bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induced ligno-suberin vascular coating and tyramine-derived hydroxycinnamic acid amides restrict Ralstonia solanacearum colonization in resistant tomato roots
Authors: Kashyap Anurag , Capellades Montserrat , Zhang Weiqi , Srinivasan Sumithra , Laromaine Anna , Serra Olga , Figueras Mercè , Rencoret Jorge , Gutiérrez Ana , Valls Marc , Coll Nuria S. 
Published: June 2021

SummaryThe soil borne pathogen Ralstonia solanacearum is the causing agent of bacterial wilt, a devastating disease affecting major agricultural crops. R. solanacearum enters plants through the roots and reaches the vasculature, causing rapid wilting. We recently showed that tomato varieties resistant to bacterial wilt restrict bacterial movement in the plant. In the present work we go a step forward by identifying the physico-chemical nature of the barriers induced in resistant tomato roots in response to R. solanacearum. We describe that resistant tomato specifically responds to infection by assembling de novo a structural barrier at the vasculature formed by a ligno-suberin coating and tyramine-derived hydroxycinnamic acid amides (HCAAs). On the contrary, susceptible tomato does not form these reinforcements in response to the pathogen but instead displays lignin structural changes compatible with its degradation. Further, we show that overexpressing genes of the ligno-suberin pathway in a commercial susceptible variety of tomato restricts R. solanacearum movement inside the plant and slows disease progression, enhancing resistance to the pathogen. We thus propose that the induced barrier in resistant plants does not only restrict the movement of the pathogen, but may also prevent cell wall degradation by the pathogen and confer anti-microbial properties.
Integrated Metabolomics to Reveal the Impacts of Common Antibiotics based on Drug Resistance Prediction of Gut Microbiota
Authors: Gao Pei , Huang Ming , Ono Naoaki , Kanaya Shigehiko , Altaf-Ul-Amin MD 
Published: June 2021

AbstractDue to the close interaction between the host and the gut microbiota, the alterations in gut microbiota metabolism may therefore contribute to various diseases. How to use antibiotics more wisely in clinical practice is a promising task in the field of pathophysiology related to gut microbiota. The hope fueling this research is that the alteration of gut microbial communities are paralleled by their capacity on metabolomic from the combined perspective of microbiome and metabolomics. In order to reveal the impacts of antibiotics on microbiota-associated host metabolomic phenotypes, a feasible methodology should be well developed to assess the pervasive effects of antibiotics on the population structure of gut microbial communities. Our attempt starts from predicting specific resistance phenotypes of the individuals in isolation from the rest of the gut microbiota community, according to their resistant genotypes. Once resistance phenotypes of microbiome is determined, we integrated metabolomics with machine learning by applying various analysis algorithms to explore the relationship between the predicted resistance and metabolites, including what the microbial community is after medication, which microbes produce metabolites, and how these metabolites enrich.
Through hawks’ eyes: reconstructing a bird’s visual field in flight to study gaze strategy and attention during perching and obstacle avoidance
Authors: Miñano Sofía , Taylor Graham K. 
Published: June 2021

AbstractWe present a method to analyse visual attention of a bird in flight, that combines motion capture data with renderings from virtual cameras. We applied it to a small subset of a larger dataset of perching and obstacle avoidance manoeuvres, and studied visual field stabilisation and gaze shifts. Our approach allows us to synthesise visual cues available to the bird during flight, such as depth information and optic flow, which can lead to novel insights into the bird’s gaze strategy in flight. This preliminary work demonstrates the method and suggests several new hypotheses to investigate with the full dataset.
Oxytocin receptor antagonism during song tutoring in zebra finches reduces preference for and learning of the tutor’s song
Authors: Pilgeram Natalie R. , Baran Nicole M. , Bhise Aditya , Davis Matthew T. , Kim Emily , Lee Sumin , Rodriguez-Saltos Carlos A. , Maney Donna L. 
Published: June 2021

AbstractIn species with vocal learning, acquiring species-typical vocalizations relies on early social orienting. In zebra finches (Taeniopygia guttata), for example, learning song requires dynamic social interactions with a “tutor” during an early sensitive period. The oxytocin system plays a central role in social orienting across species, yet it is unknown whether this system participates in the attentional and motivational processes that support vocal learning. Here, we tested whether blocking oxytocin receptors during exposure to tutors would impact learning from those tutors. Juvenile, song-naïve males were each tutored by two unfamiliar adults. During exposure to one tutor, juveniles were treated with oxytocin receptor antagonist (OTA) and during exposure to the other, saline (control). We found that OTA significantly reduced behaviors associated with approach and attention during tutoring sessions. Next, using an operant assay in which exposure to the two songs was balanced, we found that the juveniles preferred the control song over the OTA song. The developmental trajectory of preference for the control song resembled the pattern shown by father-reared birds choosing to hear their father’s song. Finally, the adult songs of the tutored birds more closely resembled control song than OTA song. The magnitude of this difference was significantly predicted by the early preference for the control song. Overall, oxytocin antagonism during exposure to a tutor seemed to bias juveniles against that tutor and his song. Our results suggest that oxytocin receptors play a role in socially-guided vocal learning in zebra finches, perhaps by affecting attention and motivation during tutoring.
Peripheral CB1 receptor blockade acts as a memory enhancer through an adrenergic-dependent mechanism
Authors: Martínez-Torres Sara , Bergadà-Martínez Araceli , Ortega Jorge E. , Galera-López Lorena , Hervera Arnau , Ortega-Álvaro Antonio , Remmers Floortje , Muñoz-Moreno Emma , Soria Guadalupe , del Río José Antonio , Lutz Beat , Ángel Ruíz-Ortega Jose , Meana J. Javier , Maldonado Rafael , Ozaita Andrés 
Published: June 2021

AbstractPeripheral inputs to the brain continuously shape its function and can influence the formation of non-emotional memory, but the underlying mechanisms have not been fully understood. Cannabinoid type-1 receptors (CB1R), widely distributed in the organism, is a well-recognized player in memory performance, and its systemic modulation significantly influences memory function. By assessing non-emotional memory in mice, we have now found a relevant role of peripheral CB1R in the formation of persistent memory. Indeed, peripherally restricted CB1R antagonism by using AM6545 showed a mnemonic effect that was occluded in adrenalectomized mice, after peripheral adrenergic blockade, or when vagus nerve was chemogenetically inhibited. Genetic CB1R deletion in dopamine β-hydroxylase-expressing cells enhanced the formation of persistent memory, supporting a role of peripheral CB1R modulating the adrenergic tone. Notably, brain connectivity was affected by peripheral CB1R inhibition, and locus coeruleus activity and extracellular hippocampal norepinephrine, were increased. In agreement, intra-hippocampal β-adrenergic blockade prevented AM6545 mnemonic effects. Together, we disclose a novel peripheral mechanism relevant for the modulation of the formation of persistent non-emotional memory.
Insights into early stages of the establishment of host:algal endosymbioses: Genetic responses to live versus heat-killed algae and bacterial prey in a sponge host
Authors: Camilli Sara , Koutsouveli Vasiliki , Hall Chelsea , Chang Lillian , Sacristan-Soriano Oriol , Hill Malcolm , Riesgo Ana , Hill April 
Published: June 2021

ABSTRACTThe freshwater sponge Ephydatia muelleri and its Chlorella-like green algal partner is an emerging model for studying animal:algal endosymbiosis. The sponge host is a highly tractable laboratory organism, and the symbiotic algae are easily cultured. We took advantage of these traits to experimentally interrogate fundamental questions about cellular mechanisms that govern the establishment of durable intracellular partnerships between hosts and symbionts in facultative symbioses. We modified a classical experimental approach to discern the phagocytotic mechanisms that might be co-opted to permit persistent infections, and identified genes differentially expressed in E. muelleri sponges early in the establishment of endosymbiosis. We exposed algal-free E. muelleri to live native algal symbionts, native heat-killed algae, and bacteria, and then performed RNASeq so we could compare patterns of gene expression in each treatment. We contrasted differential gene expression patterns between potential food items (bacteria and heat-killed algae) and the live native Chlorella-like symbiont. We found a relatively small but interesting suite of genes that are uniquely and differentially expressed in the host exposed to live algal symbionts, and a larger number of genes uniquely triggered by host exposure to heat-killed algae. One of the host genes, an ABC transporter that is downregulated in response to live algal symbionts, was further evaluated for its possible role in establishment of the algal symbiosis. We discuss the gene expression profiles associated with host responses to living algal cells in the context of conditions necessary for long-term residency within host cells by phototrophic symbionts as well as the genetic responses to sponge phagocytosis and immune driven pathways.
Comparative proteome analysis revealed the differences in responses of bovine alveolar macrophages to both M.tb and Mb infection
Authors: Cai Yurong , Li Yong , Gao Weifeng , Wang Pu , Zhang Gang , Jiang Lingling 
Published: June 2021

AbstractBovine tuberculosis, caused by both MTB(Mycobacterium tuberculosis) and MB(Mycobacterium bovis), is one of the most serious zoonotic diseases in the world. Both pathogenic MTB and MB interact closely with the host alveolar macrophages. However, the mechanisms of defense response of macrophages to MTB or MB still need further researches. Presently, in-depth comparative proteome analysis was performed on the MB- and MTB- infected macrophage. We identified that macrophages was more sensitive to the MB infection. Both pathogens could induce strong energy metabolism of macrophages. To eliminate MB and protect the host, a bunch of proteins and signaling which involved in autophagy- and inflammatory-related progresses were highly activated in macrophages following MB infection. In contrast, only proteins relevant to energy metabolisms were highly expressed in macrophages following MTB infection. In summary, we proposed that macrophages were more sensitive to MB attacks and could deployed proteins functioned in autophagy- and inflammatory-related progresses to protect the host. Our research provide a novel insight into the different mechanisms of defense responses of macrophages to both MTB and MB infection.
Impacts of dietary exposure to pesticides on faecal microbiome metabolism in adult twins
Authors: Mesnage Robin , Bowyer Ruth C E , El Balkhi Souleiman , Saint-Marcoux Franck , Gardere Arnaud , Ducarmon Quinten Raymond , Geelen Anoecim Robecca , Zwittink Romy Daniëlle , Tsoukalas Dimitris , Sarandi Evangelia , Paramera Efstathia I. , Spector Timothy , Steves Claire J , Antoniou Michael N 
Published: June 2021

AbstractConcerns have been raised as to whether the consumption of foodstuffs contaminated with pesticides can contribute to the development of chronic human diseases by affecting microbial community function in the gut. We provide the first associations between urinary pesticide excretion and the composition and function of the faecal microbiome in 65 twin pairs in the UK. Biomonitoring of exposure to 186 common insecticide, herbicide, or fungicide residues showed the presence of pyrethroid and/or organophosphorus insecticide residues in all urine samples, while the herbicide glyphosate was found in 45% of individuals. Other pesticides such as DEET, imidacloprid or dithiocarbamate fungicides were less frequently detected. While the geographic location or the rural/urban environment had no influence on pesticide urinary excretion, food frequency questionnaires showed that DMTP levels, a metabolite of organophosphates, was higher with increased consumption of fruit and vegetables. Multivariable association between urinary pesticide excretion and faecal microbial composition and function were determined with shotgun metagenomics and metabolomics. A total of 34 associations between pesticide residues concentrations and faecal metabolite concentrations were detected. Glyphosate excretion was positively associated to an increased bacterial species richness, as well as to fatty acid metabolites and phosphate levels. The insecticide metabolite Br2CA, reflecting deltamethrin exposure, was positively associated with the mammalian phytoestrogens enterodiol and enterolactone, and negatively associated with some N-methyl amino acids. Urine metabolomics performed on a subset of samples did not reveal associations with the excretion of pesticide residues. Our results highlight the need for future interventional studies to understand effects of pesticide exposure on the gut microbiome and possible health consequences.
Wearables-Only Analysis of Muscle and Joint Mechanics: An EMG-Driven Approach
Authors: Gurchiek Reed D. , Donahue Nicole , Fiorentino Niccolo M. , McGinnis Ryan S. 
Published: June 2021

AbstractComplex sensor arrays prohibit practical deployment of existing wearables-based algorithms for free-living analysis of muscle and joint mechanics. Machine learning techniques have been proposed as a potential solution, however, they are less interpretable and generalizable when compared to physics-based techniques. Herein, we propose a hybrid method utilizing inertial sensor- and electromyography (EMG)-driven simulation of muscle contraction to characterize knee joint and muscle mechanics during walking gait. Machine learning is used only to map a subset of measured muscle excitations to a full set thereby reducing the number of required sensors. We demonstrate the utility of the approach for estimating net knee flexion moment (KFM) as well as individual muscle moment and work during the stance phase of gait across nine unimpaired subjects. Across all subjects, KFM was estimated with 0.91 %BW•H RMSE and strong correlations (r = 0.87) compared to ground truth inverse dynamics analysis. Estimates of individual muscle moments were strongly correlated (r = 0.81-0.99) with a reference EMG-driven technique using optical motion capture and a full set of electrodes as were estimates of muscle work (r = 0.88-0.99). Implementation of the proposed technique in the current work included instrumenting only three muscles with surface electrodes (lateral and medial gastrocnemius and vastus medialis) and both the thigh and shank segments with inertial sensors. These sensor locations permit instrumentation of a knee brace/sleeve facilitating a practically deployable mechanism for monitoring muscle and joint mechanics with performance comparable to the current state-of-the-art.
A Co-Fractionation Mass Spectrometry-based Prediction of Protein Complex Assemblies in the Developing Rice Aleurone-subaleurone
Authors: Lee Youngwoo , Okita Thomas W. , Szymanski Daniel B. 
Published: June 2021

AbstractMultiprotein complexes execute and coordinate diverse cellular processes such as organelle biogenesis, vesicle trafficking, cell signaling, and metabolism. Knowledge about their composition and localization provides useful clues about the mechanisms of cellular homeostasis and systems-level control. This is of great biological importance and practical significance in heterotrophic rice endosperm and aleurone-subaleurone tissues that are a primary source of seed vitamins and stored energy. Dozens of protein complexes have been implicated in the synthesis, transport, and storage of seed proteins, lipids, vitamins, and minerals. Mutations in protein complexes that control RNA transport result in aberrant endosperm with shrunken and floury phenotypes, significantly reducing seed yield and quality. The purpose of this research is to broadly predict protein complex composition in the aleurone-subaleurone layers of developing rice seeds using co-fractionation mass spectrometry. Following orthogonal chromatographic separations of biological replicates, thousands of protein elution profiles were subjected to distance-based clustering to enable a large-scale determination of multimerization state and complex composition. Predictions included evolutionarily conserved proteins across diverse functional categories, including novel heteromeric RNA binding protein complexes that influence seed quality. This effective and open-ended proteomics pipeline provides useful clues about systems-level controls in the early stage of rice seed development.One-sentence summaryA co-fractionation mass spectrometry pipeline predicts compositions of cytosolic protein complexes present in the early stages of rice seed development.
Metabolic model of nitrogen-fixing obligate aerobe Azotobacter vinelandii demonstrates adaptation to oxygen concentration and metal availability
Authors: Alleman Alexander B. , Mus Florence , Peters John W. 
Published: June 2021

AbstractThere is considerable interest in promoting biological nitrogen fixation as a mechanism to reduce the inputs of nitrogenous fertilizers in agriculture, a problem of agronomic, economic, and environmental importance. For the potential impact of biological nitrogen fixation in agriculture to be realized, there are considerable fundamental knowledge gaps that need to be addressed. Biological nitrogen fixation or the reduction of N2 to NH3 is catalyzed by nitrogenase which requires a large amount of energy in the form of ATP and low potential electrons. Nitrogen-fixing organisms that respire aerobically have an advantage in meeting the energy demands of biological nitrogen fixation but face challenges of protecting nitrogenase from inactivation in the presence of oxygen. Here, we have constructed a genome-scale metabolic model of the aerobic metabolism of nitrogen-fixing bacteria Azotobacter vinelandii, which uses a complex electron transport system, termed respiratory protection, to consume oxygen at a high rate keeping intracellular conditions microaerobic. Our model accurately determines growth rate under high oxygen and high substrate concentration conditions, demonstrating the large flux of energy directed to respiratory protection. While respiratory protection mechanisms compensate the energy balance in high oxygen conditions, it does not account for all substrate intake, leading to increased maintenance rates. We have also shown how A. vinelandii can adapt under different oxygen concentrations and metal availability by rearranging flux through the electron transport system. Accurately determining the energy balance in a genome-scale metabolic model is required for future engineering approaches.ImportanceThe world’s dependence on industrially produced nitrogenous fertilizers has created a dichotomy of issues. Some parts of the globe lack access to fertilizers and associated poor crop yields, significantly limiting nutrition, contributing to disease and starvation. In contrast, in other parts of the world, abundant nitrogenous fertilizers and associated overuse result in compromised soil quality and downstream environmental issues. There is considerable interest in expanding the impacts of biological nitrogen fixation to promote improved crop yields in places struggling with access to industrial fertilizers and reducing fertilizers’ inputs in areas where overuse is resulting in the degradation of soil health and other environmental problems. A more robust and fundamental understanding of biological nitrogen fixation’s biochemistry and microbial physiology will enable strategies to promote new and more robust associations between nitrogen-fixing microorganisms and crop plants.
Land-use change from food to energy: meta-analysis unravels effects of bioenergy on biodiversity and amenity
Authors: Donnison Caspar , Holland Robert A. , Harris Zoe M. , Eigenbrod Felix , Taylor Gail 
Published: June 2021

AbstractMost decarbonization scenarios of energy systems necessitate more than 500 Mha of land converted to non-food bioenergy crops to provide both energy substitutes for fossil fuels and negative emissions through bioenergy with carbon capture and storage (BECCS). Understanding the environmental and societal impact of this significant land-use change (LUC) is important in determining where and how bioenergy crops should be deployed, and the trade-offs and co-benefits to the environment and society. Here, we use two systematic reviews and a meta-analysis to assess the existing literature on impacts that are likely to have an important effect on public perceptions of the acceptability of such land use change: biodiversity and amenity value. We focus on the impact of LUC to non-food bioenergy crops on agricultural landscapes, where large-scale bioenergy planting may be required. Our meta-analysis finds strong benefits for biodiversity overall (up 75 % ± 13 %), with particular benefits for bird abundance (+ 81 % ± 32 %), bird species richness (+ 100 % ± 31 %), arthropod abundance (+ 52 % ± 36 %), microbial biomass (+ 77 % ± 24 %), and plant species richness (+ 25 % ± 22 %), when land moves out of either arable crops or grassland to bioenergy production. Conversions from arable land to energy trees led to particularly strong benefits, providing an insight into how future LUC to bioenergy crops could support biodiversity. There were inadequate data to complete a meta-analysis on the effects of bioenergy crops on landscape amenity value, and few generalizable conclusions from a systematic review of the literature, however, findings highlight the importance of landscape context and planting strategies in determining amenity values. Our findings demonstrate improved farm-scale biodiversity on agricultural land with bioenergy crops, but also limited knowledge concerning public response to this land use change which could prove crucial to the effective deployment of bioenergy crops for BECCS.