bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic determinants of endophytism in the Arabidopsis root mycobiome
Authors: Mesny Fantin , Miyauchi Shingo , Thiergart Thorsten , Pickel Brigitte , Atanasova Lea , Karlsson Magnus , Hüttel Bruno , Barry Kerrie W. , Haridas Sajeet , Chen Cindy , Bauer Diane , Andreopoulos William , Pangilinan Jasmyn , LaButti Kurt , Riley Robert , Lipzen Anna , Clum Alicia , Drula Elodie , Henrissat Bernard , Kohler Annegret , Grigoriev Igor V. , Martin Francis M. , Hacquard Stéphane 
Published: April 2021

AbstractRoots of Arabidopsis thaliana do not engage in symbiotic associations with mycorrhizal fungi but host taxonomically diverse fungal communities that influence health and disease states. We sequenced the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with 79 other plant-associated fungi. We report that root mycobiota members evolved from ancestors with diverse lifestyles and retained large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identified a set of 84 gene families predicting best endophytism, including families encoding PCWDEs acting on xylan (GH10) and cellulose (AA9). These genes also belong to a core transcriptional response induced by phylogenetically-distant mycobiota members in A. thaliana roots. Recolonization experiments with individual fungi indicated that strains with detrimental effects in mono-association with the host not only colonize roots more aggressively than those with beneficial activities but also dominate in natural root samples. We identified and validated the pectin degrading enzyme family PL1_7 as a key component linking aggressiveness of endophytic colonization to plant health.
A strategy for mapping biophysical to abstract neuronal network models applied to primary visual cortex
Authors: Chizhov Anton V. , Graham Lyle J. 
Published: April 2021

AbstractA fundamental challenge for the theoretical study of neuronal networks is to make the link between complex biophysical models based directly on experimental data, to progressively simpler mathematical models that allow the derivation of general operating principles. We present a strategy that successively maps a relatively detailed biophysical population model, comprising conductance-based Hodgkin-Huxley type neuron models with connectivity rules derived from anatomical data, to various representations with fewer parameters, finishing with a firing rate network model that permits analysis. We apply this methodology to primary visual cortex of higher mammals, focusing on the functional property of stimulus orientation selectivity of receptive fields of individual neurons. The mapping produces compact expressions for the parameters of the abstract model that clearly identify the impact of specific electrophysiological and anatomical parameters on the analytical results, in particular as manifested by specific functional signatures of visual cortex, including input-output sharpening, conductance invariance, virtual rotation and the tilt after effect. Importantly, qualitative differences between model behaviours point out consequences of various simplifications. The strategy may be applied to other neuronal systems with appropriate modifications.Author summaryA hierarchy of theoretical approaches to study a neuronal network depends on a tradeoff between biological fidelity and mathematical tractibility. Biophysically-detailed models consider cellular mechanisms and anatomically defined synaptic circuits, but are often too complex to reveal insights into fundamental principles. In contrast, increasingly abstract reduced models facilitate analytical insights. To better ground the latter to the underlying biology, we describe a systematic procedure to move across the model hierarchy that allows understanding how changes in biological parameters - physiological, pathophysiological, or because of new data - impact the behaviour of the network. We apply this approach to mammalian primary visual cortex, and examine how the different models in the hierarchy reproduce functional signatures of this area, in particular the tuning of neurons to the orientation of a visual stimulus. Our work provides a navigation of the complex parameter space of neural network models faithful to biology, as well as highlighting how simplifications made for mathematical convenience can fundamentally change their behaviour.
Quantitative multidimensional phenotypes improve genetic analysis of laterality traits
Authors: Schmitz Judith , Zheng Mo , Lui Kelvin F. H. , McBride Catherine , Ho Connie S.-H. , Paracchini Silvia 
Published: April 2021

AbstractHandedness is the most commonly investigated lateralised phenotype and is usually measured as a binary left/right category. Its links with psychiatric and neurodevelopmental disorders prompted studies aimed at understanding the underlying genetics, while other measures and side preferences have been less studied. We investigated the heritability of hand, as well as foot, and eye preference by assessing parental effects (n≤ 5 028 family trios) and SNP-based heritability (SNP-h2,n≤ 5 931 children) in the Avon Longitudinal Study of Parents and Children (ALSPAC). An independent twin cohort from Hong Kong (n= 358) was used to replicate results from structural equation modelling (SEM). Parental left-side preference increased the chance of an individual to be left-sided for the same trait, with stronger maternal than paternal effects for footedness. By regressing out the effects of sex, age, and ancestry, we transformed laterality categories into quantitative measures. The SNP-h2for quantitative handedness and footedness was .21 and .23, respectively, which is higher than the SNP-h2reported in larger genetic studies using binary handedness measures. The heritability of the quantitative measure of handedness increased (.45) compared to a binary measure for writing hand (.27) in the Hong Kong twins. Genomic and behavioural SEM identified a shared genetic factor contributing to handedness, footedness, and eyedness, but no independent effects on individual phenotypes. Our analysis demonstrates how quantitative multidimensional laterality phenotypes are better suited to capture the underlying genetics than binary traits.
Formic acid modulates latency and accuracy of nestmate recognition in carpenter ants
Authors: Baracchi David , Giurfa Martin , d’Ettorre Patrizia 
Published: April 2021

AbstractDecision-making processes face the dilemma of being accurate or faster, a phenomenon that has been described as speed-accuracy trade-off (SAT) in numerous studies on animal behaviour. In social insects, discriminating between colony members and aliens is subjected to this trade-off as rapid and accurate rejection of enemies is of primary importance for the maintenance and ecological success of insect societies. Recognition cues distinguishing aliens from nestmates are embedded in the cuticular hydrocarbon (CHC) layer and vary among colonies. In walking carpenter ants, exposure to formic acid (FA), an alarm pheromone, improves accuracy of nestmate recognition by decreasing both alien acceptance and nestmate rejection. Here we studied the effect of FA exposure on the spontaneous aggressive mandible opening response of harnessedCamponotus aethiopsants presented with either nestmate or alien CHCs. FA modulated both MOR accuracy and the latency to respond to odours of conspecifics. In particular, FA decreased MOR towards nestmates but increased it towards aliens. Furthermore, FA decreased MOR latency towards aliens but not towards nestmates. As response latency can be used as a proxy of response speed, we conclude that contrary to the prediction of the SAT theory, ants did not trade off speed against accuracy in the process of nestmate recognition.Summary statementExposure to an alarm pheromone increases both latency and accuracy of the response to recognition cues in ants
Suboptimal proteome allocation during changing environments constrains bacterial response and growth recovery
Authors: Balakrishnan Rohan , Hwa Terence , Cremer Jonas 
Published: April 2021

AbstractTo sustain growth in fluctuating environments microbial organisms must respond appropriately. The response generally requires the synthesis of novel proteins, but this synthesis can be impeded due to the depletion of biosynthetic precursors when growth conditions vary. Microbes must thus devise effective response strategies to manage depleting precursors. To better understand these strategies, we here investigate the active response ofEscherichia colito changes in nutrient conditions, connecting transient gene-expression behavior to growth phenotypes. By synthetically modifying the gene expression during changing growth conditions, we show how the competition by genes for the limited protein synthesis capacity constrains the cellular response. Despite this constraint, cells substantially express genes that are not required, severely slowing down the response. These findings highlight that cells do not optimize growth and recovery in every encountered environment but rather exhibit hardwired response strategies that may have evolved to promote growth and fitness in their native environment and include the regulation of multiple genes. The constraint and the suboptimality of the cellular response uncovered in this study provides a conceptual framework relevant for many research applications, from the prediction of evolution and adaptation to the improvement of gene circuits in biotechnology.
Illuminati, a novel form of gene expression plasticity inDrosophilaneural stem cells
Authors: Goupil Alix , Heinen Jan Peter , Rossi Fabrizio , Salame Riham , Pennetier Carole , Simon Anthony , Skorski Patricia , Lauzao Anxela , Bardin Allison , Basto Renata , Gonzalez Cayetano 
Published: April 2021

ABSTRACTWith the aim of developing a genetic instability (GI) sensor invivowe used the well-established Gal80/Gal4-UAS system combined with a visual GFP marker inDrosophila. We generated a collection of 25Drosophilalines carrying GAL80 transgenes in different locations in all major chromosomes (X, Y, II, and III). We found low rates of GFP cells in epithelial tissues such as wing discs. In contrast, in larval brains, GFP positive clusters containing neural stem cells- also called neuroblasts (NBs)- and their offspring, were highly frequent. Using genetic and imaging-based approaches, we show that GFP NBs do not result from aneuploidy or mutations in theGAL80gene, but rather by stochastic repression ofGAL80expression. We named this novel type of gene expression instability Illuminati. Importantly, Illuminati frequency is influenced by environmental and stress conditions. Further, we found that once established, Illuminati can be propagated over many cell cycles.
DE-STRESS: A user-friendly web application for the evaluation of protein designs
Authors: Stam Michael J. , Wood Christopher W. 
Published: April 2021

AbstractDe novo protein design is a rapidly growing field and there are now many interesting and useful examples of designed proteins in the literature. However, most designs could be classed as failures when characterised in the lab, usually as a result of low expression, misfolding, aggregation or lack of function. This high attrition rate makes protein design unreliable and costly. It is possible that some of these failures could be caught earlier in the design process if it were quick and easy to generate information and a set of high-quality metrics regarding designs, which could be used to make reproducible and data-driven decisions about which designs to characterise experimentally.We present DE-STRESS (DEsigned STRucture Evaluation ServiceS), a web application for evaluating structural models of designed and engineered proteins. DE-STRESS has been designed to be simple, intuitive to use and responsive. It provides a wealth of information regarding designs, as well as tools to help contextualise the results and formally describe the properties that a design requires to be fit for purpose.AvailabilityDE-STRESS is available for non-commercial use, without registration, through the following website: https://pragmaticproteindesign.bio.ed.ac.uk/de-stress/. Source code for the application is available on GitHub: https://github.com/wells-wood-research/de-stress. The data used to generate reference sets is available through a GraphQL API, with the following URL: https://pragmaticproteindesign.bio.ed.ac.uk/big-structure/graphql.
An organelle inheritance pathway during polarized cell growth
Authors: Li Kathryn W , Pedersen Ross TA , Lu Michelle S , Drubin David G 
Published: April 2021

AbstractSome organelles cannot be synthesized anew, so they are segregated into daughter cells during cell division. InSaccharomyces cerevisiae, daughter cells bud from mother cells and are populated by organelles inherited from the mothers. To determine whether this organelle inheritance occurs in a stereotyped manner, we tracked organelles using fluorescence microscopy. We describe a program for organelle inheritance in budding yeast. The cortical endoplasmic reticulum (ER) and peroxisomes are inherited concomitant with bud emergence. Next, vacuoles are inherited in small buds, followed closely by mitochondria. Finally, the nucleus and perinuclear ER are inherited when buds have nearly reached their maximal size. Because organelle inheritance timing correlates with bud morphology, which is coupled to the cell cycle, we tested whether organelle inheritance order is controlled by the cell cycle. By arresting cell cycle progression but allowing continued bud growth, we determined that organelle inheritance still occurs without cell cycle progression past S-phase, and that the general inheritance order is maintained. Thus, organelle inheritance follows a preferred order during polarized cell division, but it is not controlled exclusively by cell cycle signaling.Summary statementOrganelles are interconnected by contact sites, but they must be inherited from mother cells into buds during budding yeast mitosis. We report that this process occurs in a preferred sequence.
Cannabis Vapour Exposure Alters Neural Circuit Oscillatory Activity In A Neurodevelopmental Model Of Schizophrenia: Exploring The Differential Impact Of Cannabis Constituents
Authors: Jenkins Bryan W. , Buckhalter Shoshana , Perreault Melissa L. , Khokhar Jibran Y. 
Published: April 2021

AbstractCannabis use is highly prevalent in patients with schizophrenia and worsens the course of the disorder. To understand the causal impacts of cannabis on schizophrenia-related oscillatory disruptions, we herein investigated the impact of exposure to cannabis vapour (containing delta-9-tetrahydrocannabinol [THC] or balanced THC and cannabidiol [CBD]) on oscillatory activity in the neonatal ventral hippocampal lesion (NVHL) rat model of schizophrenia. Male Sprague Dawley rats underwent NVHL or sham surgeries on postnatal day 7. In adulthood, electrodes were implanted targeting the cingulate cortex (Cg), the prefrontal cortex (PFC), the dorsal hippocampus (HIP), and the nucleus accumbens (NAc). Local field potential recordings were obtained following exposure to two strains of vapourized cannabis flower (with ~10% THC or ~10% balanced THC:CBD) in a cross-over design with a two-week wash-out period between exposures. Compared to controls, NVHL rats had reduced baseline gamma power in the Cg, dHIP, and NAc, and reduced high-gamma coherence between the dHIP-Cg. THC-only vapour broadly suppressed oscillatory power and coherence, even beyond the baseline suppressions observed in NHVL rats. Balanced THC:CBD vapour appeared to ameliorate the THC-induced impacts on power and coherence in both sham and NVHL rats. For NVHL rats, THC-only vapour also normalized the baseline dHIP-Cg high-gamma coherence deficits. NHVL rats also demonstrated a 20ms delay in dHIP theta to high-gamma phase coupling, which was ameliorated by both exposures in the PFC and NAc. In conclusion, THC-only cannabis vapour suppressed oscillatory activity in NVHL and sham rats, while balanced THC:CBD vapour may ameliorate some of these effects.
Recombination patterns in coronaviruses
Authors: Müller Nicola F. , Kistler Kathryn E. , Bedford Trevor 
Published: April 2021

AbstractAs shown during the SARS-CoV-2 pandemic, phylogenetic and phylodynamic methods are essential tools to study the spread and evolution of pathogens. One of the central assumptions of these methods is that the shared history of pathogens isolated from different hosts can be described by a branching phylogenetic tree. Recombination breaks this assumption. This makes it problematic to apply phylogenetic methods to study recombining pathogens, including, for example, coronaviruses. Here, we introduce a Markov chain Monte Carlo approach that allows inference of recombination networks from genetic sequence data under a template switching model of recombination. Using this method, we first show that recombination is extremely common in the evolutionary history of SARS-like coronaviruses. We then show how recombination rates across the genome of the human seasonal coronaviruses 229E, OC43 and NL63 vary with rates of adaptation. This suggests that recombination could be beneficial to fitness of human seasonal coronaviruses. Additionally, this work sets the stage for Bayesian phylogenetic tracking of the spread and evolution of SARS-CoV-2 in the future, even as recombinant viruses become prevalent.
Quantifying the potential for red blood cell β-adrenergic sodium-proton exchangers to protect oxygen transport in hypoxic and hypercapnic white seabass
Authors: Harter Till S. , Clifford Alexander M. , Tresguerres Martin 
Published: April 2021

AbstractWhite seabass (Atractoscion nobilis) are increasingly experiencing periods of low oxygen (O2; hypoxia) and high carbon dioxide (CO2, hypercapnia) due to climate change and eutrophication of the coastal waters of California. Hemoglobin (Hb) is the principal O2carrier in the blood and in many teleost fishes Hb-O2binding is compromised at low pH; however, the red blood cells (RBC) of some species regulate intracellular pH with adrenergically-stimulated sodium-proton-exchangers (β-NHE). We hypothesized that RBC β-NHEs in white seabass are an important mechanism that can protect the blood O2-carrying capacity during hypoxia and hypercapnia. We determined the O2-binding characteristics of white seabass blood, the response of RBCs to adrenergic stimulation, and quantified the protective effect of β-NHE activity on Hb-O2saturation. White seabass had typical teleost Hb characteristics, with a moderate O2affinity (PO2at half-saturation; P502.9 kPa) that was highly pH-sensitive (Bohr coefficient -0.92; Root effect 52%). The presence of RBC β-NHEs was confirmed by functional, molecular and bioinformatic data and super-resolution imaging revealed, for the first time, the subcellular location of β-NHE protein in vesicle-like structures and on the RBC membrane, and its translocation after adrenergic stimulation. The activation of RBC β-NHEs increased Hb-O2saturation by ∼8% in normoxia at 1 kPa PCO2, and by up to 20% in hypoxia. Our results confirm that RBC β-NHE activity in white seabass has great potential to protect arterial O2transport in environmentally relevant conditions of hypoxia and hypercapnia, but also reveal a potential vulnerability of fish to combinations of these stressors.
Systematic morphological and morphometric analysis of identified olfactory receptor neurons inDrosophila melanogaster
Authors: Gonzales Cesar Nava , McKaughan Quintyn , Bushong Eric A , Cauwenberghs Kalyani , Ng Renny , Madany Matthew , Ellisman Mark H , Su Chih-Ying 
Published: April 2021

ABSTRACTThe biophysical properties of sensory neurons are influenced by their morphometric and morphological features, whose precise measurements require high-quality volume electron microscopy (EM). However, systematic surveys of these nanoscale characteristics for identified neurons are scarce. Here, we characterize the morphology ofDrosophilaolfactory receptor neurons (ORNs) across the majority of genetically identified sensory hairs. By analyzing serial block-face electron microscopy (SBEM) images of cryofixed antennal tissues, we compile an extensive morphometric dataset based on 122 reconstructed 3D models of 33 identified ORN types. In addition, we observe multiple novel features—including extracellular vacuoles within sensillum lumen, intricate dendritic branching, mitochondria enrichment in select ORNs, novel sensillum types, and empty sensilla containing no neurons—which raise new questions pertinent to cell biology and sensory neurobiology. Our systematic survey is critical for future investigations into how the size and shape of sensory neurons influence their responses, sensitivity and circuit function.
Behavioural variability and cortical electrophysiological signals depend on recent outcomes during human reinforcement motor learning
Authors: Wiegel Patrick , Spedden Meaghan Elizabeth , Ramsenthaler Christina , Beck Mikkel Malling , Lundbye-Jensen Jesper 
Published: April 2021

AbstractThe history of our actions and the outcomes of these represent important information, which can inform choices, and efficiently guide future behaviour. While unsuccessful (S-) outcomes are expected to lead to more explorative motor states and increased behavioural variability, successful (S+) outcomes lead to reinforcement of the previous action and thus exploitation. Here, we show that during reinforcement motor learning, humans attribute different values to previous actions when they experience S- vs. S+ outcomes. Behavioural variability after S- outcomes is influenced more by the previous outcomes compared to what is observed after S+ outcomes. Using electroencephalography, we show that neural oscillations of the prefrontal cortex encode the level of reinforcement (high beta frequencies) and reflect the detection of reward prediction errors (theta frequencies). The results suggest that S+ experiences ‘overwrite’ previous motor states to a greater extent than S- experiences and that modulations in neural oscillations in the prefrontal cortex play a potential role in encoding the (changes in) movement variability state during reinforcement motor learning.
UBP12 and UBP13 deubiquitinases destabilize the CRY2 blue-light receptor to regulate growth
Authors: Norén Lindbäck Louise , Artz Oliver , Ackermann Amanda , Pedmale Ullas V. 
Published: April 2021

ABSTRACTAll organisms undergo growth, which is precisely controlled by exogenous and endogenous signals. Unchecked growth often leads to neoplasia and other developmental defects, severely affecting an organism’s fitness. Light is a vital exogenous signal sensed by cryptochrome (CRY) blue light receptors to modulate growth and the circadian clock in plants and animals. Yet, how CRYs interpret light quantity to regulate growth in plants remains poorly understood. We show that UBP12 and UBP13 deubiquitinases physically interact with CRY2 in light. UBP12/13 negatively regulated CRY2 protein levels by promoting its ubiquitination and turnover to fine-tune growth. Unexpectedly, the destabilization of CRY2 by UBP12/13 is contrary to the general view that deubiquitinases stabilize proteins by preventing their degradation. Growth and development were explicitly affected in blue light when UBP12/13 was disrupted or overexpressed, indicating their role alongside CRY2. UBP12/13 also interacted and stabilized COP1, which is partially required for the turnover of CRY2. Despite decades of studies on deubiquitinases, the knowledge on how they are regulated is limited. Our study offers an insight into how exogenous signals and their receptors regulate deubiquitinase activity by protein-protein interaction. Altogether, our results provide a new module of cryptochromes and deubiquitinases in sensing and interpreting light cues to control growth at the most appropriate time.