bluuebunny/crossref_metadata_2025_split huggingface dataset:
SaccuFlow – A High-throughput Analysis Platform to Investigate Bacterial Cell Wall Interactions
Authors: Apostolos Alexis J. , Ferraro Noel J. , Dalesandro Brianna E. , Pires Marcos M. 
Published: April 2021

AbstractBacterial cell walls are formidable barriers that protect bacterial cells against external insults and oppose internal turgor pressure. While cell wall composition is variable across species, peptidoglycan is the principal component of all cell walls. Peptidoglycan is a mesh-like scaffold composed of crosslinked strands that can be heavily decorated with anchored proteins. The biosynthesis and remodeling of peptidoglycan must be tightly regulated by cells because disruption to this biomacromolecule is lethal. This essentiality is exploited by the human innate immune system in resisting colonization and by a number of clinically relevant antibiotics that target peptidoglycan biosynthesis. Evaluation of molecules or proteins that interact with peptidoglycan can be a complicated and, typically, qualitative effort. We have developed a novel assay platform (SaccuFlow) that preserves the native structure of bacterial peptidoglycan and is compatible with high-throughput flow cytometry analysis. We show that the assay is facile and versatile as demonstrated by its compatibility with sacculi from Gram-positive bacteria, Gram-negative bacteria, and mycobacteria. Finally, we highlight the utility of this assay to assess the activity of sortase A fromStaphylococcus aureusagainst potential anti-virulence agents.
The allosteric activation of α7 nAChR by α-conotoxin MrIC is modified by mutations at the vestibular site
Authors: Gulsevin Alican , Papke Roger L. , Stokes Clare , Tran Hue N. T. , Jin Ai-Hua , Vetter Irina , Meiler Jens 
Published: April 2021

Abstractα-conotoxins are 13-19 amino acid toxin peptides that bind various nicotinic acetylcholine receptor (nAChR) subtypes. α-conotoxin Mr1.7c (MrIC) is a 17 amino acid peptide that targets α7 nAChR. Although MrIC has no activating effect on α7 nAChR when applied by itself, it evokes a large response when co-applied with the type II positive allosteric modulator PNU-120596, which potentiates α7 nAChR response by recovering it from a desensitized state. Lack of standalone activity despite activation upon co-application with a positive allosteric modulator was previously observed for molecules that bind to an extracellular domain allosteric activation (AA) site at the vestibule of the receptor. We hypothesized that MrIC may activate α7 nAChR allosterically through this site. We ran voltage-clamp electrophysiology experiments and in silico peptide docking calculations to gather evidence in support of α7 nAChR activation by MrIC through the AA site. The experiments with the wild-type α7 nAChR supported an allosteric mode of action, which was confirmed by the increased MrIC + PNU-120596 responses of three α7 nAChR AA site mutants that were designed in silico to improve MrIC binding. Overall, our results shed light on allosteric activation of α7 nAChR by MrIC and suggest involvement of the AA site.Significance Statementα-conotoxin MrIC (MrIC) is an allosteric agonist of the α7 nicotinic acetylcholine receptor (nAChR). This mode of action is unique among α-conotoxins since these peptides typically act as orthosteric antagonists of nAChR. However, the mechanism of α7 nAChR activation by MrIC has been elusive so far. This work demonstrates that activation by MrIC is independent of the α7 nAChR orthosteric site and is related to a vestibular allosteric activation site at the extracellular domain of the receptor. Our experimental and computational studies identified the residues that play a role in allosteric activation and confirmed the utility of ensemble docking methods in understanding peptide – nAChR interactions, thus providing a basis for the design of peptides for allosteric modulation of nAChR.
A quantile integral linear model to quantify genetic effects on phenotypic variability
Authors: Miao Jiacheng , Lin Yupei , Wu Yuchang , Zheng Boyan , Schmitz Lauren L. , Fletcher Jason M. , Lu Qiongshi 
Published: April 2021

AbstractDetecting genetic variants associated with the variance of complex traits, i.e. variance quantitative trait loci (vQTL), can provide crucial insights into the interplay between genes and environments and how they jointly shape human phenotypes in the population. We propose a quantile integral linear model (QUAIL) to estimate genetic effects on trait variability. Through extensive simulations and analyses of real data, we demonstrate that QUAIL provides computationally efficient and statistically powerful vQTL mapping that is robust to non-Gaussian phenotypes and confounding effects on phenotypic variability. Applied to UK Biobank (N=375,791), QUAIL identified 11 novel vQTL for body mass index (BMI). Top vQTL findings showed substantial enrichment for interactions with physical activities and sedentary behavior. Further, variance polygenic scores (vPGS) based on QUAIL effect estimates showed superior predictive performance on both population-level and within-individual BMI variability compared to existing approaches. Overall, QUAIL is a unified framework to quantify genetic effects on the phenotypic variability at both single-variant and vPGS levels. It addresses critical limitations in existing approaches and may have broad applications in future gene-environment interaction studies.
Towards guided mutagenesis: Gaussian process regression predicts MHC class II antigen mutant binding
Authors: Bell David R. , Chen Serena H. 
Published: April 2021

AbstractAntigen-specific immunotherapies (ASI) require successful loading and presentation of antigen peptide into the major histocompatibility complex (MHC) binding cleft. One route of ASI design is to mutate native antigens for either stronger or weaker binding interaction to MHC. Exploring all possible mutations is costly both experimentally and computationally. To reduce experimental and computational expense, here we investigate the minimal amount of prior data required to accurately predict the relative binding affinity of point mutations for peptide-MHC class II (pMHCII) binding. Using data from different residue subsets, we interpolate pMHCII mutant binding affinities by Gaussian process (GP) regression of residue volume and hydrophobicity. We apply GP regression to an experimental dataset from the Immune Epitope Database, and theoretical datasets from NetMHCIIpan and Free Energy Perturbation calculations. We find that GP regression can predict binding affinities of 9 neutral residues from a 6-residue subset with an average R2coefficient of determination value of 0.62 ± 0.04 (±95% CI), average error of 0.09 ± 0.01 kcal/mol (±95% CI), and with an ROC AUC value of 0.92 for binary classification of enhanced or diminished binding affinity. Similarly, metrics increase to an R2value of 0.69 ± 0.04, average error of 0.07 ± 0.01 kcal/mol, and an ROC AUC value of 0.94 for predicting 7 neutral residues from an 8-residue subset. Our work finds that prediction is most accurate for neutral residues at anchor residue sites without register shift. This work holds relevance to predicting pMHCII binding and accelerating ASI design.
An mRNA SARS-CoV-2 vaccine employing Charge-Altering Releasable Transporters with a TLR-9 agonist induces neutralizing antibodies and T cell memory
Authors: Haabeth Ole A.W. , Lohmeyer Julian J.K. , Sallets Adrienne , Blake Timothy R. , Sagiv-Barfi Idit , Czerwinski Debra K. , McCarthy Blaine , Powell Abigail E. , Wender Paul A. , Waymouth Robert M. , Levy Ronald 
Published: April 2021

AbstractThe SARS-CoV-2 pandemic has necessitated the rapid development of prophylactic vaccines. Two mRNA vaccines have been approved for emergency use by the FDA and have demonstrated extraordinary effectiveness. The success of these mRNA vaccines establishes the speed of development and therapeutic potential of mRNA. These authorized vaccines encode full-length versions of the SARS-CoV-2 spike protein. They are formulated with Lipid Nanoparticle (LNP) delivery vehicles that have inherent immunostimulatory properties. Different vaccination strategies and alternative mRNA delivery vehicles would be desirable to ensure flexibility of future generations of SARS-CoV-2 vaccines and the development of mRNA vaccines in general.Here, we report on the development of an alternative mRNA vaccine approach using a delivery vehicle called Charge-Altering Releasable Transporters (CARTs). Using these inherently nonimmunogenic vehicles we can tailor the vaccine immunogenicity by inclusion of co-formulated adjuvants such as oligodeoxynucleotides with CpG motifs (CpG-ODN). Mice vaccinated with the mRNA-CART vaccine developed therapeutically relevant levels of RBD-specific neutralizing antibodies in both the circulation and in the lung bronchial fluids. In addition, vaccination elicited strong and long lasting RBD-specific TH1 T cell responses including CD4+and CD8+T cell memory.
Nodal is a short-range morphogen with activity that spreads through a relay mechanism in human gastruloids
Authors: Liu Lizhong , Nemashkalo Anastasiia , Jung Ji Yoon , Chhabra Sapna , Guerra M. Cecilia , Heemserk Idse , Warmflash Aryeh 
Published: April 2021

AbstractMorphogens are signaling molecules that convey positional information and dictate cell fates during development. Little is known about how morphogen gradients are created and interpreted during mammalian embryogenesis. Here we take advantage of a human gastruloid model to visualize endogenous Nodal protein in living cells. We show that Nodal is extremely short range so that Nodal protein is limited to the immediate neighborhood of source cells. Nodal activity spreads through a relay mechanism in which Nodal production induces neighboring cells to transcribe Nodal. We further show that the Nodal inhibitor Lefty, while biochemically capable of long-range diffusion, also acts locally to control the timing of Nodal spread and therefore of mesoderm differentiation during patterning. Our study establishes a novel paradigm for tissue patterning by an activator-inhibitor pair.
Drp1 SUMO/deSUMOylation by Senp5 isoforms influences ER tubulation and mitochondrial dynamics to regulate brain development
Authors: Yamada Seiya , Sato Ayaka , Akiyama Hiroki , Sakakibara Shin-ichi 
Published: April 2021

ABSTRACTBrain development is a highly orchestrated process requiring spatiotemporally regulated mitochondrial dynamics. Drp1, a key molecule in the mitochondrial fission machinery, undergoes various post-translational modifications including conjugation to the small ubiquitin-like modifier (SUMO). However, the functional significance of SUMOylation/deSUMOylation on Drp1 remains controversial. SUMO-specific protease 5 (Senp5L) catalyzes the deSUMOylation of Drp1. We revealed that a splicing variant of Senp5L, Senp5S, which lacks peptidase activity, prevents deSUMOylation of Drp1 by competing against other Senps. The altered SUMOylation level of Drp1 induced by Senp5L/5S affects Drp1 ubiquitination and tubulation of the endoplasmic reticulum (ER), thereby influencing mitochondrial morphology. A dynamic SUMOylation/deSUMOylation balance controls neuronal polarization and migration during the development of the cerebral cortex. These findings suggest a novel role of post translational modification, in which a deSUMOylation enzyme isoform competitively regulates mitochondrial dynamics and ER tubulation via Drp1 SUMOylation levels in a tightly controlled process of neuronal differentiation and corticogenesis.
Fast leaps between millisecond confinements govern Ase1 diffusion along microtubules
Authors: Bujak Łukasz , Holanová Kristýna , Marín Antonio García , Henrichs Verena , Barvík Ivan , Braun Marcus , Lánský Zdenĕk , Piliarik Marek 
Published: April 2021

AbstractDiffusion is the most fundamental mode of protein translocation within cells. Confined diffusion of proteins along the electrostatic potential constituted by the surface of microtubules, although modeled meticulously in molecular dynamics simulations, has not been experimentally observed in real-time. Here, we used interferometric scattering microscopy to directly visualize the movement of the microtubule-associated protein Ase1 along the microtubule surface at nanometer and microsecond resolution. We resolved millisecond confinements of Ase1 and fast leaps between these positions of dwelling preferentially occurring along the microtubule protofilaments, revealing Ase1’s mode of diffusive translocation along the microtubule’s periodic surface. The derived interaction potential closely matches the tubulin-dimer periodicity and the distribution of the electrostatic potential on the microtubule lattice. We anticipate that mapping the interaction landscapes for different proteins on microtubules, finding plausible energetic barriers of different positioning and heights, will provide valuable insights into regulating the dynamics of essential cytoskeletal processes, such as intracellular cargo trafficking, cell division, and morphogenesis, all of which rely on diffusive translocation of proteins along microtubules.
Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment
Authors: Ross Jennifer , McIver Zak , Lambert Thomas , Piergentili Cecilia , Bird Jasmine Emma , Gallagher Kelly J. , Cruickshank Faye L. , James Patrick , Zarazúa-Arvizu Efrain , Horsfall Louise E. , Waldron Kevin J. , Wilson Marcus D. , Mackay C. Logan , Baslé Arnaud , Clarke David J. , Marles-Wright Jon 
Published: April 2021

AbstractEncapsulins are protein nanocompartments that house various cargo enzymes, including a family of decameric ferritin-like proteins. Here, we study a recombinantHaliangium ochraceumencapsulin:encapsulated ferritin complex using electron cryo-microscopy and hydrogen/deuterium exchange mass spectrometry to gain insight into the structural relationship between the encapsulin shell and its protein cargo. An asymmetric single particle reconstruction reveals four encapsulated ferritin decamers in a tetrahedral arrangement within the encapsulin nanocompartment. This leads to a symmetry mismatch between the protein cargo and the icosahedral encapsulin shell. The encapsulated ferritin decamers are offset from the interior face of the encapsulin shell. Using HDX-MS, we observed dynamic behavior of the major five-fold pore in the encapsulin shell and show the pore opening via the movement of the encapsulin A-domain. These data will accelerate efforts to engineer the encapsulation of heterologous cargo proteins and to alter the permeability of the encapsulin shell via pore modifications.TeaserCryo-EM and HDX-MS analysis of an encapsulin nanocompartment shows that the pores at the five-fold icosahedral vertex of the shell are flexible.
Public contributions to early detection of new invasive pests
Authors: Epanchin‐Niell Rebecca , Thompson Alexandra L. , Treakle Tyler 
Published: April 2021

AbstractEarly detection of new invasive pest incursions enables faster management responses and more successful outcomes. Formal surveillance programs—such as agency‐led pest detection surveys—are thus key components of domestic biosecurity programs for managing invasive species. Independent sources of pest detection, such as members of the public and farm operators, also contribute to early detection efforts, but their roles are less understood. To assess the relative contributions of different detection sources, we compiled a novel dataset comprising reported detections of new plant pests in the US from 2010 through 2018 and analyze when, where, how, and by whom pests were first detected. While accounting for uncertainties arising from data limitations, we find that agency‐led activities detected 32–56% of new pests, independent sources detected 27–60%, and research/extension detected 8–17%. We highlight the value of independent sources in detecting high impact pests, diverse pest types, and narrowly distributed pests—with contributions comparable with agency‐led surveys. However, in the US, independent sources detect a smaller proportion of new pests than in New Zealand. We suggest opportunities to further leverage independent pest detection sources, including by citizen science, landscaping contractors, and members of the public.
Relationship between work–family conflict and turnover intention in nurses: A meta‐analytic review
Authors: Yildiz Bora , Yildiz Harun , Ayaz Arda Ozlem 
Published: April 2021

AbstractAimThis meta‐analytic review aimed to synthesize and analyse studies that explored the relationship between nurses’ work–family conflicts and turnover intentions.DesignThis meta‐analytical review was conducted according to the Joanna Briggs Institute guidelines and PRISMA checklist.Data SourcesA total of 191 (k = 14) publications published between 2005 and 2019 in English, including grey literature on turnover intention and work–family conflict, were retrieved from PubMed, PsycINFO, Web of Science, ProQuest and Scopus databases.Review MethodsStudies on the relationship between work–family conflict and turnover intention were summarized.ResultsAn overall effect size of r = .28 (N = 5781, 95% CI [0.23−0.33]) was obtained, indicating a moderate, positive and significant relationship between work–family conflict and turnover intention. The moderator analysis showed that individualism and long‐term orientation accounted for 90% of effect size heterogeneity of work–family conflict and turnover intention relationship.ConclusionExploring the correlation between work–family conflict and turnover intention can provide guidelines and recommendations for the development of strategies to promote nurse retention and alleviate the nursing shortage. National culture, particularly individualism and long‐term orientation, were found to play a significant moderator role in this relationship. Cultures that are highly individualistic and have a long‐term orientation have a diminishing effect on the relationship between work–family conflict and turnover intention.ImpactWork–family conflict and turnover intention are significantly correlated factors regardless of the studies’ cultural characteristics examined in this study. Policymakers and managers should consider this finding and develop strategies that provide a balance‐oriented work design to prevent nurse shortage.
The aesthetics of country music
Authors: Dyck John 
Published: April 2021

AbstractCountry music has not gotten much attention in philosophy. I introduce two philosophical issues that country music raises. First, country music is simple. Some people might think that its simplicity makes country music worse; I argue that simplicity is aesthetically valuable. The second issue is country music’s ideal of authenticity; fans and performers think that country should be real or genuine in a particular way. But country music scholars have debunked the idea that country authenticity gets at anything real; widespread ideas about country authenticity are rooted in a racist and fabricated picture of country music. In discussing these two issues, I highlight the importance of community in country music.
Abnormal corneal properties in osteogenesis imperfecta and glaucoma: a case series
Authors: Doolan Emer , O’Brien Colm 
Published: April 2021

ObjectiveWe aimed to carry out ocular examination and genetic studies in a family in which some members are affected with osteogenesis imperfecta (OI) and primary open-angle glaucoma (POAG). We compared the corneal properties of affected and unaffected members (ie, cases and controls).MethodsEight family members from two generations, both affected and unaffected, were examined. Corneal hysteresis (CH), intraocular pressure (IOP) measured with Goldmann applanation tonometer, central corneal thickness (CCT) and cornea-corrected IOP (IOPcc) were recorded. Blood samples were obtained from seven family members, both affected and unaffected, and tested for a panel of genes associated with OI.ResultsFamily members affected with OI (n=6) had a heterozygous splice site mutation in intron 26 of the COL1A1 gene. The family members affected with OI had reduced CCT (476.5±24.6 µm) and CH (7.9 ±1.4 mmHg) compared with the unaffected controls (CCT, 575.8±10.8 µm; CH, 12.3±0.8 mmHg). Two of the six patients affected with OI had a glaucoma diagnosis and were on topical therapy and under regular clinical review.ConclusionsPatients affected with OI have a significant risk of developing POAG due to the effects of abnormal collagen on various ocular structures. Two of these effects which place them at risk are reduced CCT and CH. They should be screened and monitored for glaucoma from a young age, and the examination should include corneal biomechanical measurements and CCT to identify those most at risk. IOPcc may be a more accurate way to monitor IOP in the presence of abnormal corneal properties.
To prescribe or not to prescribe for paediatric sore throat: a retrospective cohort study comparing clinician-led antibiotic prescriptions to FeverPAIN and Centor scoring in a tertiary paediatric emergency department and a national review of practice
Authors: Malley Michael , Driver Katie , Costelloe Megan , Monaghan Isla , Jefferson Lucy , Poole Louise , Lewis Cliona , Salt Rachael , Marlow Robin 
Published: April 2021

BackgroundTonsillopharyngitis is a common presentation to paediatric emergency departments (PEDs). FeverPAIN (FP) and Centor scoring systems are recommended in the UK to help delineate bacterial aetiology, despite being primarily evidenced in adult populations. We investigate how the use of FP or Centor compares to actual clinician practice in guiding antibiotic prescription rates in PED. We establish current national practice in English PEDs.MethodsWe performed a retrospective cohort study of tonsillopharyngitis presentations to a tertiary PED in January–February 2020. Investigators retrospectively assigned each patient FP and Centor scores using documented symptoms. We compared antibiotic prescription rates guided by FP/Centor against the actual rate prescribed by clinicians, and assessed agreement between these strategies using kappa analysis. We contacted 153 English emergency departments to establish national practice.ResultsWe identified 632 consecutive patients aged 6 months to 15 years. Actual clinician-prescribed antibiotics numbered 116 (18.4%). Prescriptions predicted by FP score numbered 124 (19.6%) and Centor 112 (17.7%). Kappa (K) analysis indicated only moderate agreement between clinician choice versus FP (K=0.434) and clinician choice versus Centor (K=0.476). This was similar for cohorts aged under and over 3 years.National practice was reportedly heterogeneous, with 70 emergency departments (45.8%) not employing a specific system.ConclusionCurrent guidance is variably interpreted and inconsistently implemented in paediatric populations. FeverPAIN and Centor scoring systems may not rationalise antibiotics as much as previously reported compared with judicious clinician practice. Producing clear paediatric-specific national guidelines, especially for under-5s who are omitted from NICE sore throat guidance, may help further rationalise and standardise antibiotic use in paediatric tonsillopharyngitis.