bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spatialised agent-based model of NOTCH signalling pathway in Endothelial Cells predicts emergent heterogeneity due to continual dynamic phenotypic adjustments
Authors: Chesnais Francois , Sego Timothy J , Engstler Elena , Battilocchi Matteo , Danovi Davide , Glazier James A , Veschini Lorenzo 
Published: August 2022

AbstractVascular Endothelial Cells (EC) plasticity is key to homeostasis and its disruption is a hallmark of diseases such as cancer, atherosclerosis, and diabetes. The EC lineage has evolved to address in parallel sensor and actuator functions. This ability is reflected in remarkable phenotypical heterogeneity of EC across different tissues, within the same tissue, and within the same vascular bed as demonstrated by single cell image analysis and transcriptomics studies. However, how the molecular signalling dynamics in EC could generate and maintain such heterogeneity in different contexts is still largely unexplored. Recently we reported that confluent EC have spatially heterogeneous NOTCH signalling pathway (NSP) levels in vitro as confirmed from analysis of available OMICS databases. Here, we show that spatial heterogeneity of NSP levels is a feature of aortic murine endothelia in vivo and recapitulated by human EC in culture despite absence of signalling from mural cells. We study lateral induction and inhibition, cis-interactions and signalling, and target genes autoregulation in NSP. Using mathematical models and experimental observations we report that NSP dynamics can generate stable, periodic, and asynchronous oscillations of the NSP target HES1. Importantly, we observe that cell contact dependent NSP signal oscillations is the most likely parsimonious mechanistic hypothesis justifying observed spatial heterogeneity in endothelia. We propose that NSP is sufficient to enable individual EC in monolayers to acquire different phenotypes dynamically explaining robustness of quiescent endothelia in performing parallel functions.
Factors associated with peri-neonatal mortality in Sao Tome & Principe: a prospective cohort study
Authors: Vasconcelos Alexandra , Sousa Swasilanne , Bandeira Nelson , Alves Marta , Papoila Ana Luísa , Pereira Filomena , Machado Maria Céu 
Published: August 2022

AbstractBackgroundNeonatal mortality reduction is a global goal but its factors in high-burden nations vary and are poorly understood. This study was conducted to identify the factors affecting peri- neonatal mortality in Sao Tome & Principe (STP), one of the smallest African countries.MethodsInstitution-based prospective cohort study conducted at Hospital Dr. Ayres Menezes. Maternal-neonate dyads enrolled were followed up after the 28thday of life (n=194) for identification of neonatal death-outcome (n=22) and alive-outcome groups (n=172). Data were collected from pregnancy cards, hospital records and face-to-face interviews. After the 28thday of birth, a phone call was made to evaluate the newborn’s health status. A logistic regression model was used to identify the relevant factors associated with mortality, a p value <0.05 was considered statistically significant.ResultsThe mean gestational age of the death-outcome and alive-outcome groups was 36 (SD=4.8) and 39 (SD=1.4) weeks, respectively. Death-outcome group (n=22) included sixteen stillbirths, four early and two late neonatal deaths. High-risk pregnancy score [cOR 2.91, 95%CI:1.18-7.22], meconium-stained fluid [cOR 4.38, 95%CI:1.74–10.98], prolonged rupture of membranes [cOR 4.84, 95%CI:1.47–15.93], transfer from another unit [cOR 6.08, 95%CI:1.95–18.90], and instrumental vaginal delivery [cOR 8.90, 95%CI:1.68–47.21], were factors significantly associated with mortality. The odds of experiencing death were higher for newborns with infectious risk, IUGR, resuscitation maneuvers, fetal distress at birth, birth asphyxia, and unit care admission. Female newborn [cOR 0.37, 95%CI:0.14-1.00] and birth weight of more than 2500 g [cOR 0.017, 95%CI:0.002-0.162] were found to be protective factors. In the multivariable model, meconium-stained fluid was significantly associated with death outcome.ConclusionFactors such as having a high-risk pregnancy score, meconium-stained amniotic fluid, prolonged rupture of membranes, being transferred from another unit, and an instrumental- assisted vaginal delivery increased 4– to 9–fold the risk of stillbirth and neonatal death. Of the factors associated with peri-neonatal mortality in this study, avoiding health-worker- related factors associated with delays in prompt intrapartum care is a key strategy to implement in Sao Tome & Principe.
A Comprehensive Survey of C. elegans Argonaute Proteins Reveals Organism-wide Gene Regulatory Networks and Functions
Authors: Seroussi Uri , Lugowski Andrew , Wadi Lina , Lao Robert X. , Willis Alexandra R. , Zhao Winnie , Sundby Adam E. , Charlesworth Amanda G. , Reinke Aaron W. , Claycomb Julie M. 
Published: August 2022

SummaryArgonaute (AGO) proteins associate with small RNAs to direct their effector function on complementary transcripts. The nematode C. elegans contains an expanded family of 19 functional AGO proteins, many of which have not been fully characterized. In this work we systematically analyzed every C. elegans AGO, using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG tags. We have characterized the expression patterns of each AGO throughout development, identified small RNA binding complements, and determined the effects of ago loss on small RNA populations and developmental phenotypes. Our analysis indicates stratification of subsets of AGOs into distinct regulatory modules, and integration of our data led us to uncover novel stress-induced fertility and pathogen response phenotypes due to ago loss.
Dynamic allosteric networks drive adenosine A1receptor activation and G-protein coupling
Authors: Maria-Solano Miguel A. , Choi Sun 
Published: August 2022

ABSTRACTG-protein coupled receptors (GPCRs) present specific activation pathways and signaling among receptor subtypes. Hence, an extensive knowledge of the structural dynamics of the receptor is critical for the development of therapeutics. Here, we target the adenosine A1receptor (A1R), for which a negligible number of drugs have been approved. We combine molecular dynamics simulations, enhanced sampling techniques, network theory and pocket detection to decipher the activation pathway of A1R, decode the allosteric networks and identify transient pockets. The A1R activation pathway reveal hidden intermediate and pre-active states together with the inactive and fully-active states observed experimentally. The protein energy networks computed throughout these conformational states successfully unravel the extra and intracellular allosteric centers and the communication pathways that couples them. We observe that the allosteric networks are dynamic, being increased along activation and fine-tuned in presence of the trimeric G-proteins. Overlap of transient pockets and energy networks uncover how the allosteric coupling between pockets and distinct functional regions of the receptor is altered along activation. By an in-depth analysis of the bridge between activation pathway, energy networks and transient pockets, we provide a further understanding of A1R. This information can be useful to ease the design of allosteric modulators for A1R.
UNC-45 assisted myosin folding depends on a conserved FX3HY motif implicated in Freeman Sheldon Syndrome
Authors: Vogel Antonia , Arnese Renato , Gudino Carrillo Ricardo M. , Sehr Daria , Bylicki Andrzej , Meinhart Anton , Clausen Tim 
Published: August 2022

SummaryMyosin motors are critical for diverse motility functions ranging from cytokinesis and endocytosis to muscle contraction. The UNC-45 chaperone controls myosin function mediating the folding, assembly, and degradation of the muscle protein. Here, we analyze the molecular mechanism of UNC-45 as a hub in myosin quality control. We show that UNC-45 forms discrete complexes with folded and unfolded myosin, forwarding them to downstream chaperones and E3 ligases. Structural analysis of a minimal chaperone:substrate complex reveals that UNC-45 binds to a conserved FX3HY motif in the myosin motor domain. Disrupting the observed interface by mutagenesis prevents myosin maturation leading to protein aggregation in vivo. We also show that a mutation in the FX3HY motif linked to the Freeman Sheldon Syndrome impairs UNC-45 assisted folding, reducing the level of functional myosin. These findings demonstrate that a faulty myosin quality control is a critical yet unexplored cause of human myopathies.
Asymmetry and ion selectivity properties of bacterial channel NaK mutants mimicking ionotropic glutamate receptors
Authors: Minniberger Sonja , Abdolvand Saeid , Braunbeck Sebastian , Sun Han , Plested Andrew J.R. 
Published: August 2022

AbstractIonotropic glutamate receptors are ligand-gated cation channels that play essential roles in the excitatory synaptic transmission throughout the central nervous system. A number of open-pore structures of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic-acid (AMPA)-type glutamate receptors became recently available by cryo-electron microscopy (cryo-EM). These structures provide valuable insights into the conformation of the selectivity filter (SF), the part of the ion channel that determines the ion selectivity. Nonetheless, due to the moderate resolution of the cryo-EM structures, detailed information such as ion occupancy of monovalent and divalent cations as well as exact displacement of the side-chains in the SF is still missing. Here, in order to resolve high-resolution crystal structures of the AMPA SF in its open-state, we incorporated the partial SF sequence of the AMPA receptor into the bacterial tetrameric cation channel NaK, which served as a structural scaffold. We determined a series of X-ray structures of NaK-CDI, NaK-SDI and NaK-SELM mutants at 1.42-2.10 Å resolution, showing distinct ion occupation of different monovalent cations. Molecular dynamics (MD) simulations of NaK-CDI indicated the channel to be conductive to monovalent cations, which agrees well with our electrophysiology recordings. Moreover, unique structural asymmetry of the SF was revealed by the X-ray structures and MD simulations, implying its importance in ion non-selectivity of tetrameric cation channels.
Analysis of genetic relatedness between gastric and oral H. pylori in patients with early gastric cancer using multilocus sequence typing
Authors: Nagata Ryoko , Sato Hiroki , Takenaka Shoji , Yokoyama Junji , Terai Shuji , Mimuro Hitomi , Noiri Yuichiro 
Published: August 2022

AbstractAlthough oral cavity is the second most colonized site after the stomach, the association between gastric and oral Helicobacter pylori remains unclear. This study aimed to compare the genetic relatedness between gastric and oral H. pylori in Japanese patients with early gastric cancer by multilocus sequence typing (MLST) analysis using seven housekeeping genes. Gastric biopsy specimens and oral samples, including saliva, supragingival dental biofilm, and superficial layers of the tongue, were collected from 21 patients positive for H. pylori by a fecal antigen test. The number of H. pylori allelic profiles of seven loci obtained from oral and gastric samples ranged from zero to seven since the yield of DNA was small even when the nested PCR was performed. The alleles of seven loci from both collection sites were determined from only one patient, and two out of seven alleles matched between oral and gastric samples. MLST analysis revealed that only one sample had a matching oral and gastric H. pylori genotype, suggesting that different genotypes of H. pylori inhabit the oral cavity and gastric mucosa. The phylogenetic analysis showed that oral H. pylori in two patients was markedly similar to gastric H. pylori, implying that the the origins of two strains may be the same, and the stomach and the oral cavity may be infected at the same time. In brief, although different genotypes of H. pylori exist in the oral cavity independently of H. pylori present in the stomach, there are rare cases in which the same H. pylori is present in the stomach and the oral cavity. It is necessary to establish a culture method for oral H. pylori for elucidating whether the oral cavity will act as the source of the gastric infection, as our analysis was based on a limited number of allele sequences.Author summaryHericobacter pylori is a clinically important pathogen that causes chronic gastritis and peptic ulcers, which are associated with gastric carcinoma. Oral H. pylori DNA has also been detected in a range of oral specimens, including saliva, supra- or sub-gingival biofilm, dentin caries, dental pulp, infected root canal, and coating of the tongue. Thus, researchers speculate that the main route of transmission of gastric H. pylori infections is via the oral cavity, however, there is inadequate evidence to support this suggestion. This study aimed to investigate if the oral and gastric H. pylori have the same origin using multilocus sequence typing. The results of this study provided some insight into the role of oral cavity as the source of H. pylori infections in stomach.
Single-molecule tracking of Nanog and Oct4 in mouse embryonic stem cells
Authors: Okamoto Kazuko , Fujita Hideaki , Okada Yasushi , Shinkai Soya , Onami Shuichi , Abe Kuniya , Fujimoto Kenta , Watanabe Tomonobu M 
Published: August 2022

AbstractNanog and Oct4 are core transcription factors in a gene regulatory network that regulate hundreds of target genes for pluripotency maintenance in mouse embryonic stem cells. To understand their function as a gatekeeper or a pioneer factor at the molecular scale, we quantified the residence time on target loci, fluctuation at the loci, and interaction clustering by visualizing single molecules of Nanog and Oct4 in a living nucleus during the pluripotency loss. Interestingly, Nanog interacted longer with its target loci in the lower Nanog expression state or at the onset of differentiation, indicating the possibility of a new feedback mechanism to maintain Nanog expression. The interaction time of Nanog and Oct4 corresponded to their fluctuation and interaction clustering, which depended on their expression or differentiation state, respectively. The DNA viscoelasticity near the Oct4 target locus remained flexible during the differentiation, reflecting its role as a pioneer factor. Based on these results, we propose a new feedback mechanism for pluripotency maintenance in which Nanog function is prolonged, corresponding to chromatin condensation, and Oct4 reopens the condensation.
Cotranslational folding of human growth hormone in vitro and in Escherichia coli
Authors: Mermans Daphne , Nicolaus Felix , Baygin Aysel , von Heijne Gunnar 
Published: August 2022

AbstractHuman growth hormone (hGH) is a four-helix bundle protein of considerable pharmacological interest. Recombinant hGH is produced in bacteria, yet little is known about its folding during expression in E. coli. We have studied the cotranslational folding of hGH using Force Profile Analysis (FPA), both during in vitro translation in the absence and presence of the chaperone trigger factor (TF), and when expressed in E. coli. We find that the main folding transition starts before hGH is completely released from the ribosome, and that it can interact with TF and possibly other chaperones.
Purine-rich RNA sequences in the 5’UTR site-specifically regulate eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation
Authors: Schmidt Tobias , Dabrowska Adrianna , Waldron Joseph A. , Hodge Kelly , Koulouras Grigorios , Gabrielsen Mads , Munro June , Tack David C. , Harris Gemma , McGhee Ewan , Scott David , Carlin Leo M. , Huang Danny , Le Quesne John , Zanivan Sara , Wilczynska Ania , Bushell Martin 
Published: August 2022

AbstractOncogenic translational programmes underpin cancer development and are often driven by dysregulation of oncogenic signalling pathways that converge on the eukaryotic translation initiation (eIF) 4F complex. Altered eIF4F activity promotes translation of oncogene mRNAs that typically contain highly structured 5’UTRs rendering their translation strongly dependent on RNA unwinding by the DEAD-box helicase eIF4A1 subunit of the eIF4F complex. While eIF4A1-dependent mRNAs have been widely investigated, it is still unclear how highly structured mRNAs recruit and activate eIF4A1 unwinding specifically to facilitate their preferential translation.Here, we show that RNA sequence motifs regulate eIF4A1 unwinding activity in cells. Our data demonstrate that eIF4A1-dependent mRNAs contain AG-rich motifs within their 5’UTR which recruit and stimulate eIF4A1 unwinding of localised RNA structure to facilitate mRNA translation. This mode of eIF4A1 regulation is used by mRNAs encoding components of mTORC-signalling and cell cycle progression and renders these mRNAs particularly sensitive to eIF4A1-inhibition. Mechanistically, we show that binding of eIF4A1 to AG-rich sequences leads to multimerization of eIF4A1 with eIF4A1 subunits performing distinct enzymatic activities. Our structural data suggest that RNA-binding of multimeric eIF4A1 induces conformational changes in the RNA substrate resulting in an optimal positioning of eIF4A1 proximal to the RNA duplex region that supports efficient unwinding.Hence, we conclude a model in which mRNAs utilise AG-rich sequences to specifically recruit eIF4A1, enabling assembly of the helicase-active multimeric eIF4A1 complex, and positioning these complexes proximal to stable localised RNA structure allowing ribosomal subunit scanning.
Static stability and swim bladder volume in the bluegill sunfish Lepomis macrochirus
Authors: Fath Michael , Nguyen Stacy , Donahue Joan , McMenamin Sarah , Tytell Eric 
Published: August 2022

AbstractThe static stability of a fish in the water is determined by the relative locations of its center of mass and center of buoyancy. These locations may not be constant, but may depend on the volume of the swim bladder. Changes in swim bladder volume affect both the distribution of mass and the overall volume of the fish, thus affecting the location of the center of mass and center of buoyancy, respectively. To determine the static stability and to examine the influence of the swim bladder on static stability, we used micro-computed tomography to estimate the locations of the center of mass and center of buoyancy in bluegill sunfish (Lepomis macrochrius). In fish oriented head up in the scanner, we found that the center of buoyancy is located 0.441 body lengths from the snout and 0.19 body lengths above the ventral surface of the pelvic girdle, and that the center of mass is 0.0012 BL posterior to and 0.00045 BL ventral to the center of buoyancy. Swim bladders from our specimens ranged in size from 1.9% to 7.6% total body volume, and we found no correlation between swim bladder volume and the distance between the center of mass and center of buoyancy. However, in fish scanned in a head-down orientation, the center of mass is anterior and dorsal to the center of buoyancy—the opposite configuration of that found in fish oriented head up. This change in center of mass and center of buoyancy seems to be caused by changes in the location of the swim bladder in the body: the centroid of the swim bladder is located more posteriorly in fish oriented head-down. The air in the bladder “rises” while heavier tissues “sink,” driving a change in tissue distribution and changing the location of the center of mass relative to the center of buoyancy. We conclude that while static stability does not change with swim bladder volume, pitch angle could have a marked effect on static stability.
A replicon RNA vaccine induces durable protective immunity from SARS-CoV-2 in nonhuman primates after neutralizing antibodies have waned
Authors: O’Connor Megan A. , Hawman David W. , Meade-White Kimberly , Leventhal Shanna , Song Wenjun , Randall Samantha , Archer Jacob , Lewis Thomas B. , Brown Brieann , Iwayama Naoto , Ahrens Chul , Garrison William , Wangari Solomon , Guerriero Kathryn A. , Hanley Patrick , Lovaglio Jamie , Saturday Greg , Edlefsen Paul T. , Khandhar Amit , Feldmann Heinz , Fuller Deborah Heydenburg , Erasmus Jesse H. 
Published: August 2022

AbstractThe global SARS-CoV-2 pandemic prompted rapid development of COVID-19 vaccines. Although several vaccines have received emergency approval through various public health agencies, the SARS-CoV-2 pandemic continues. Emergent variants of concern, waning immunity in the vaccinated, evidence that vaccines may not prevent transmission and inequity in vaccine distribution have driven continued development of vaccines against SARS-CoV-2 to address these public health needs. In this report, we evaluated a novel self-amplifying replicon RNA vaccine against SARS-CoV-2 in a pigtail macaque model of COVID-19 disease. We found that this vaccine elicited strong binding and neutralizing antibody responses. While binding antibody responses were sustained, neutralizing antibody waned to undetectable levels after six months but were rapidly recalled and conferred protection from disease when the animals were challenged 7 months after vaccination as evident by reduced viral replication and pathology in the lower respiratory tract, reduced viral shedding in the nasal cavity and lower concentrations of pro-inflammatory cytokines in the lung. Cumulatively, our data demonstrate in pigtail macaques that a self-amplifying replicon RNA vaccine can elicit durable and protective immunity to SARS-CoV-2 infection. Furthermore, these data provide evidence that this vaccine can provide durable protective efficacy and reduce viral shedding even after neutralizing antibody responses have waned to undetectable levels.
UNIQmin, an alignment-free tool to study viral sequence diversity across taxonomic lineages: a case study of monkeypox virus
Authors: Chong Li Chuin , Khan Asif M. 
Published: August 2022

AbstractSequence changes in viral genomes generate protein sequence diversity that enable viruses to evade the host immune system, hindering the development of effective preventive and therapeutic interventions. Massive proliferation of sequence data provides unprecedented opportunities to study viral adaptation and evolution. Alignment-free approach removes various restrictions, otherwise posed by an alignment-dependent approach for the study of sequence diversity. The publicly available tool, UNIQmin offers an alignment-free approach for the study of viral sequence diversity at any given rank of taxonomy lineage and is big data ready. The tool performs an exhaustive search to determine the minimal set of sequences required to capture the peptidome diversity within a given dataset. This compression is possible through the removal of identical sequences and unique sequences that do not contribute effectively to the peptidome diversity pool. Herein, we describe a detailed three-part protocol utilizing UNIQmin to generate the minimal set for the purpose of viral diversity analyses, alignment-free at any rank of the taxonomy lineage, using the latest global public health threat monkeypox virus (MPX) as a case study. This protocol enables systematic diversity study across the taxonomic lineage, which are much needed for our future preparedness of a viral epidemic, in particular when data is in abundance, freely available, and alignment is not an option.