate. To assess the influence of task complexity, participants perform two tasks. The simpler of the two requires participants to choose between two alternatives with two attributes each (four items to consider). The more complex one requires a choice between four alternatives with four attributes each (16 items to consider). We then compare a large set of model classes, of different levels of complexity, by considering the dynamic interactions between uncertainty, attention and pairwise comparisons between attribute values. The task of all models is to predict what choices humans make, using the sequence of observed eye movements for each participant as input to the model. We find that two models outperform all others. The first is the two-layer leaky accumulator which predicts human choices on the simpler task better than any other model. We call the second model, which is introduced in this study, TNPRO. It is modified from a previous model from management science and designed to deal with highly complex decision problems. Our results show that this model performs well in the simpler of our two tasks (second best, after the accumulator model) and best for the complex task. Our results suggest that, when faced with complex choice problems, people prefer to accumulate preference based on attention-guided pairwise comparisons.
Atypical mediofrontal theta oscillations underlying cognitive control in kindergarteners with autism spectrum disorder
Authors: Buzzell George A. , Thomas Hannah R. , Choi Yeo Bi , Kim So Hyun 
Published: December 2020

AbstractBackgroundChildren with autism spectrum disorder (ASD) often exhibit deficits in cognitive control. Neuroimaging approaches have implicated disruptions to medio-frontal cortex (MFC) structure and function. However, prior work has not directly tested whether young children with ASD exhibit disruptions to task-related theta oscillations thought to arise from the MFC.MethodsForty-three children with ASD and 24 age- and gender-matched typically developing (TD) peers performed a child-friendly Go/No-go task while 64-channel electroencephalography (EEG) was recorded at kindergarten-entry. Time-frequency approaches were employed to assess the magnitude of mediofrontal theta oscillations immediately following error (vs. correct) responses (“early theta”), as well as later emerging theta oscillations (“late theta”). We tested whether error-related mediofrontal theta oscillations differed as a function of diagnosis (ASD/typical) and timing (early/late theta). Additionally, links to social and academic outcomes were tested.ResultsOverall, children showed increased theta power following error vs. correct responses. Compared to TD children, children with ASD exhibited a selective reduction in error-related mediofrontal theta power during the late theta time window. There were no significant group differences for early theta power. Moreover, reduced error-related theta power during the late, butnotearly, time window significantly predicted poorer academic and social skills.ConclusionsKindergarteners with ASD demonstrated a selective reduction in error-related mediofrontal theta power during a relatively late time window, which is consistent with impairments in specific cognitive processes that recruit top-down control. Targeting these particular cognitive control processes via intervention prior to school-entry may promote more successful functional outcomes for children with ASD.
Cardiomyopathy Mutations Impact the Power Stroke of Human Cardiac Myosin
Authors: Tang W. , Ge J. , Unrath W.C. , Desetty R. , Yengo C. M. 
Published: December 2020

AbstractCardiac muscle contraction is driven by the molecular motor myosin that uses the energy from ATP hydrolysis to generate a power stroke when interacting with actin filaments, while it is unclear how this mechanism is impaired by mutations in myosin that can lead to heart failure. We have applied a Förster resonance energy transfer (FRET) strategy to investigate structural changes in the lever arm domain of human β-cardiac myosin subfragment 1 (M2β-S1). We exchanged the human ventricular regulatory light chain labeled at a single cysteine (V105C) with Alexa 488 onto M2β-S1, which served as a donor for Cy3ATP bound to the active site. We monitored the FRET signal during the actin-activated product release steps using transient kinetic stopped-flow measurements. We proposed that the fast phase measured with our FRET probes represents the structural change associated with rotation of the lever arm during the power stroke in M2β-S1. Our results demonstrated human cardiac muscle myosin has a slower power stroke compared with fast skeletal muscle myosin and myosin V. Measurements at different temperatures comparing the rate constants of the power stroke and phosphate release revealed that the power stroke occurs before phosphate release, and the two steps are tightly coupled. We speculate that the slower power stroke rate constant in cardiac myosin may correlate with the slower force development and/or unique thin filament activation properties in cardiac muscle. Additionally, we demonstrated that HCM (R723G) and DCM (F764L) associated mutations both reduced actin-activation of the power stroke in M2β-S1. We also demonstrate that both mutations decrease ensemble force development in the loaded in vitro motility assay. Thus, examining the structural kinetics of the power stroke in M2β-S1 has revealed critical mutation-associated defects in the myosin ATPase pathway, suggesting these measurements will be extremely important for establishing structure-based mechanisms of contractile dysfunction.SignificanceMutations in human beta-cardiac myosin are known to cause various forms of heart disease, while it is unclear how the mutations lead to contractile dysfunction and pathogenic remodeling of the heart. In this study, we investigated two mutations with opposing phenotypes and examined their impact on ATPase cycle kinetics, structural changes associated with the myosin power stroke, and ability to slide actin filaments in the presence of load. We found that both mutations impair the myosin power stroke and other key kinetic steps as well as the ability to produce ensemble force. Thus, our results provide a structural basis for how mutations disrupt molecular level contractile dysfunction.
Structure-based mapping of the TβRI and TβRII receptor binding sites of the parasitic TGF-β mimic, Hp-TGM
Authors: Mukundan Ananya , Byeon Chang-Hyeock , Hinck Cynthia S. , Smyth Danielle J. , Maizels Rick M. , Hinck Andrew P. 
Published: December 2020

AbstractTGF-β is a secreted signaling protein involved in many physiological processes: organ development, production and maintenance of the extracellular matrix, as well as regulation of the adaptive immune system. As a cytokine, TGF-β stimulates the differentiation of CD4+T-cells into regulatory T-cells (Tregs) that act to promote peripheral immune tolerance. The murine parasiteHeligmosomoides polygyrustakes advantage of this pathway to induce inducing Foxp3+Tregsin a similar manner using a TGF-β mimic (TGM), comprised of five tandem complement control protein (CCP) domains, designated D1-D5. Despite having no structural homology to TGF-β or to TGF-β family proteins, TGM binds directly to the TGF-β type I and type II receptors, TβRI and TβRII. To further investigate, NMR titration, and SPR and ITC binding experiments were performed, showing that TGM-D2, with the aid of D1, binds TβRI and TGM-D3 binds TβRII. Competition ITC experiments showed that TGM-D3 competes with TGF-β for binding to TβRII, consistent with TGM-D3-induced NMR chemical shift perturbations of TβRII which aligned with the solvent inaccessible areas of TβRII upon binding TGF-β. Thus, TGM-D3 binds to the same edged β-strand of TβRII that is used to bind TGF-β. Competition ITC experiments demonstrated that TGM-D1D2 and TGF-β3:TβRII compete for binding to TβRI, while TGM-D2-induced NMR chemical shift perturbation of TβRI showed that TGM-D2 binds to the same pre-helix extension of TβRI as does the TGF-β/TβRII binary complex. The solution structure of TGM-D3 revealed that while it has the overall structure of a CCP domain, TGM-D3 has an insertion in the hypervariable loop uncommon to CCP domains. These findings suggest that parasitic TGM, despite its lack of structural similarity to TGF-β, evolved to take advantage of the binding regions of the mammalian TGF-β type I and type II receptors. The structure of this TGM domain, along with the predicted structure of otherH. polygyrussecreted proteins reported in the literature, suggest that TGM is part of a larger family of evolutionarily-adapted immunomodulatory CCP-containing proteins.
Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases
Authors: Tarke Alison , Sidney John , Kidd Conner K , Dan Jennifer M. , Ramirez Sydney I. , Yu Esther Dawen , Mateus Jose , da Silva Antunes Ricardo , Moore Erin , Rubiro Paul , Methot Nils , Phillips Elizabeth , Mallal Simon , Frazier April , Rawlings Stephen A. , Greenbaum Jason A. , Peters Bjoern , Smith Davey M. , Crotty Shane , Weiskopf Daniela , Grifoni Alba , Sette Alessandro 
Published: December 2020

SUMMARYT cells are involved in control of SARS-CoV-2 infection. To establish the patterns of immunodominance of different SARS-CoV-2 antigens, and precisely measure virus-specific CD4+and CD8+T cells, we studied epitope-specific T cell responses of approximately 100 convalescent COVID-19 cases. The SARS-CoV-2 proteome was probed using 1,925 peptides spanning the entire genome, ensuring an unbiased coverage of HLA alleles for class II responses. For HLA class I, we studied an additional 5,600 predicted binding epitopes for 28 prominent HLA class I alleles, accounting for wide global coverage. We identified several hundred HLA-restricted SARS-CoV-2-derived epitopes. Distinct patterns of immunodominance were observed, which differed for CD4+T cells, CD8+T cells, and antibodies. The class I and class II epitopes were combined into new epitope megapools to facilitate identification and quantification of SARS-CoV-2-specific CD4+and CD8+T cells.
Absent expansion of pericentral hepatocytes and altered physiology in Axin2CreERT2 mice
Authors: May Stephanie , Müller Miryam , Livingstone Callum R , Skalka George , Nixon Colin , Hedley Ann , Shaw Robin , Clark William , Drake Thomas M , Kiourtis Christos , Rocha Ana Sofia , Sansom Owen J , Bird Thomas G 
Published: December 2020

Abstract/IntroductionUnderstanding how the liver regenerates is a key biological question. Hepatocytes are the principle regenerative population in the liver. Recently, numerous lineage tracing studies (which apply genetic tagging to a restricted population and track its descendants over time) have reported conflicting results using a variety of hepatocyte based reporting systems in mice1,2. The first significant lineage tracing from a distinct subpopulation of hepatocytes in homeostasis reported hyper-proliferation of self-renewing pericentral hepatocytes with their subsequent expansion across the liver lobule3. This study used a CreERT2 construct knocked into the endogenousAxin2locus; here termed Axin2CreERT2. Subsequent studies, using either a different pericentral marker (Lgr54) or a different AxinCreERT2 transgene5, did not show lineage tracing. Here we aim to reconcile these discrepancies by re-evaluating lineage tracing in the Axin2CreERT2 knock-in model and explore the physiological consequences of this mutant allele. We were unable to find evidence of expansion of an Axin2CreERT2 labelled population and show that this population, whilst zonated, is spread throughout the lobule rather than being zonally restricted. Finally, we report that this allele results in profound perturbation of the Wnt pathway and physiology in the mouse.
Large and interacting effects of temperature and nutrient addition on stratified microbial ecosystems in a small, replicated, and liquid dominated Winogradsky column approach
Authors: Suleiman Marcel , Choffat Yves , Daugaard Uriah , Petchey Owen L 
Published: December 2020

AbstractAquatic ecosystems are often stratified, with cyanobacteria in oxic layers and phototrophic sulfur bacteria in anoxic ones. Changes in stratification caused by global environmental change are an ongoing concern. Increasing understanding how such aerobic and anaerobic microbial communities, and associated abiotic conditions, respond to multifarious environmental changes is an important endeavor in microbial ecology. Insights can come from observational and experimental studies of naturally occurring stratified aquatic ecosystems, from theoretical models of ecological processes, and from experimental studies of replicated microbial communities in the laboratory. Here we demonstrate a laboratory-based approach with small, replicated, and liquid dominated Winogradsky columns, with distinct oxic/anoxic strata in a highly replicable manner. Our objective is to apply simultaneous global change scenarios (temperature, nutrient addition) on this micro-ecosystem to report how the microbial communities (full-length 16SrRNA-seq.) and the abiotic conditions (O2, H2S, TOC) of the oxic/anoxic layer responded to these environmental changes. Composition of the strongly stratified microbial communities was greatly affected by temperature and by the interaction of temperature and nutrient addition, demonstrating the need of investigating global change treatments simultaneously. Especially phototrophic sulfur bacteria dominated the water column at higher temperatures, and may indicate the presence of alternative stable states. We show that the establishment of such a micro-ecosystem has potential to test global change scenarios in stratified eutrophic limnic systems.
Metabolic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing
Authors: Waschulin Valentin , Borsetto Chiara , James Robert , Newsham Kevin K. , Donadio Stefano , Corre Christophe , Wellington Elizabeth 
Published: December 2020

AbstractThe growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster (BGC) diversity in metagenomes. However, few complete BGCs from uncultivated bacteria have been recovered, making assessment of BGC diversity difficult. Here, long-read sequencing and genome mining were used to recover >1400 mostly complete BGCs that demonstrate the rich diversity of BGCs from uncultivated lineages present in soil from Mars Oasis, Antarctica. The phyla Acidobacteriota, Verrucomicrobiota and Gemmatimonadota, but also the actinobacterial classes Acidimicrobiia, Thermoleophilia, and the gammaproteobacterial order UBA7966, were found to encode a large number of highly divergent BGCs. Our findings underline the biosynthetic potential of underexplored phyla as well as unexplored lineages within seemingly well-studied producer phyla. They also showcase long-read metagenomic sequencing as a promising way to access the untapped reservoir of specialised metabolites of the uncultured majority of microbes.
Moment-by-moment tracking of naturalistic learning and its underlying hippocampo-cortical interactions
Authors: Michelmann Sebastian , Price Amy R. , Aubrey Bobbi , Doyle Werner K. , Friedman Daniel , Dugan Patricia C. , Devinsky Orrin , Devore Sasha , Flinker Adeen , Hasson Uri , Norman Kenneth A. 
Published: December 2020

AbstractEvery day our memory system achieves a remarkable feat: We form lasting memories of stimuli that were only encountered once. Here we investigate such learning as it naturally occurs during story listening, with the goal of uncovering when and how memories are stored and retrieved during processing of continuous, naturalistic stimuli. In behavioral experiments we confirm that, after a single exposure to a naturalistic story, participants can learn about its structure and are able to recall upcoming words in the story. In patients undergoing electrocorticographic recordings, we then track mnemonic information in high frequency activity (70 – 200Hz) as patients listen to a story twice. In auditory processing regions we demonstrate the rapid reinstatement of upcoming information after a single exposure; this neural measure of predictive recall correlates with behavioral measures of event segmentation and learning. Connectivity analyses on the neural data reveal information-flow from cortex to hippocampus at the end of events. On the second time of listening information-flow from hippocampus to cortex precedes moments of successful reinstatement.
Paternal hypoxia exposure primes offspring for increased hypoxia resistance
Authors: Ragsdale Alexandria , Ortega-Recalde Oscar , Dutoit Ludovic , Besson Anne A. , Chia Jolyn H.Z. , King Tania , Nakagawa Shinichi , Hickey Anthony , Gemmell Neil J. , Hore Timothy , Johnson Sheri L. 
Published: December 2020

ABSTRACTIn a time of rapid environmental change, understanding how the challenges experienced by one generation can influence the fitness of future generations is critically needed. Using tolerance assays, transcriptomic and methylome approaches, we use zebrafish as a model to investigate transgenerational acclimation to hypoxia. We show that short-term paternal exposure to hypoxia endows offspring with greater tolerance to acute hypoxia. We detected two hemoglobin genes that are significantly upregulated by more than 7-fold in the offspring of hypoxia exposed males. Moreover, the offspring which maintained equilibrium the longest showed greatest upregulation in hemoglobin expression. We did not detect differential methylation at any of the differentially expressed genes, suggesting that another epigenetic mechanism is responsible for alterations in gene expression. Overall, our findings suggest that a ‘memory’ of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations, pre-acclimating progeny to cope with hypoxic conditions.
Increased seed carbohydrate reserves associated with domestication influence the optimal seminal root number ofZea mays
Authors: Perkins Alden C. , Lynch Jonathan P. 
Published: December 2020

AbstractBackground and AimsDomesticated maize (Zea maysssp.mays) generally forms between two and six seminal roots, while its wild ancestor, Mexican annual teosinte (Zea maysssp.parviglumis), typically lacks seminal roots. Maize also produces larger seeds than teosinte, and it generally has higher growth rates as a seedling. Maize was originally domesticated in the tropical soils of southern Mexico, but it was later brought to the Mexican highlands before spreading to other parts of the continent, where it experienced different soil resource constraints. The aims of this study were to understand the impact of increased seminal root number on seedling nitrogen acquisition and to model how differences in maize and teosinte phenotypes might have contributed to increased seminal root number in domesticated maize.MethodsSeedling root architectural models of a teosinte accession and a maize landrace were constructed by parameterizing the functional-structural plant modelOpenSimRootusing plants grown in mesocosms. Seedling growth was simulated in a low-phosphorus environment, multiple low-nitrogen environments, and at variable planting densities. Models were also constructed to combine individual components of the maize and teosinte phenotypes.Key ResultsSeminal roots contributed about 35% of the nitrogen and phosphorus acquired by maize landrace seedlings in the first 25 days after planting. Increased seminal root number improved plant N acquisition under low-N environments with varying precipitation patterns, fertilization rates, soil textures, and planting densities. Models suggested that the optimal number of seminal roots for nutrient acquisition in teosinte is constrained by its limited seed carbohydrate reserves.ConclusionsSeminal roots can improve the acquisition of both nitrogen and phosphorus in maize seedlings, and the increase in seed size associated with maize domestication may have facilitated increased seminal root number.
Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of a nosocomial pathogen
Authors: Haudiquet Matthieu , Buffet Amandine , Rendueles Olaya , Rocha Eduardo P.C. 
Published: December 2020

ABSTRACTMobile genetic elements (MGEs) drive genetic transfers between bacteria using mechanisms that are affected by the cell envelope composition, notably the capsule. Here, we show that capsules constrain phage-mediated gene flow between closely related serotypes inKlebsiella pneumoniae, a high-priority nosocomial enterobacteria. Serotype-specific phage pressure may also explain the inactivation of capsule genes, which occur frequently and recapitulate the capsule biosynthetic pathway. We show that plasmid conjugation is increased upon capsule inactivation and that capsule re-acquisition leaves long recombination tracts around the capsular locus. This suggests that capsule inactivation by phage pressure facilitates its subsequent re-acquisition by conjugation, a process re-wiring gene flow towards novel lineages whenever it leads to serotype swaps. These results reveal the basis of trade-offs between the evolution of virulence and multidrug resistance. They also caution that some alternatives to antibiotic therapy may select for capsule inactivation, thus decreasing virulence but facilitating antibiotic resistance genes acquisition.