bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced production of recombinant HALT-1 pore-forming toxin using two-step chromatographic procedure
Authors: Yap Wei Yuen , Loo Lok Wenn , Sha Hong Xi , Hwang Jung Shan 
Published: August 2022

AbstractHydra actinoporin-like toxin-1 (HALT-1) has been isolated from Hydra magnipapillata and is highly cytolytic against various human cells including erythrocyte. Previously, recombinant HALT-1 (rHALT-1) was expressed in Escherichia coli and purified by the nickel affinity chromatography. In this study, we improved the purification of rHALT-1 by two-step purifications. Bacterial cell lysate containing rHALT-1 was subjected to the sulphopropyl (SP) cation exchange chromatography with different buffers, pHs, and NaCl concentrations. The results indicated that both phosphate and acetate buffers facilitated the strong binding of rHALT-1 to SP resins, and the buffers containing 150 mM and 200 mM NaCl, respectively, removed protein impurities but retain most rHALT-1 in the column. When combining the nickel affinity chromatography and the SP cation exchange chromatography, the purity of rHALT-1 was highly enhanced. In subsequent cytotoxicity assays, 50% of cells could be lysed at ∼18 and ∼22 μg/ml of rHALT-1 purified with phosphate and acetate buffers, respectively.HALT-1 is a soluble α-pore-forming toxin of 18.38 kDa.rHALT-1 was purified by nickel affinity chromatography followed by SP cation exchange chromatography.The cytotoxicity of purified rHALT-1 using 2-step purifications via either phosphate or acetate buffer was comparable to those previously reported.Graphical abstractSpecifications table
lncRNAHOTAIRM1Coordinates with RNA Processing Factors in DNA Damage Repair
Authors: Chuang Tzu-Wei , Wu Pei-Yu , Chang Yao-Ming , Tarn Woan-Yuh 
Published: August 2022

SUMMARYThe eukaryotic RNA processing factor Y14 participates in double-strand break (DSB) repair via its RNA-dependent interaction with the non-homologous end-joining (NHEJ) complex. We identified the long non-coding RNAHOTAIRM1as a candidate that mediates this interaction.HOTAIRM1localized to DNA damage sites induced by ionizing radiation. Depletion ofHOTAIRM1delayed the recruitment of DNA damage response and repair factors to DNA lesions and reduced DNA repair efficiency. Identification of theHOTAIRM1interactome revealed a large set of RNA processing factors including mRNA surveillance factors. The surveillance factors Upf1 and SMG6 localized to DNA damage sites in aHOTAIRM1-dependent manner. Depletion of Upf1 or SMG6 increased the level of DSB-induced non-coding transcripts at damaged sites, indicating a pivotal role for Upf1/SMG6-mediated RNA degradation in DNA repair. We conclude thatHOTAIRM1serves as an assembly scaffold for both DNA repair and RNA processing factors that act in concert to repair DSBs.
Structural basis and dynamics of Chikungunya alphavirus RNA capping by the nsP1 capping pores
Authors: Jones Rhian , Homs Michael , Rabat Nadia , Zamarreño Noelia , Arranz Rocio , Reguera Juan 
Published: August 2022

ABSTRACTAlphaviruses are emerging positive stranded RNA virus which replicate and transcribe their genomes in membranous organelles formed in the cell cytoplasm. The non-structural protein 1 (nsP1) is responsible for RNA capping and the gating of replication organelles by assembling into monotopic membrane-associated dodecameric pores (Jones R. et al. Nature 2021). The capping path is unique for Alphavirus; beginning with the N7 methylation of a GTP molecule, followed by the covalent linkage of a m7GMP group to a conserved histidine in nsP1 and the transfer of this cap structure to a diphosphate RNA (Ahola T. et al. PNAS 1995). Here we provide structural snapshots of different stages of the reaction pathway showing how nsP1 pores recognize the substrates of the methyl-transfer reaction, GTP and SAM, how it reaches a metastable post-methylation state with SAH and m7GTP in the active site, the subsequent covalent transfer of m7GMP to nsP1 and post-reaction conformational changes triggering the opening of the pore. In addition, we biochemically characterize the capping reaction, demonstrating specificity for the RNA substrate and the reversibility of the cap transfer resulting in decapping activity and the release of intermediates of the reaction. Our data identify the molecular determinants allowing each pathway transition, provide explanation for the need for the SAM methyl donor all along the pathway and new clues about the conformational rearrangements associated to the enzymatic activity of nsP1. Together our results set new ground for the structural and functional understanding of alphavirus RNA-capping and the design of antivirals.Significance statementHere we present biochemical and structural characterization of the capping pathway carried out by the Chikungunya virus nsP1 capping pores. We provide five Cryo-EM structures representative of the different steps of the reaction. These structures reveal the molecular determinants and dynamics associated with the alphavirus capping process. In addition, we biochemically show the RNA capping specificity and the reversibility of the reaction which allow nsP1 to cap and decap RNAs and to release intermediates of the reaction. These data provide a new biochemical clues on the enzymatic activity of nsP1 capping pores and a new structural landscape that will be instrumental for the design of effective antivirals targeting the viral RNA capping for blocking the infection.
Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates
Authors: Watson Zoe L. , Knudson Isaac , Ward Fred R. , Miller Scott J. , Cate Jamie H. D. , Schepartz Alanna , Abramyan Ara M. 
Published: August 2022

AbstractAs genetic code expansion advances beyond L-α-amino acids to backbone modifications and new polymerization chemistries, the field faces an increasingly broad challenge to discover what the ribosome can accommodate. Although the E. coli ribosome tolerates non-L-α-amino acids in vitro, few structural insights are available, and the boundary conditions for efficient bond formation are unknown. We describe a 2.1 Å cryo-EM structure of the E. coli ribosome containing well-resolved α-amino acid monomers coupled with a computational approach for which energy surface minima produced by metadynamics trend in agreement with established incorporation efficiencies. Reactive monomers across diverse structural classes favor a conformational space characterized by an A-site nucleophile to P-site carbonyl distance of < 4 Å and a Bürgi-Dunitz angle of 90-110°. Monomers whose free energy minima fall outside these regions do not react. Application of this model should accelerate the in vivo and in vitro ribosomal synthesis and application of sequence-defined, non-peptide heterooligomers.
Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification
Authors: Lee Sungeun , Sieradzki Ella T. , Nicol Graeme W. , Hazard Christina 
Published: August 2022

AbstractAmmonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO2-derived13C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of13C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of13C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in13C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.
Phylogenetic Association and Genetic Factors in Cold Stress Tolerance in Campylobacter jejuni
Authors: Hur Jeong In , Kim Jinshil , Ryu Sangryeol , Jeon Byeonghwa 
Published: August 2022

ABSTRACTCampylobacter jejuni is a major foodborne pathogen transmitted to humans primarily via contaminated poultry meat. Since poultry meat is generally processed, distributed, and stored in the cold chain, the survival of C. jejuni at refrigeration temperatures crucially affects human exposure to C. jejuni. Here, we investigated genetic factors associated with cold stress tolerance in C. jejuni. Seventy-nine C. jejuni strains isolated from retail raw chicken exhibited different survival levels at 4°C for 21 days. Multilocus sequence typing (MLST) clonal complex (CC)-21 and CC-443 were dominant among cold stress-tolerant strains, whereas CC-45 was common among cold stress-sensitive strains. Genome-wide average nucleotide identity (ANI) analysis identified a phylogenetic cluster associated with cold stress tolerance. Moreover, a pan-genome analysis revealed 58 genes distinctively present in the cold stress-tolerant phylogenetic cluster. Among the 58 genes, cfrA, encoding the ferric enterobactin receptor involved in ion transport and metabolism, was selected for further analysis. Remarkably, the viability of a ΔcfrA mutant at 4°C was significantly decreased, while the levels of total reactive oxygen species and intracellular iron exceeded those in the wild type. Additionally, a knockout mutation of cfrA also significantly decreased the viability of three cold stress-tolerant isolates at 4°C, confirming the role of cfrA in cold stress tolerance. The results of this study demonstrate that unique phylogenetic clusters of C. jejuni associated with cold stress tolerance exist and that cfrA is a genetic factor contributing to cold stress tolerance in C. jejuni.IMPORTANCEThe tolerance of foodborne pathogens to environmental stresses significantly affects food safety. Several studies have demonstrated that C. jejuni survives extended exposure to low temperatures, but the mechanisms of cold stress tolerance are not fully understood. Here, we demonstrate that C. jejuni strains in certain phylogenetic groups exhibit increased tolerance to cold stress. Notably, cfrA is present in the phylogenetic cluster associated with cold stress tolerance and plays a role in C. jejuni survival at low temperatures by alleviating oxidative stress. This is the first study to discover phylogenetic associations involving cold stress tolerance and identify genetic elements conferring cold stress tolerance in C. jejuni.
Monitoring of nighttime EEG slow‐wave activity during dexmedetomidine infusion in patients with hyperactive ICU delirium: An observational pilot study
Authors: Ala‐Kokko Tero , Erikson Kristo , Koskenkari Juha , Laurila Jouko , Kortelainen Jukka 
Published: August 2022

AbstractBackgroundThe disturbance of sleep has been associated with intensive care unit (ICU) delirium. Monitoring of EEG slow‐wave activity (SWA) has potential in measuring sleep quality and quantity. We investigated the quantitative monitoring of nighttime SWA and its association with the clinical evaluation of sleep in patients with hyperactive ICU delirium treated with dexmedetomidine.MethodsWe performed overnight EEG recordings in 15 patients diagnosed with hyperactive delirium during moderate dexmedetomidine sedation. SWA was evaluated by offline calculation of the C‐Trend Index, describing SWA in one parameter ranging 0 to 100 in values. Average and percentage of SWA values <50 were categorized as poor. The sleep quality and depth was clinically evaluated by the bedside nurse using the Richards‐Campbell Sleep Questionnaire (RCSQ) with scores <70 categorized as poor.ResultsNighttime SWA revealed individual sleep structures and fundamental variation between patients. SWA was poor in 67%, sleep quality (RCSQ) in 67%, and sleep depth (RCSQ) in 60% of the patients. The category of SWA aligned with that of RCSQ‐based sleep quality in 87% and RCSQ‐based sleep depth in 67% of the patients.ConclusionBoth, SWA and clinical evaluation suggested that the quality and depth of nighttime sleep were poor in most patients with hyperactive delirium despite dexmedetomidine infusion. Furthermore, the SWA and clinical evaluation classifications were not uniformly in agreement. An objective mode such as practical EEG‐based solution for sleep evaluation and individual drug dosing in the ICU setting could offer potential in improving sleep for patients with delirium.
Anatomo‐comparative study of formaldehyde, alcohol, and saturated salt solution as fixatives in Wistar rat brains
Authors: Martins‐Costa Camila , Nunes Thauane Carvalho , Anjos‐Ramos Luana dos 
Published: August 2022

AbstractAlthough formaldehyde is the most widely used and largely available fixative for preserving cadavers through decomposition prevention, it promotes darkening and weight gain, in addition to being considered carcinogenic. Ethyl alcohol has been proven a potential substitute to formaldehyde due to its effectiveness in tissue penetration, thus preventing proliferation of microorganisms; however, it can only be used alone for fixation of small parts. In view of such fixatives limitations, saturated salt solution has been widely employed based on its antimicrobial effect and ability to maintain tissue similar to the original one, in addition to exerting no hazardous effects as there is no evaporation of harmful substances. This research aimed to observe anatomical brain behaviour submitted to formaldehyde, alcohol, and saturated salt solution as fixatives. Fixatives were tested in 15 adult Wistar rats’ brain, submerged in 10 ml of intended solution after removal for 4 weeks. Weight of the brains fixed in saturated salt did not change over the weeks. However, the weight of formaldehyde‐fixed brains increased and the weight in alcohol‐fixed brains decreased; in addition, modifications in all solutions measures were also observed. Alcohol provides a peculiar dehydrating effect as formaldehyde clearly increases the length of the pieces. Thus, since the saturated salt solution showed no important adjustment over the experimental time, it proved an efficient alternative for replacing formaldehyde and alcohol as fixative solutions of anatomical study of the brain.
Circ_0077109 sponges miR‐139‐5p and upregulates HOXD10 in trophoblast cells as potential mechanism for preeclampsia progression
Authors: Zhang Liping , Liu Mengxu 
Published: August 2022

AbstractBackgroundOne of the important reasons for the development of preeclampsia (PE) is the abnormal function of trophoblast cells. Many circular RNAs (circRNAs) have been confirmed to participate in the regulation of trophoblast cell function to mediate PE progression. However, whether circ_0077109 is involved in PE progression through regulating trophoblast cell function remains unclear.MethodsQuantitative real‐time PCR was utilized for measuring the expression of circ_0077109, microRNA (miR)‐139‐5p and homeobox D10 (HOXD10). Trophoblast cell proliferation, apoptosis, invasion, and angiogenesis was assessed cell counting kit 8 assay, EdU assay, flow cytometry, transwell assay and tube formation assay. In addition, western blot analysis was used to determine protein expression. The interaction between miR‐139‐5p and circ_0077109 or HOXD10 was verified by dual‐luciferase reporter assay and RIP assay.ResultsOur results pointed out that circ_0077109 was a circRNA with upregulated expression in PE patients. Overexpression of circ_0077109 suppressed trophoblast cell proliferation, invasion, and angiogenesis, while increased apoptosis. MiR‐139‐5p was found to be sponged by circ_0077109, and its mimic reversed the suppressive effect of circ_0077109 on trophoblast cell function. HOXD10 was a target of miR‐139‐5p, and its overexpression inhibited trophoblast cell proliferation, invasion, and angiogenesis. MiR‐139‐5p inhibitor could repress trophoblast cell function, while this effect could be reversed by HOXD10 knockdown.ConclusionIn summary, we confirmed that circ_0077109 inhibited trophoblast cell function through the regulation of miR‐139‐5p/HOXD10 axis, which might be a potential target for PE treatment.
Crowd Cohesion and Protest Outcomes
Authors: Mueller Lisa 
Published: August 2022

AbstractAmidst an unprecedented swell in global protest, scholars and activists wrestle with the question of why protests succeed or fail. I explore a new answer: more cohesive crowds, where protesters agree on their demands, are more likely to win concessions than less cohesive crowds. Drawing on psychology and linguistics, I theorize that cohesive demands are more comprehensible and thus persuasive. I test this theory with a multimethod approach. First, I use cross‐national data from 97 protests to estimate the relationship between crowd cohesion and subsequent concessions, applying natural language processing to measure cohesion in participants’ self‐reported motivations. Second, a survey experiment in South Africa tests the causal effects of crowd cohesion and assesses comprehensibility of demands as the mechanism driving concessions. Third, case studies of two British protests demonstrate the theory in real‐world settings. My findings suggest that activists can improve their odds of success by coordinating around a common goal.
Light or Fire? Frederick Douglass and the Orator's Dilemma
Authors: Hawley Michael C. 
Published: August 2022

AbstractMost scholarship on political rhetoric views it as an exercise in changing the minds of an audience. However, we see numerous examples of political speech aimed at those who already agree with the speaker, to motivate them to act on judgments they have already made. This kind of discourse is often dismissed as pandering, or the “red meat” rabble‐rousing that contributes to polarization. I draw upon Frederick Douglass to render a more complete account of this speech, which I term “hortatory rhetoric.” Douglass draws upon the prophetic tradition of Black Christian preaching to develop an alternative for when persuasion has reached its limit. This kind of speech raises a set of normative difficulties that differ from those raised by the rhetoric of persuasion, which Douglass helps us to think through. He provides a framework for understanding when it might be permissible or even desirable to abandon persuasion for exhortation.
Dimension Reduction for Integrative Survival Analysis
Authors: Molstad Aaron J. , Patra Rohit K. 
Published: August 2022

Abstract
We propose a constrained maximum partial likelihood estimator for dimension reduction in integrative (e.g., pan-cancer) survival analysis with high-dimensional predictors. We assume that for each population in the study, the hazard function follows a distinct Cox proportional hazards model. To borrow information across populations, we assume that each of the hazard functions depend only on a small number of linear combinations of the predictors (i.e., “factors”). We estimate these linear combinations using an algorithm based on “distance-to-set” penalties. This allows us to impose both low-rankness and sparsity on the regression coefficient matrix estimator. We derive asymptotic results that reveal that our estimator is more efficient than fitting a separate proportional hazards model for each population. Numerical experiments suggest that our method outperforms competitors under various data generating models. We use our method to perform a pan-cancer survival analysis relating protein expression to survival across 18 distinct cancer types. Our approach identifies six linear combinations, depending on only 20 proteins, which explain survival across the cancer types. Finally, to validate our fitted model, we show that our estimated factors can lead to better prediction than competitors on four external datasets.
The many faces of knowledge: Do science and traditional ecological knowledge coexist in federal assessments?
Authors: Beaulieu‐Guay Louis‐Robert 
Published: August 2022

AbstractTraditional Ecological Knowledge is officially recognized as a legitimate source of information when legislating on wildlife management at the federal level. This study assesses the extent to which this kind of information is mobilized by administrators when writing regulations. Analyzing the use of traditional knowledge in classifying endangered species shows that although Indigenous individuals and organizations are systematically consulted, traditional knowledge is rarely a factor in impact assessments. However, for scientific examinations conducted before these regulatory impact assessments, traditional ecological knowledge does appear to be considered a reliable source of information, even if it is not widely used.
The mediating role of social capital in socioeconomic inequalities of oral health behaviours among Brazilian older adults
Authors: do Amaral Júnior Orlando Luiz , Fagundes Maria Laura Braccini , Menegazzo Gabriele Rissotto , do Amaral Giordani Jessye Melgarejo 
Published: August 2022

AbstractObjectivesKnowledge of the possible pathways linking socioeconomic status (SES) to oral health‐related behaviours can improve the understanding of inequalities in oral health. Therefore, in this study, it was investigated whether social capital mediates the relationship between SES and oral health behaviours.MethodsThrough a cross‐sectional study, data were analysed from participants aged ≥60 years from the Brazilian National Health Survey 2019 (n = 21 575). Structural equation modelling was used to test the direct and indirect pathways from a latent variable for SES to a latent variable for oral health behaviours: daily flossing, toothbrushing frequency and the use of dental care services.ResultsThe maximum likelihood estimator was used for complex samples with robust standard errors, and the final model demonstrated an adequate fit. The findings demonstrated that a higher SES was directly associated with better oral health‐related behaviours (standardized coefficient [SC]: 0.82; [90% CI: 0.78–0.85]) and indirectly via structural social capital (SC: 0.05; [90% CI: 0.02–0.07]). The total effect of SES on oral health‐related behaviours was (SC: 0.87, [90% CI: 0.85–0.89]).ConclusionThe findings demonstrate that structural social capital in older Brazilian adults might partly mediate the pathways to socioeconomic inequalities in oral health behaviours. However, there is a direct effect on oral health behaviours, reinforcing the hypothesis that SES is associated with oral health, based on paths that link income inequality to oral health.