bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical activity and aerobic fitness show different associations with brain processes underlying anticipatory selective visuospatial attention in adolescents
Authors: Hernández Doris , Heinilä Erkka , Muotka Joona , Ruotsalainen Ilona , Lapinkero Hanna-Maija , Syväoja Heidi , Tammelin Tuija H. , Parviainen Tiina 
Published: July 2020

ABSTRACTUnderlying brain processes of exercise-related benefits on executive functions and the specific contribution of physical activity vs. aerobic fitness are poorly understood, especially during adolescence. We explored whether and how physical activity and aerobic fitness are associated with selective attention and the oscillatory dynamics induced by an anticipatory spatial cue. Further, we studied whether the link between physical exercise level and cognitive control in adolescents is mediated by the task-related oscillatory activity. Magnetoencephalographic alpha oscillations during a modified Posner’s cueing paradigm were measured in 59 adolescents (37 females and 22 males, 12 to 17 years). Accelerometer-measured physical activity and aerobic fitness (20-m shuttle run test) were used to divide the sample into higher and lower performing groups. The interhemispheric alpha asymmetry during selective attention was larger in the high than in the low physical activity group, but there was no difference between the high and low aerobic fitness groups. Exploratory mediation analysis suggested that anticipatory interhemispheric asymmetry mediates the association between physical activity status and drift rate in the selective attention task. Higher physical activity was related to increased cue-induced asymmetry, which in turn was associated with less efficient processing of information. Behaviorally, higher physically active males showed stronger dependence on the cue while higher fit females showed more efficient processing of information. Our findings suggest that physical activity may be associated with a neural marker of anticipatory attention in adolescents. These findings have implications for understanding the varying results on the association between physical activity and attention in adolescents.HIGHLIGHTSPhysical activity and aerobic fitness link differently with attention in adolescents.Higher physical activity relates with stronger cue-induced oscillatory asymmetry.Brain hemispheric interaction mediates the link between physical activity and attention.
Single-Molecule Micromanipulation Studies of Methylated DNA
Authors: Zaichuk T. , Marko J. F. 
Published: July 2020

AbstractCytosine methylated at the 5-carbon position is the most widely studied reversible DNA modification. Prior findings indicate that methylation can alter mechanical properties. However, those findings were qualitative and sometimes contradictory, leaving many aspects unclear. By applying single-molecule magnetic force spectroscopy techniques allowing for direct manipulation and dynamic observation of DNA mechanics and mechanically driven strand separation, we investigated how CpG and non-CpG cytosine methylation affects DNA micromechanical properties. We quantitatively characterized DNA stiffness using persistence length measurements from force-extension curves in the nanoscale length regime and demonstrated that cytosine methylation results in increased DNA flexibility (i.e., decreased persistence length). In addition, we observed the preferential formation of plectonemes over unwound single-stranded “bubbles” of DNA, under physiologically relevant stretching forces and supercoiling densities. The stiffness and high structural stability of methylated DNA is likely to have significant consequences on the recruitment of proteins recognizing cytosine methylation and DNA packaging.Statement of SignificanceDespite countless structural and functional studies of DNA methylation, a key epigenetic mark in higher organisms, research towards the understanding of DNA intrinsic structural properties in the context of methylation layout representing different epigenetic landscapes is still in its initial stage. We utilize single molecule spectroscopy to analyze the effect of sparse symmetric and asymmetric 5-mC modification on the mechanical stability of long double-stranded DNA. Our findings establish that at physiologically relevant forces and supercoiling densities increased DNA flexibility of non-CpG methylated DNA translates to the high structural stability.
Exosomes are predominantly loaded with mRNA transcript encoding cytoplasmic proteins and exclude mRNA transcript encoding nuclear proteins
Authors: Haque Shabirul , Vaiselbuh Sarah R. 
Published: July 2020

AbstractExosomes are nanovesicles (∼30-150 nm diameters) released via an endocytic pathway in almost all mammalian cell types. Exosomes are composed of a lipid bilayer membrane that encloses RNA, miRNA, proteins and DNA. This manuscript unravels how exosome cargo is collected by a highly precise process delineating two separate mRNA transcript entities encoding cytoplasmic and nuclear proteins separately.Ultracentrifuge isolated exosomes were directly converted into cDNA (Exo-cDNA), by a method developed in our laboratory. Cellular RNA was extracted from each cell line and cDNA was prepared (Cell-cDNA). We amplified mRNA transcripts translatingcytoplasmicproteins CD10 and CXCR4 and mRNA transcripts translatingnuclearproteins such as proliferating cell nuclear antigen (PCNA), CREB-BP, activation induced cytidine deaminase (AID), and terminal deoxynucleotidyl transferase (TdT). We amplified all four different mRNA transcripts (PCNA, CREB-BP, AID, and TdT) fromcellularcDNA but none fromexosomalcDNA (Exo-cDNA). These findings suggest that exosomes carry mRNA transcripts encodingcytoplasmicproteins only but mRNA transcripts encodingnuclearproteins could not be detected. This important observation could prove to be crucial for the exosome research community since it sheds light on one of the limitations relating to the use of exosomes as biomarkers in cancer biology and other diseases.Graphical Abstract
Disease-Linked Super-Trafficking of a Mutant Potassium Channel
Authors: Huang Hui , Chamness Laura M. , Vanoye Carlos G. , Kuenze Georg , Meiler Jens , George Alfred L. , Schlebach Jonathan P. , Sanders Charles R. 
Published: July 2020

ABSTRACTGain-of-function (GOF) mutations in the KCNQ1 voltage-gated potassium channel can induce cardiac arrhythmia. We tested whether any of the known GOF disease mutations in KCNQ1 act by increasing the amount of KCNQ1 that reaches the cell surface—“super-trafficking”. We found that levels of R231C KCNQ1 in the plasma membrane are 5-fold higher than wild type KCNQ1. This arises from both enhanced translocon-mediated membrane integration of the S4 voltage-sensor helix and an energetic linkage of C231 with the V129 and F166 side chains. Whole-cell electrophysiology recordings confirmed that R231C KCNQ1 in complex with KCNE1 is constitutively active, but also revealed the single channel activity of this mutant to be only 20% that of WT. The GOF phenotype associated with R231C therefore reflects the net effects of super-trafficking, reduced single channel activity, and constitutive channel activation. These investigations document membrane protein super-trafficking as a contributing mechanism to human disease.
Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry
Authors: Aguilar-Pineda Jorge Alberto , Albaghdadi Mazen , Jiang Wanlin , Lopez Karin J. Vera , Del-Carpio Gonzalo Davila , Valdez Badhin Gómez , Lindsay Mark E. , Malhotra Rajeev , Lino Cardenas Christian L. 
Published: July 2020

AbstractEmerging evidence suggests that males are more susceptible to severe infection by the SARS-CoV-2 virus than females. A variety of mechanisms may underlie the observed gender-related disparities including differences in sex hormones. However, the precise mechanisms by which female sex hormones may provide protection against SARS-CoV-2 infectivity remains unknown. Here we report new insights into the molecular basis of the interactions between the SARS-CoV-2 spike (S) protein and the human ACE2 receptor. We further observed that glycosylation of the ACE2 receptor enhances SARS-CoV-2 infectivity. Importantly estrogens can disrupt glycan-glycan interactions and glycan-protein interactions between the human ACE2 and the SARS-CoV2 thereby blocking its entry into cells. In a mouse model, estrogens reduced ACE2 glycosylation and thereby alveolar uptake of the SARS-CoV-2 spike protein. These results shed light on a putative mechanism whereby female sex hormones may provide protection from developing severe infection and could inform the development of future therapies against COVID-19.
High-Pressure NMR Reveals Volume and Compressibility Differences Between Two Stably Folded Protein Conformations
Authors: Xu Xingjian , Gagné Donald , Aramini James M. , Gardner Kevin H. 
Published: July 2020

ABSTRACTProteins often interconvert between different conformations in ways critical to their function. While manipulating such equilibria for biophysical study is often challenging, the application of pressure is a potential route to achieve such control by favoring the population of lower volume states. Here, we use this feature to study the interconversion of ARNT PAS-B Y456T, which undergoes a dramatic beta-strand slip as it switches between two stably-folded conformations. Coupling high pressure and biomolecular NMR, we obtained the first quantitative data testing two key hypotheses of this process: the slipped conformation is both smaller and less compressible than the wildtype equivalent, and the interconversion proceeds through a chiefly-unfolded intermediate state. Our work exemplifies how these approaches, which can be generally applied to protein conformational switches, can provide unique information that is not easily accessible through other techniques.
Dissection of the corticotroph transcriptome in a mouse model of glucocorticoid-induced suppression of the HPA axis
Authors: Romanò N , Duncan PJ , McClafferty H , Nolan O , Ding Q , Homer NZ , Le Tissier P , Walker BR , Shipston MJ , Chambers TJG 
Published: July 2020

ABSTRACTGlucocorticoids (GC) are prescribed for periods >3 months to 1-3% of the UK population; 10-50% of these patients develop hypothalamus-pituitary-adrenal (HPA) axis suppression, which may last over 6 months and is associated with morbidity and mortality. Recovery of higher nodes of the axis is necessary for recovery of adrenal function. We developed a mouse model of Dexamethasone (DEX)-induced HPA axis dysfunction in order to further explore recovery in the pituitary. Adult male C57BL6/J or those crossed withPomc-eGFP mice were randomly assigned to receive DEX (~0.4 mg/kg bodyweight/day) or vehicle via drinking water for 4 weeks following which treatment was withdrawn. Tissues were harvested at 0, 1, and 4 weeks following withdrawal of treatment. Corticotrophs were isolated fromPomc-eGFP pituitaries using FACS, and RNA extracted for RNA-seq. DEX treatment suppressed corticosterone production, which remained partially suppressed at least 1 week following DEX withdrawal. In the adrenal, at time 0,Hsd3b2, Cyp11a1, andMc2rmRNA levels were significantly reduced, withMc2randCyp11a1remaining reduced 1 week following DEX withdrawal. The corticotroph transcriptome was modified by DEX treatment with some differences between groups persisting 4 weeks following withdrawal. No genes supressed by DEX exhibited ongoing attenuation 1 and 4 weeks following withdrawal, whilst only 2 genes were upregulated and remained so following withdrawal. A pattern of rebound at 1 and 4 weeks was observed in 14 genes that increased following suppression, and 6 genes that were reduced by DEX and then increased. Chronic GC treatment may induce persistent changes in the pituitary that may influence future response to GC treatment or stress.
Intrinsically disordered protein ensembles shape evolutionary rates revealing conformational patterns
Authors: Palopoli Nicolas , Marchetti Julia , Monzon Alexander M. , Zea Diego J. , Tosatto Silvio C.E. , Fornasari Maria S. , Parisi Gustavo 
Published: July 2020

AbstractIntrinsically disordered proteins (IDPs) lack stable tertiary structure under physiological conditions. The unique composition and complex dynamical behaviour of IDPs make them a challenge for structural biology and molecular evolution studies. Using NMR ensembles, we found that IDPs evolve under a strong site-specific evolutionary rate heterogeneity, mainly originated by different constraints derived from their inter-residue contacts. Evolutionary rate profiles correlate with the experimentally observed conformational diversity of the protein, allowing the description of different conformational patterns possibly related to their structure-function relationships. The correlation between evolutionary rates and contact information improves when structural information is taken not from any individual conformer or the whole ensemble, but from combining a limited number of conformers. Our results suggest that residue contacts in disordered regions constrain evolutionary rates to conserve the dynamic behaviour of the ensemble and that evolutionary rates can be used as a proxy for the conformational diversity of IDPs.Significance StatementIntrinsically disordered proteins (IDPs) challenge the structure-function relationship paradigm. In this work we found that individual sites of IDPs evolve under a strong rate heterogeneity, mainly due to the structural constraints imposed by contacts between their residues. This can be better explained if the contacts are taken from selected subsets of their alternative native conformations, rather than from individual conformations or the whole native ensemble. From an evolutionary point of view, this result indicates that experimentally-based ensembles are redundant. We also observed that the evolutionary rates follow the structural variability between conformers, unveiling conformational preferences. Our results set the stage for establishing novel evolutionary-based methods to study IDP ensembles.
Gut Phageome Analysis Reveals Disease-Specific Hallmarks in Childhood Obesity
Authors: Bikel Shirley , López-Leal Gamaliel , Cornejo-Granados Fernanda , Gallardo-Becerra Luigui , Sánchez Filiberto , Equihua-Medina Edgar , Ochoa-Romo Juan Pablo , López-Contreras Blanca Estela , Canizales-Quinteros Samuel , Leyva Adrian Ochoa 
Published: July 2020

AbstractChanges in the composition of the human gut microbiome are recognized to have a significant association with obesity and metabolic syndrome. Mexico leads worldwide childhood-obesity rankings representing an epidemic problem for public health. To this date, it is still unclear how the gut phageome, the bacteriophage component of the virome, influences childhood obesity and obesity with metabolic syndrome. We characterized the gut phageome of 28 school-age children with healthy normal-weight (NW), obese (O), and obese with metabolic syndrome (OMS) profiles, using metagenomic sequencing of virus-like particles (VLPs) from fecal samples. Viromes derived from VLPs were mainly dominated by Caudovirales, and only Inoviridae family was significantly increased in obesity. The three groups showed a similar number of VLPs, while a significant increase in phage richness and diversity was found in obesity groups compared NW. Few phage contigs dominated the phageome composition in NW, being increased in obesity groups. Interestingly, the majority of the phageome was shared among all individuals, establishing a core and common phageome, which abundances correlated with anthropometric and biochemical traits and bacteria previously associated with obesity and metabolic syndrome. We also established a healthy core phageome shared in >80% of NW samples, with a decreased prevalence in the O and OMS groups. Our data support that changes in the gut phageome may contribute to obesity and metabolic syndrome development via bacterial dysbiosis. We consider the phageome characterization provides the basis for novel diagnostic and therapeutic strategies for managing obesity and preventing metabolic syndrome development in obese children through potential phage manipulation. To the best of our knowledge, this study represents the most in-depth sequenced dataset of human bacteriophages, demonstrating for the first time that alterations of the gut phageome characterize obesity.
Nanoscale curvature promotes high yield spontaneous formation of cell-mimetic giant vesicles
Authors: Pazzi Joseph , Subramaniam Anand Bala 
Published: July 2020

AbstractTo date, surface-assisted assembly of cell-like giant vesicles use planar surfaces and require the application of electric fields or dissolved molecules to obtain adequate yields. Here, we present the use of nanoscale surface curvature and hydrophilic surface chemistry to promote the high yield assembly of GUVs. We show that assembly on surfaces composed of entangled hydrophilic nanocellulose fibers results in an unprecedented 100,000-fold reduction in costs while increasing yields compared to extant techniques. Quantitative measurements of yields provide mechanistic insight on the effect of nanoscale curvature and the effect of surface chemistry. We present a thermodynamic ‘budding and merging’, BNM, model that unifies observations of assembly. The BNM model considers the change in free energy by balancing elastic, adhesion, and membrane edge energies in the formation of surface-attached spherical buds. Due to curvature and the hydrophilicity of cellulose, energetically unfavorable formation of buds on planar and spherical surfaces becomes favorable (spontaneous) on surfaces composed of cylindrical cellulose nanofibers.TOC Graphic
MafF is an antiviral host factor that suppresses transcription from Hepatitis B Virus core promoter
Authors: Ibrahim Marwa K. , Abdelhafez Tawfeek H. , Takeuchi Junko S. , Wakae Kosho , Sugiyama Masaya , Tsuge Masataka , Ito Masahiko , Watashi Koichi , Kassas Mohamed El , Kato Takanobu , Murayama Asako , Suzuki Tetsuro , Chayama Kazuaki , Shimotohno Kunitada , Muramatsu Masamichi , Aly Hussein H. , Wakita Takaji 
Published: July 2020

AbstractHepatitis B Virus (HBV) is a stealth virus that exhibits only minimal induction of the interferon system that is required for both innate and adaptive immune responses. However, 90% of acutely infected adults can clear the virus, suggesting the presence of additional mechanisms that facilitate viral clearance. Herein, we report that Maf bZIP transcription factor F (MafF) promotes host defense against infection with HBV. Using siRNA library and an HBV/NL reporter virus, we screened to identify anti-HBV host factors. Our data showed that silencing ofMafFled to a 6-fold increase in luciferase activity after HBV/NL infection. Overexpression of MafF reduced HBV core promoter transcriptional activity, which was relieved upon mutating the putative MafF binding region. Loss of MafF expression by CRISPR/CAS9 (in HepG2-hNTCP-C4 cells) or siRNA silencing (in primary hepatocytes [PXB]), induced HBV core and HBV pregenomic RNA (pgRNA) levels, respectively, after HBV infection. MafF physically binds to HBV core promoter and competitively inhibits HNF-4α binding to an overlapping sequence in HBV enhancer II sequence (EnhII) as seen by ChIP analysis. MafF expression was induced by IL-1β/TNF-α treatment in both HepG2 and PXB cells, in an NF-κB-dependent manner. Consistently,MafFexpression levels were significantly enhanced and positively correlated with the levels of these cytokines in patients with chronic HBV infection, especially in the immune clearance phase.ImportanceHBV is a leading cause of chronic liver diseases, infecting about 250 million people worldwide. HBV has developed strategies to escape interferon-dependent innate immune responses. Hence, the identification of other anti-HBV mechanisms is important for understanding HBV pathogenesis, and developing anti-HBV strategies. MafF was shown to suppress transcription from HBV core promoter, leading to a significant suppression of HBV life cycle. Furthermore, MafF expression was induced in chronic HBV patients and in primary human hepatocytes (PXB). This induction correlated with the levels of inflammatory cytokines (IL-1β and TNF-α). These data suggest that the induction of MafF contributes to the host’s antiviral defense by suppressing transcription from selected viral promoters. Our data shed light on a novel role for MafF as anti-HBV host restriction factor.
Application of CRISPR/Cas9 nuclease in amphioxus genome editing
Authors: Su Liuru , Shi Chenggang , Huang Xin , Wang Yiquan , Li Guang 
Published: July 2020

AbstractThe cephalochordate amphioxus is a promising animal model for studying the origin of vertebrate due to its key phylogenetic position among chordates. Although transcription activator-like effector nucleases (TALENs) has been adopted in amphioxus genome editing, its labor intensive construction of the TALEN proteins limits its usage in many laboratories. We here report an application of the CRISPR/Cas9 system, a more amenable genome editing method, in this group of animals. Our data show that while co-injection ofCas9mRNAs and sgRNAs into amphioxus unfertilized eggs causes no detectable mutations at targeted loci, injections ofCas9mRNAs and sgRNAs at two cell stage, or of Cas9 protein and sgRNAs before fertilization can executes efficient disruptions of targeted genes. Among the nine tested sgRNAs (targeting five genes) co-injected with Cas9 protein, seven introduced mutations at efficiency ranging from 18.4% to 90% and four caused specific phenotypes in the injected embryos. We also demonstrate that monomerization of sgRNAs via thermal treatment or integration of sgRNAs into a longer backbone could increase mutation efficacies. Our study will not only promote application of genome editing method in amphioxus research, but also provide valuable experiences for other organisms in which the CRISPR/Cas9 system has not been successfully applied.