bluuebunny/crossref_metadata_2025_split huggingface dataset:
SAMBA: Structure-Learning of Aquaculture Microbiomes using a Bayesian Approach
Authors: Soriano Beatriz , Hafez Ahmed Ibrahem , Naya-Català Fernando , Moroni Federico , Moldovan Roxana Andreea , Toxqui-Rodríguez Socorro , Piazzon M. Carla , Arnau Vicente , Llorens Carlos , Pérez-Sánchez Jaume 
Published: December 2022

AbstractIn aquaculture systems, microbiomes of farmed fishes may contain thousands of bacterial taxa that establish complex networks of interactions among each other and among the host and the environment. Gut microbiomes in many fish species consist of thousands of bacterial taxa that interact among each other, their environment, and the host. These complex networks of interactions are regulated by a diverse range of factors, yet little is known about the hierarchy of these interactions. Here, we introduce SAMBA (Structure-Learning of Aquaculture Microbiomes using a Bayesian Approach), a computational tool that uses a unified Bayesian network approach to model the network structure of fish gut microbiomes and their interactions with biotic and abiotic variables associated with typical aquaculture systems. SAMBA accepts input data on microbial abundance from 16S rRNA amplicons as well as continuous and categorical information from distinct farming conditions. From this, SAMBA can create and train a network model scenario that can be used to: i) infer information how specific farming conditions influence the diversity of the gut microbiome or pan-microbiome, and ii) predict how the diversity and functional profile of that microbiome would change under other experimental variables. SAMBA also allows the user to visualize, manage, edit, and export the acyclic graph of the modelled network. Our study presents examples and test results of bayesian network scenarios created by SAMBA using data from: a) a microbial synthetic experiment; and b) the pan-microbiome of the gilthead sea bream (Sparus aurata) under different experimental feeding trials. It is worth noting that the usage of SAMBA is not limited to aquaculture systems and can be used for modelling microbiome-host network relationships in any vertebrate organism, including humans, in any system and/or ecosystem.
Functionally dissecting claustrum along anterior-posterior axis in anxiety and higher sensitivity to cocaine
Authors: Zhao Ziheng , Liu Zhaoyu , Chen Liying , Chen Wenwen , Guo Hao , Wang Jingjing , Mai Yuning , Wei Xiaoyan , Ding Jianhua , Ge Feifei , Fan Yu , Guan Xiaowei 
Published: December 2022

AbstractAdolescent cocaine exposure (ACE) induce anxiety and higher sensitivity to drug addiction during adulthood. Here, we show that the claustrum is crucial for control of these two distinct psychiatric disorders in ACE mice. In the process of anxiety test, the CaMKII-positive neurons in median portion of claustrum (MClaustrum) were obviously triggered, and chemogenetic suppressing these neurons efficiently reduced ACE-induced anxiety in adulthood. While, the CaMKII-positive neurons in anterior portion of claustrum (AClaustrum) were obviously activated in response to cocaine-induced conditioned place preference (CPP), and chemogenetic suppressing these neurons efficiently blocked cocaine CPP in ACE mice during adulthood. Our findings dissociating specific sub-portions of claustrum for drug-related anxiety and susceptibility of addiction, extending our understanding to diverse functions of claustrum subregions.
The anti-platelet drug cilostazol enhances interrenal steroidogenesis and exerts a scant effect on innate immune responses in zebrafish
Authors: Chang Wei-Chun , Chen Mei-Jen , Chen Yu-Fu , Chou Chih-Wei , Chuang Yung-Jen , Liu Yi-Wen 
Published: December 2022

AbstractRationaleCilostazol, an anti-platelet phosphodiesterase-3 inhibitor used for the treatment of intermittent claudication, is known for its pleiotropic effects on platelets, endothelial cells and smooth muscle cells. However, how cilostazol impacts the endocrine system and the injury-induced inflammatory processes remains unclear.MethodsWe used the zebrafish, a simple transparent model that demonstrates rapid development and a strong regenerative ability, to test whether cilostazol influences steroidogenesis, and the temporal and dosage effects of cilostazol on innate immune cells during tissue damage and repair.ResultsWhile dosages of cilostazol from 10 to 100 μM did not induce any noticeable morphological abnormality in the embryonic and larval zebrafish, the heart rate and adrenal/interrenal steroidogenesis in larval zebrafish was increased in a dose-dependent manner. During larval fin amputation and regeneration, cilostazol treatments did not affect the immediate injury-induced recruitment of either neutrophils or macrophages, followed by a subtle yet significant effect on reducing the neutrophil retention at the lesion site.ConclusionsOur results indicate that cilostazol has a significant effect on the growth and endocrine function of steroidogenic tissue; and a limited effect on the neutrophil retention without affecting neutrophil and macrophage recruitment during tissue damage and repair.
Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function
Authors: Aderounmu Adedeji M. , Aruscavage P. Joseph , Kolaczkowski Bryan , Bass Brenda L. 
Published: December 2022

AbstractAntiviral defense in ecdysozoan invertebrates requires Dicer with a helicase domain capable of ATP hydrolysis. But despite well-conserved ATPase motifs, human Dicer is incapable of ATP hydrolysis, consistent with a muted role in antiviral defense. To investigate this enigma, we used ancestral protein reconstruction to resurrect Dicer’s helicase in animals and trace the evolutionary trajectory of ATP hydrolysis. Biochemical assays indicated ancient Dicer possessed ATPase function, that like extant invertebrate Dicers, is stimulated by dsRNA. Analyses revealed that dsRNA stimulates ATPase activity by increasing ATP affinity, reflected in Michaelis constants. Deuterostome Dicer-1 ancestor, while exhibiting lower dsRNA affinity, retained ATPase activity; importantly, ATPase activity was undetectable in the vertebrate Dicer-1 ancestor, which had even lower dsRNA affinity. Reverting residues in the ATP hydrolysis pocket was insufficient to rescue hydrolysis, but including additional substitutions distant from the ATPase pocket rescued vertebrate Dicer-1’s ATPase function. Our work suggests Dicer lost ATPase function in the vertebrate ancestor due to loss of ATP affinity, involving motifs distant from the active site, important for coupling dsRNA binding to the active conformation. RLRs important for interferon signaling, and their competition with Dicer for viral dsRNAs, possibly provided incentive to jettison an active helicase in vertebrate Dicer.
Phenotypical Rescue of Bmp15 Deficiency by Mutation of Inhibinα(inha) Provides Novel Clues to How Bmp15 Controls Zebrafish Folliculogenesis
Authors: Zhai Yue , Zhao Cheng , Geng Ruijing , Wu Kun , Yuan Mingzhe , Ai Nana , Ge Wei 
Published: December 2022

AbstractAs an oocyte-specific growth factor, bone morphogenetic protein 15 (BMP15) plays a critical role in controlling folliculogenesis. However, the mechanism of BMP15 action remains elusive. Using zebrafish as the model, we created abmp15mutant using CRISPR/Cas9 and demonstrated thatbmp15deficiency caused a significant delay in follicle activation and puberty onset followed by complete arrest of follicle development at previtellogenic stage without yolk accumulation. The mutant females eventually underwent female-to-male sex reversal to become functional males, which was accompanied by a series of changes in secondary sexual characteristics. Interestingly, the blockade of folliculogenesis and sex reversal inbmp15mutant could be rescued by the loss of inhibin (inha-/-). The follicles of double mutant (bmp15-/-;inha-/-) could progress to mid-vitellogenic stage with yolk accumulation and the fish maintained their femaleness without sex reversal. Transcriptome analysis revealed up-regulation of pathways related to TGF-β signaling and endocytosis in the double mutant follicles. Intriguingly, the expression of inhibin/activin βAa subunit (inhbaa) increased significantly in the double mutant ovary. Further knockout ofinhbaain the triple mutant (bmp15-/-;inha-/-;inhbaa-/-) resulted in the loss of yolk granules again in the oocytes although the follicles could continue to grow beyond the size range of previtellogenic stage. The serum levels of estradiol (E2) and vitellogenin (Vtg) both decreased significantly inbmp15single mutant females, returned to normal in the double mutant (bmp15-/-;inha-/-), but reduced again significantly in the triple mutant (bmp15-/-;inha-/-;inhbaa-/-). E2 treatment could rescue the vitellogenic follicles inbmp15-/-, and fadrozole (a nonsteroidal aromatase inhibitor) treatment blocked yolk accumulation inbmp15-/-;inha-/-fish. In summary, the present study provided comprehensive genetic evidence for the interaction ofbmp15pathways and the activin-inhibin system in regulating folliculogenesis, in particular E2 production from the follicle, Vtg biosynthesis in the liver and its update by the developing oocytes.
Behavioral responses of free flyingDrosophila melanogasterto shiny, reflecting surfaces
Authors: Mathejczyk Thomas , Babo Edouard J. , Schönlein Erik , Grinda Nikolai V. , Greiner Andreas , Okrožnik Nina , Belušič Gregor , Wernet Mathias F. 
Published: December 2022

AbstractActive locomotion plays an important role in the life of many animals since it permits to explore the environment and find vital resources. Most insect species rely on a combination of visual cues such as celestial bodies, landmarks, or linearly polarized light to navigate or to orient themselves in their surroundings. In nature, linearly polarized light can arise either from atmospheric scattering or from reflections off shiny non-metallic surfaces like water or shiny foil. Although multiple reports described different behavioral responses of various insects to such shiny surfaces, little is known about the retinal detectors or the underlying neural circuits. Our goal was to quantify the behavioral responses of free flyingDrosophila melanogaster, a molecular genetic model organism that allows for systematic dissection of neural circuitry. Fruit flies were placed in a custom-built arena with controlled environmental parameters (temperature, humidity, and light intensity). Flight densities and landings were quantified for hydrated and dehydrated fly populations when separately exposed to three different stimuli such as a diffusely-reflecting matt plate, a small patch of shiny foil, versus real water. Our analysis reveals for the first time that flying fruit flies indeed use vision to guide their flight maneuvers around shiny surfaces.
Brain Electrical Bioactivity Informational Specifics in Relation to Behavioural and Cognitive Functions in Children with Learning Difficulties
Authors: Tolmacha Nelli , Pudvosky Konstantin , Vandans Janis , Bondarenko Andrey 
Published: December 2022

AnnotationThe current paper performs a comprehensive assessment of electroencephalogram (EEG) parameters and features of cognitive functions of the brain in children of preschool (6-7) and primary school age (7-8) years with learning difficulties are considered. Spectral and coherent EEG analysis is conducted as well as particularities of gamified orientation in the maze. Spectral analysis of the EEG in children with learning difficulties revealed a speed decrease in the formation of almost all indicators of alpha activity and an increase in the power of slow-wave activity in the EEG, which was more pronounced in the left hemisphere of the brain. EEG coherence analysis revealed early differences in the spatial organization of the coherence function both in EEG rhythms and the cerebral hemispheres. A high level of motor activity in the maze, fragmented perception, unstable attention, low volume of operational memory, and poor optimization of skills in mastering a new space in children with learning difficulties correlated with indicators of age-related neurophysiological immaturity in terms of EEG.
Structural basis for the mechanism and antagonism of receptor signaling mediated by Interleukin-9 (IL-9)
Authors: De Vos Tatjana , Godar Marie , Bick Fabian , Papageorgiou Anna C. , Evangelidis Thomas , Marković Iva , Mortier Eva , Dumoutier Laure , Tripsianes Konstantinos , Blanchetot Christophe , Savvides Savvas N. 
Published: December 2022

AbstractInterleukin-9 (IL-9) is the hallmark cytokine in Th9 immunity and is also central to Innate Lymphocyte 2 (ILC2) biology. Furthermore, receptor signaling mediated by IL-9 has been linked to inflammatory and autoimmune diseases, and cancer. Despite its functional pleiotropy, the structure-function landscape of IL-9 had remained enigmatic. Here, we show via a combination of X-ray crystallography and NMR that human IL-9 adopts a helical bundle fold with unprecedented structural features among helical cytokines, including five disulfide bridges. Binding of IL-9 to the interdomain junction of IL-9Rα results in marked structural changes on the opposite face of IL-9 that prime the binary complex for recruiting the common gamma chain (γc) for signaling. Surprisingly, this tripartite cytokine-receptor assembly displays a markedly lower affinity than the IL-9: IL-9Rα complex, which we trace to distinct features of IL-9Rα that might destabilize the ternary complex. Furthermore, we developed monoclonal antibodies that antagonize IL-9 activity by sterically competing for the binding footprint of IL-9Rα. Collectively, we here provide a structural and mechanistic blueprint to facilitate interrogation and modulation of pleiotropic signaling outputs of IL-9 in physiology and disease.
Temporal Regulation of Organelle Biogenesis
Authors: Dixit Smruti , Aniruddha N , Choubey Sandeep 
Published: December 2022

AbstractOrganelle abundance is tightly regulated in eukaryotic cells in response to external stimuli. The underlying mechanisms responsible for this regulation remains less understood. Time-lapse imaging of fluorescently labelled organelles allow for counting individual organelle copies at a single-cell level. These experiments contain information about the time evolution of distribution of organelle number across a population of cells. To tap onto such data, we build upon a recently proposed kinetic model of organelle biogenesis that explicitly incorporates de novo synthesis, fission, fusion and degradation of organelles. Different limits of this general model correspond to distinct mechanisms of organelle biogenesis. We compute the first two moments of organelle number distribution for these different mechanisms. Interestingly, different mechanisms of biogenesis lead to qualitatively distinct temporal behavior of cell-to-cell variability (noise), thereby allowing us to discern between these mechanisms. Notably, noise in temporal organelle abundance exhibits strikingly more complex behaviour as compared to the steady state. Our modeling framework paves the way for extracting quantitative information about the dynamics of organelle biogenesis from time-lapse experiments that can measure organelle abundance at single-molecule resolution.
Acidophilic nitrification alleviates phosphorus deficiency in hydroponics using biogas digestates
Authors: Sakuma Satoru , Endo Ryosuke , Shibuya Toshio 
Published: December 2022

AbstractBiogas digestates can be applied to hydroponics via nitrification. However, the low solubility of phosphorus in digestates can cause phosphorus deficiency in plants. Here, we hypothesized that acidophilic nitrification might prevent this deficiency by dissolving phosphorus in the digestate. Acidophilic and neutrophilic nitrification were conducted at a pH of 3.27 and 6.25 using biogas digestates from food wastes. Acidophilic nitrification dissolved about 3.5 times more phosphorus than neutrophilic nitrification, but the increased acidity also reduced the nitrification rate, resulting in residual ammonium. We then grew lettuce hydroponically with filtrates of these digestates. The growth performance suggested that the increased phosphorus improved growth and that the residual ammonium did not inhibit it. Acidophilic nitrification was shown to be effective for use in hydroponics, particularly to alleviate phosphorus deficiency. These findings should provide new insights into resource recycling, which is essential in both urban and space environments.Graphical abstract
Aedes aegyptieggs use rewired polyamine and lipid metabolism to survive extreme desiccation
Authors: Prasad Anjana , Sreedharan Sreesa , Bakthavachalu Baskar , Laxman Sunil 
Published: December 2022

AbstractUpon extreme water loss, some organisms pause their life cycles and escape death, in a process called anhydrobiosis. While widespread in microbes, this is uncommon in animals. Mosquitoes of theAedesgenus are vectors for several viral diseases in humans. These mosquitoes lay eggs that survive extreme desiccation and this property greatly enhances geographical expansion of these insects. The molecular principles of egg survival and hatching post-desiccation in these insects remain obscure. In this report, we find that eggs ofAedes aegypti, in contrast to those ofAnopheles stephensi, are true anhydrobiotes.Aedesembryos acquire desiccation tolerance at a late developmental stage. We uncover unique proteome-level changes inAedesembryos during desiccation. These changes reflect a metabolic state with reduced central carbon metabolism, and precise rewiring towards polyamine production, altered lipid levels and enhanced lipid utilization for energy. Using inhibitor-based approaches targeting these processes in blood-fed mosquitoes that lay eggs, we infer a two-step process of anhydrobiosis inAedeseggs, where polyamine accumulation as well as lipid breakdown confer desiccation tolerance, and rapid lipid breakdown fuels energetic requirements enabling the revival of mosquito larvae post rehydration.
Intra- and inter-species interactions drive early phases of invasion in mice gut microbiota
Authors: Gencel Melis , Cofino Gisela Marrero , Hui Cang , Sahaf Zahra , Gauthier Louis , Tsang Derek , Philpott Dana , Ramathan Sheela , Menendez Alfredo , Bershtein Shimon , Serohijos Adrian W.R. 
Published: December 2022

AbstractThe stability and dynamics of ecological communities are dictated by interaction networks typically quantified at the level of species.1–10But how such networks are influenced by intra-species variation (ISV) is poorly understood.11–14Here, we use ~500,000 chromosomal barcodes to track high-resolution intra-species clonal lineages ofEscherichia coliinvading mice gut with the increasing complexity of gut microbiome: germ-free, antibiotic-perturbed, and innate microbiota. By co-clustering the dynamics of intra-species clonal lineages and those of gut bacteria from 16S rRNA profiling, we show the emergence of complex time-dependent interactions betweenE. coliclones and resident gut bacteria. With a new approach, dynamic covariance mapping (DCM), we differentiate three phases of invasion in susceptible communities: 1) initial loss of community stability asE. colienters; 2) recolonization of some gut bacteria; and 3) recovery of stability withE. colicoexisting with resident bacteria in a quasi-steady state. Comparison of the dynamics, stability and fitness from experimental replicates and different cohorts suggest that phase 1 is driven by mutations inE. colibefore colonization, while phase 3 is byde novomutations. Our results highlight the transient nature of interaction networks in microbiomes driven by the persistent coupling of ecological and evolutionary dynamics.One-Sentence SummaryHigh-resolution lineage tracking and dynamic covariance mapping (DCM) define three distinct phases during early gut microbiome invasion.
Neurological Disorder after Severe Pneumonia is Associated with Translocation of Bacteria from Lung to Brain
Authors: Ma Qingle , Yao Chenlu , Wu Yi , Wang Heng , Fan Qin , Yang Qianyu , Xu Jialu , Dai Huaxing , Zhang Yue , Xu Fang , Lu Ting , Wang Chao 
Published: December 2022

ABSTRACTThe neurological disorder is a common feature in patients who recovered from severe acute pneumonia. However, the underline mechanisms remain not very clear. Here we show that these neurological syndromes after severe acute pneumonia are partly attributed to the translocation of bacteria from the lung to the brain during pneumonia. We detected an emerging and increased bacteria in the brain tissue of mice with lipopolysaccharide-induced experimental severe pneumonia. Interestingly, using 16S rDNA amplification sequencing, similarities were found between the brain’s flora species and those of the lungs, indicating the bacteria in the brain may originate from the lung. We also observed the impairment of the lung-blood barrier and brain-blood barrier, simultaneously, allowing lung bacteria invade the brain during pneumonia. An elevated microglia and astrocytes activation signature through bacterial infection-related pathways is observed by single-cell RNA sequencing, indicating a bacteria-induced disruption of brain homeostasis. Rapamycin delivered by platelet-derived extracellular vesicles provides an effective strategy to rescue the dysfunction of microglia and astrocytes, and relief neurological disorders. Collectively, we identify lung bacteria that play a role in altering brain homeostasis, which provides new insight into the mechanism of neurological syndromes after severe pneumonia.
Metformin antiproliferative activity is exclusively mediated by the membrane functional expression of the Chloride Intracellular Channel 1 in glioblastoma stem cells
Authors: Verduci Ivan , Cianci Francesca , Cazzoli Riccardo , Cannavale Gaetano , Veronesi Marina , Balboni Beatrice , Ranucci Matteo , Palloni Luca Maria Giovanni , Richichi Cristina , Faletti Stefania , Osti Daniela , Ailuno Giorgia , Caviglioli Gabriele , Tacconi Carlotta , Girotto Stefania , Barbieri Federica , Fantin Alessandro , Cavalli Andrea , Pelicci Giuliana , Florio Tullio , Minucci Saverio , Mazzanti Michele 
Published: December 2022

AbstractMetformin is the first-line drug for type-2 diabetes. Retrospective analyses, based on diabetic patients’ clinical data, demonstrate that daily assumption of metformin reduces the incidence of several kinds of solid tumors. Even though it is widely agreed that metformin must be internalized to accomplish its pharmacological activity, direct evidence about metformin membrane permeability and/or the presence of a specific membrane receptor in cancer cells is still missing. Here, we show that the transmembrane form of Chloride Intracellular Channel 1 (tmCLIC1) works as a privileged metformin receptor in glioblastoma stem-like cells. We found that metformin impairs tmCLIC1 activity by a specific binding coordinated by arginine 29. Its mutation, preventing metformin to bind and block tmCLIC1, abolishes the biguanide inhibition of glioblastoma cell proliferation in 2D and 3D models and metformin dependent effect on mitochondrial respiration. In addition, we demonstrate the direct binding between the drug and its target, and byin vivoexperiments on zebrafish embryos and mice orthotopically engrafted with glioblastoma cells and treated with metformin, we prove that metformin binding to tmCLIC1 is crucial for metformin antineoplastic effect. Considering tmCLIC1’s contribution to glioblastoma progression, the present work provides the fundaments for future development of strategies aimed at improving metformin-tmCLIC1 interaction to further increase metformin therapeutic potential.