bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural basis for late maturation steps of the human mitoribosomal large subunit
Authors: Cipullo Miriam , Gesé Genís Valentín , Khawaja Anas , Hällberg B. Martin , Rorbach Joanna 
Published: March 2021

AbstractMitochondrial ribosomes (mitoribosomes) synthezise a critical set of proteins essential for oxidative phosphorylation. Therefore, their function is vital to cellular energy supply and mitoribosomal defects give rise to a large and diverse group of human diseases1. The architecture of mitoribosomes is strikingly different from that of their bacterial and eukaryotic cytosolic counterparts and display high divergence between species2–6. Mitoribosome biogenesis follows distinct molecular pathways that remain poorly understood. Here, we determined the cryo-EM structures of mitoribosomes isolated from human cell lines with either depleted or overexpressed mitoribosome assembly factor GTPBP5. This allowed us to capture consecutive steps during mitoribosomal large subunit (mt-LSU) biogenesis that involve normally short-lived assembly intermediates. Our structures provide important insights into the last steps of 16S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, which require the coordinated action of nine assembly factors. We show that mammalian-specific MTERF4 contributes to the folding of 16S rRNA, allowing 16S rRNA methylation by MRM2, while GTPBP5 and NSUN4 promote fine-tuning rRNA rearrangments leading to PTC formation. Moreover, our data reveal an unexpected role for the elongation factor mtEF-Tu in mt-LSU assembly, in which mt-EF-Tu interacts with GTPBP5 in a manner similar to its interaction with tRNA during translational elongation. Together, our approaches provide detailed understanding of the last stages of mt-LSU biogenesis that are unique to mammalian mitochondria.
Diversification of Transcription Factor NF-κB in Protists
Authors: Williams Leah M. , Sridhar Sainetra , Samaroo Jason , Adindu Ebubechi K. , Addanki Anvitha ,   BB522 Molecular Biology Laboratory, Aguirre Carrión Pablo J. , DiRusso Christopher J. , Rodriguez-Sastre Nahomie , Siggers Trevor , Gilmore Thomas D. 
Published: March 2021

AbstractIn this report, we investigate the evolution of transcription factor NF-κB by examining its structure, activity, and regulation in two protists using phylogenetic, cellular, and biochemical techniques. InCapsaspora owczarzaki(Co), we find that full-length NF-κB has an N-terminal DNA-binding domain and a C-terminal Ankyrin (ANK) repeat inhibitory domain, and its DNA-binding activity is more similar to metazoan NF-κB rather than Rel proteins. As with mammalian NF-κB proteins, removal of the ANK repeats is required forCo-NF-κB to enter the nucleus, bind DNA, and activate transcription. However, C-terminal processing ofCo-NF-κB is not induced by co-expression of IKK in human cells. Exogenously expressedCo-NF-κB localizes to the nucleus inCocells. NF-κB mRNA and DNA-binding levels differ across three life stages ofCapsaspora, suggesting distinct roles for NF-κB in these life stages. RNA-seq and GO analyses identify possible gene targets and biological functions ofCo-NF-κB. We also show that three NF-κB-like proteins from the choanoflagellateAcanthoeca spectabilis(As) all consist of primarily the N-terminal conserved Rel Homology domain sequences of NF-κB, and lack C-terminal ANK repeats. All threeAs-NF-κB proteins constitutively enter the nucleus of human and Co cells, but differ in their DNA-binding and transcriptional activation activities. Furthermore, all threeAs-NF-κB proteins can form heterodimers, indicating that NF-κB diversified into multi-subunit families at least two times during evolution. Overall, these results present the first functional characterization of NF-κB in a taxonomic kingdom other than Animalia and provide information about the evolution and diversification of this biologically important transcription factor.SignificanceThese results represent the first functional characterization of the biologically important transcription factor NF-κB in a taxonomic kingdom other than Animalia. As such, they provide information on the evolutionary origins and basal diversification of NF-κB outside of metazoans. These results suggest that NF-κB plays life stage-specific roles inCapsaspora, the closest unicellular ancestor to all metazoans. Finally, the analysis of three NF-κB proteins in a single choanoflagellate indicates that choanoflagellates have subclasses of NF-κBs, which can form heterodimers, suggesting that NF-κB subunit expansion and diversification has occurred at least twice in evolution.
Anatomical and Functional Gradients Shape Dynamic Functional Connectivity in the Human Brain
Authors: Kong Xiaolu , Kong Ru , Orban Csaba , Peng Wang , Zhang Shaoshi , Anderson Kevin , Holmes Avram , Murray John D. , Deco Gustavo , van den Heuvel Martijn , Yeo B.T. Thomas 
Published: March 2021

AbstractLarge-scale biophysical circuit models can provide mechanistic insights into the fundamental micro-scale and macro-scale properties of brain organization that shape complex patterns of spontaneous brain activity. By allowing local synaptic properties to vary across brain regions, recent large-scale circuit models have demonstrated better fit to empirical observations, such as inter-regional synchrony averaged over several minutes, i.e. static functional connectivity (FC). However, most previous models do not capture how inter-regional synchrony patterns vary over timescales of seconds, i.e., time-varying FC dynamics. Here we developed a spatially-heterogeneous large-scale dynamical circuit model that allowed for variation in local circuit properties across the human cortex. We showed that parameterizing local circuit properties with both anatomical and functional gradients was necessary for generating realistic static and dynamical properties of resting-state fMRI activity. Furthermore, empirical and simulated FC dynamics demonstrated remarkably similar sharp transitions in FC patterns, suggesting the existence of multiple attractors. We found that time-varying regional fMRI amplitude tracked multi-stability in FC dynamics. Causal manipulation of the large-scale circuit model suggested that sensory-motor regions were a driver of FC dynamics. Finally, the spatial distribution of sensory-motor drivers matched the principal gradient of gene expression that encompassed certain interneuron classes, suggesting that heterogeneity in excitation-inhibition balance might shape multi-stability in FC dynamics.
GTP and lipids control self-assembly and functional promiscuity of Dynamin2 molecular machinery
Authors: Espadas Javier , Bocanegra Rebeca , Martinez-Galvez Juan Manuel , Largo Eneko , Baños-Mateos Soledad , Arrasate Pedro , Guisasola Julene Ormaetxea , Velasco-Olmo Ariana , Lillo Javier Vera , Ibarra Borja , Shnyrova Anna V. , Frolov Vadim A. 
Published: March 2021

AbstractDynamin2 GTPase (Dyn2) is a crucial player in clathrin-mediated endocytosis. Dyn2 is tetrameric in cytoplasm and self-assembles into functional units upon membrane binding. How the curvature activities and functionality of Dyn2 emerge during self-assembly and are regulated by lipids remains unknown. Here we reconstituted the Dyn2 self-assembly process using membrane nanotubes (NT) and vesicles and characterized it using single- molecule fluorescence microscopy, optical tweezers force spectroscopy and cryo-electron microscopy. On NTs, Dyn2 first forms small subhelical oligomers, which are already curvature active and display pronounced curvature sensing properties. Conical lipids and GTP promote their further self-assembly into helical machinery mediating the NT scission. In the presence of large unilamellar vesicles (LUVs), an alternative self- assembly pathway emerges where the subhelical oligomers form membrane tethering complexes mediating LUV-NT binding. Reconstitution of tethering in the LUV system revealed that lipid mixing is controlled by conical lipid species, divalents, GTP, and SH3 binding partners of Dyn2. In membranes with a high content of lipids with negative intrinsic curvature, cryo-EM revealed putative membrane contact sites made by Dyn2 clusters. On such membranes, with GTP lowered to 0.2 mM, both membrane fission and tethering activities become possible, indicating functional promiscuity of Dyn2.We conclude that GTP and lipids control both extent and topology of Dyn2 functional self-assembly. The function of Dyn2 oligomers evolves from curvature sensing, seen in subhelical Dyn2 oligomers, to curvature creation and fission, seen in Dyn2 helices. Under specific circumstances, such as downregulation of SH3 partners of Dyn2 and GTP depletion, membrane tethering activity can emerge in membrane systems enriched with conical lipids. Hence the Dyn2 functionality is actively adapted to lipidome, explaining its large habitat in the cells and tissues.
Intertissue mechanical interactions shape the olfactory circuit in zebrafish
Authors: Monnot P , Gangatharan G , Baraban M , Pottin K , Cabrera M , Bonnet I , Breau MA 
Published: March 2021

AbstractWhile the chemical signals guiding neuronal migration and axon elongation have been extensively studied, the influence of mechanical cues on these processes remains poorly studiedin vivo. Here, we investigate how mechanical forces exerted by surrounding tissues steer neuronal movements and axon extension during the morphogenesis of the olfactory placode in zebrafish. We mainly focus on the mechanical contribution of the adjacent eye tissue, which develops underneath the placode through extensive evagination and invagination movements. Using quantitative analysis of cell movements and biomechanical manipulations, we show that the developing eye exerts lateral traction forces on the olfactory placode through extracellular matrix, mediating proper morphogenetic movements and axon extension within the placode. Our data shed new light on the key participation of intertissue mechanical interactions in the sculpting of neuronal circuits.
Mobile elements habouring heavy metal and bacitracin resistance cassettes are common amongListeria monocytogenespersisting on dairy farms
Authors: Castro Hanna , Douillard Francois , Korkeala Hannu , Lindström Miia 
Published: March 2021

AbstractListeria monocytogenesis a food-borne pathogen and a resilient environmental saprophyte. Dairy farms are a reservoir ofL. monocytogenesand strains can persist on farms for years. Here, we sequenced the genomes of 250L. monocytogenesisolates to investigate the persistence and mobile genetic elements ofListeriainhabiting dairy farms. We performed a SNP-based phylogenomic analysis to identify 14 monophyletic clades ofL. monocytogenesthat persistent on the farms for ≥ 6 months. We found that prophages and other mobile genetic elements were on average more numerous among isolates in persistent than nonpersistent clades, and demonstrated that resistance genes against bacitracin, arsenic and cadmium were significantly more prevalent among isolates in persistent than nonpersistent clades. We identified a diversity of mobile elements among the 250 farm isolates, including three novel plasmids, three novel transposons and a novel prophage harbouring cadmium resistance genes. Several of the mobile elements we identified inListeriawere identical to the mobile elements ofEnterococci, indicative of recent transfer between these genera. Finally, we demonstrated that the CRISPR-casIIa system and a type II restriction-modification system were negatively associated with persistence on farms. Our findings suggest that mobile elements support the persistence ofL. monocytogeneson dairy farms and thatL. monocytogenesinhabiting the agroecosystem is a potential reservoir of mobile elements that may spread to the food industry.ImportanceAnimal derived raw materials are an important source ofL. monocytogenesfor the food industry. Knowledge of the factors contributing to the pathogen’s transmission and persistence on farms are essential for designing effective strategies against the spread of the pathogen from farm to fork. An increasing body of evidence suggests that mobile genetic elements support the adaptation and persistence ofL. monocytogenesin the food industry, as these elements contribute to the dissemination of genes encoding favourable phenotypes, such as resilience against biocides and thermal stress. Understanding the role of farms as a potential reservoir of these elements is needed for managing the transmission of mobile elements across the food chain. BecauseL. monocytogenescoinhabits the farm ecosystem with a diversity of other bacterial species, it is important to assess the degree to which genetic elements are exchanged betweenListeriaand other species, as such exchanges may contribute to rise the novel resistance phenotypes.
Low pathogenic avian influenza virus infection retards colon microbiome diversification in two different chicken lines
Authors: Chrzastek Klaudia , Leng Joy , Zakaria Mohammad Khalid , Bialy Dagmara , La Ragione Roberto , Shelton Holly 
Published: March 2021

AbstractA commensal microbiome regulates and is in turn regulated by viruses during host infection which can influence virus infectivity. In this study, analysis of colon microbiome population changes following a low pathogenicity avian influenza virus (AIV) of the H9N2 subtype infection of two different chicken breeds was conducted. Using 16S rRNA sequencing and subsequent data analysis we found reduced microbiome alpha diversity in the acute period of AIV infection (day 2-3) in both Rhode Island Red and VALO chicken lines. From day 4 post infection a gradual increase in diversity of the colon microbiome was observed, but the diversity did not reach the same level as in uninfected chickens by day 10 post infection, suggesting that AIV infection retards the natural accumulation of colon microbiome diversity, which may further influence chicken health following recovery from infection. Beta diversity analysis indicated differences in diversity between the chicken lines during and following acute influenza infection suggesting the impact of host gut microflora dysbiosis following H9N2 influenza virus infection could differ for different breeds.
Echolocation reverses information flow in a cortical vocalization network
Authors: García-Rosales Francisco , López-Jury Luciana , Gonzalez-Palomares Eugenia , Wetekam Johannes , Cabral-Calderín Yuranny , Kiai Ava , Kössl Manfred , Hechavarría Julio C. 
Published: March 2021

AbstractThe mammalian frontal and auditory cortices are important for vocal behaviour. Here, using local field potential recordings, we demonstrate for the first time that the timing and spatial pattern of oscillations in the fronto-auditory cortical network of vocalizing bats (Carollia perspicillata) predict the purpose of vocalization: echolocation or communication. Transfer entropy analyses revealed predominantly top-down (frontal-to-auditory cortex) information flow during spontaneous activity and pre-vocal periods. The dynamics of information flow depended on the behavioural role of the vocalization and on the timing relative to vocal onset. Remarkably, we observed the emergence of predominantly bottom-up (auditory-to-frontal cortex) information transfer patterns specific echolocation production, leading to self-directed acoustic feedback. Electrical stimulation of frontal areas selectively enhanced responses to echolocation sounds in auditory cortex. These results reveal unique changes in information flow across sensory and frontal cortices, potentially driven by the purpose of the vocalization in a highly vocal mammalian model.
Microbial diversity in raw milk and Sayram Ketteki from southern of Xinjiang, China
Authors: Gao DongLa , Wang Weihua , Han ZhanJiang , Xi Qian , Guo RuiCheng , Kuang PengCheng , Li DongLiang 
Published: March 2021

AbstractRaw milk and fermented milk are rich in microbial resources, which are essential for the formation of texture, flavor and taste. In order to gain a deeper knowledge of the bacterial and fungal community diversity in local raw milk and home-made yogurts from Sayram town, Baicheng county, Akesu area, southern of Xinjiang, China,30 raw milk and 30 home-made yogurt samples were collected and experiment of high-throughput sequencing was implemented.The results of experiments revealed the species of fungi in raw milk was the most, and the species of bacteria in fermented milk was the least.Based on principal component analysis (PCA), it was found that the bacterial and fungal community structure differed in samples from two types of dairy products.And the presence of 15 bacterial and 12 fungal phyla, comprising 218 bacterial and 495 fungal genera respectively, among all samples. Firmicutes and Ascomycota,Lactobacillus and Candida were the predominant phyla and genera of bacteria and fungi, respectively. The results indicated that the microbial community of raw milk differs from home-made yogurts due to sampling location and manufacturing process. The study suggested that high-throughput sequencing could provide a better understanding of microbiological diversity as well as lay a theoretical foundation for selecting beneficial microbial resources from this natural yogurt.
Effect of nandrolone decanoate on healing of experimentally induced radial nonunion in rabbits (Oryctolagus cuniculus)
Authors: Dissenha Adrielly , Minto Bruno Watanabe , Calciolari Karina , Sargi Laís Fernanda , do Nascimento Lismara Castro , Del Lama Rocha Fabiana , Galindez Julián Andrés Sanjuán , de Lucena Dayvid Vianêis Farias , Dias Luis Gustavo Gosuen Gonçalves 
Published: March 2021

ABSTRACTThe aim of this study was to evaluate the effect of nandrolone decanoate (ND) on treatment of bone nonunion in the radius of rabbits. Thirty-one, young adult, New Zealand White rabbits (Oryctolagus cuniculus) were allocated to one of four groups: nandrolone males (NMG), nandrolone females (NFG), placebo males (NPM), and placebo females (NPF). After bone nonunion of a 10 mm ostectomy of the radius was confirmed (45 days after surgery), the animals in the NMG and NFG groups received 10 mg/kg ND intramuscular once a week for four weeks, while placebo groups received intramuscular 0.9% NaCl solution. Radiographic, histopathologic, and densitometric parameters (DXA) were used to compared groups.ResultsNo significant differences were observed radiographically. However, ND groups showed greater area (P=0.0258) and BMC (P=0.0140) in the densitometric evaluation. Histologically, the placebo group showed a predominance of primary bone tissue. Whereas, lamellary organizations of secondary bone and the presence of fibrocartilage were found in the ND group (P =0.006). In conclusion, ND promoted bone regeneration after the creation of a large defect in the radius of rabbits.
Primary brain cell infection byToxoplasma gondiireveals the extent and dynamics of parasite differentiation and its impact on neuron biology
Authors: Mouveaux Thomas , Roger Emmanuel , Gueye Alioune , Eysert Fanny , Huot Ludovic , Grenier-Boley Benjamin , Lambert Jean-Charles , Gissot Mathieu 
Published: March 2021

ABSTRACTToxoplasma gondiiis a eukaryotic parasite that forms latent cysts in the brain of immunocompetent individuals. The latent parasite infection of the immune-privileged central nervous system is linked to most complications. With no drug currently available to eliminate the latent cysts in the brain of infected hosts, the consequences of neurons’ long-term infection are unknown. It has long been known thatT. gondiispecifically differentiates into a latent form (bradyzoite) in neurons, but how the infected neuron responds to the infection remains to be elucidated. We have established a newin vitromodel resulting in the production of mature bradyzoite cysts in brain cells. Using dual, host and parasite RNA-seq, we characterized the dynamics of differentiation of the parasite, revealing the involvement of key pathways in this process. Moreover, we identified how the infected brain cells responded to the parasite infection revealing the drastic changes that take place. We showed that neuronal-specific pathways are strongly affected, with synapse signaling being particularly affected, especially glutamatergic synapse signaling. The establishment of this newin vitromodel allows investigating both the dynamics of parasite differentiation and the specific response of neurons to the long-term infection by this parasite.
Arginine induced Streptococcus gordonii biofilm detachment using a novel rotating-disc rheometry method
Authors: Gloag Erin S. , Wozniak Daniel J. , Wolf Kevin L. , Masters James G. , Daep Carlo Amorin , Stoodley Paul 
Published: March 2021

AbstractOral diseases are one of the most common pathologies affecting human health. These diseases are typically associated with dental plaque-biofilms, through either build-up of the biofilm or dysbiosis of the microbial community. Arginine can disrupt dental plaque-biofilms, and maintain plaque homeostasis, making it an ideal therapeutic to combat the development of oral disease. Despite our understanding of the actions of arginine towards dental plaque-biofilms, it is still unclear how or if arginine effects the mechanical integrity of the dental plaque-biofilm. Here we adapted a rotating-disc rheometry assay, which is routinely used in marine microbial ecology, to study how arginine treatment of Streptococcus gordonii biofilms influences biofilm detachment from surfaces. We demonstrate that the assay is highly sensitive at quantifying the presence of biofilm and the detachment or rearrangement of the biofilm structure as a function of shear stress. We demonstrate that arginine treatment leads to earlier detachment of the biofilm, indicating that arginine treatment weakens the biofilm, making it more suspectable to removal by shear stresses. Our results add to the understanding that arginine targets biofilms by multifaceted mechanisms, both metabolic and physical, further promoting the potential of arginine as an active compound in dentifrices to maintain oral health.
Modeling the three-way feedback between cellular contractility, actin polymerization, and adhesion turnover resolves the contradictory effects of RhoA and Rac1 on endothelial junction dynamics
Authors: McEvoy Eoin , Sneh Tal , Moeendarbary Emad , Marino Gloria E. , Chen Xingyu , Escribano Jorge , Spill Fabian , Garcia-Aznar Jose Manuel , Weeraratna Ashani T. , Svitkina Tatyana M. , Kamm Roger D. , Shenoy Vivek B. 
Published: March 2021

AbstractThe formation and recovery of gaps in the vascular endothelium governs a wide range of physiological and pathological phenomena, from angiogenesis to atherosclerosis and tumor cell extravasation. However, the interplay between the mechanical and signaling processes that drive dynamic behavior in vascular endothelial cells is not well understood. In this study, we propose a chemo-mechanical model to investigate the maintenance of endothelial junctions as dependent on the crosstalk between actomyosin contractility, VE-cadherin bond turnover, and actin polymerization, which mediate the forces exerted on the cell-cell interface. Our theoretical model reveals that active cell tension can stabilize cadherin bonds within an adhesion, but excessive RhoA signaling can drive bond dissociation and junction failure. While Rac1-mediated actin polymerization aids gap closure, high levels of Rac1 may also facilitate junction weakening. Combining the modeling framework with novel experiments, we identify how dynamic rupture and heal cycles emerge and, further, describe why gaps tend to localize at multi-cell contacts. Beyond, our analysis also indicates that a critical balance between RhoA and Rac1 expression is required to maintain junction stability and limit endothelial dysfunction. The model predicts how pharmacological modulation of actin polymerization and cell contractility impacts junction stability, with predictions subsequently validated experimentally. Our proposed framework can help guide the development of therapeutics that target the Rho family of GTPases and downstream active mechanical processes.