bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noncanonical usage of stop codons in ciliates expands proteins with Q-rich motifs
Authors: Chuang Chi-Ning , Liu Hou-Cheng , Woo Tai-Ting , Chao Ju-Lan , Chen Chiung-Ya , Hu Hisao-Tang , Hsueh Yi-Ping , Wang Ting-Fang 
Published: December 2020

AbstractSerine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many proteins. SCDs often are intrinsically disordered regions that mediate protein phosphorylation and protein-protein interactions. PolyQ and polyQ/N tracts are structurally flexible sequences that trigger protein aggregation. We report that due to their high percentages of STQ or STQN amino acid content, four SCDs and three prion-causing Q/N-rich motifs of yeast proteins possess autonomous protein expression-enhancing activities. Since these Q-rich motifs can endow proteins with structural and functional plasticity, we suggest that they represent useful toolkits for evolutionary novelty. Comparative Gene Ontology (GO) analyses of the near-complete proteomes of 27 representative model eukaryotes reveal that Q-rich motifs prevail in proteins involved in specialized biological processes, includingSaccharomyces cerevisiaeRNA-mediated transposition and pseudohyphal growth,Candida albicansfilamentous growth, ciliate peptidyl-glutamic acid modification and microtubule-based movement,Tetrahymena thermophilaxylan catabolism and meiosis,Dictyostelium discoideumdevelopment and sexual cycles,Plasmodium falciparuminfection, and the nervous systems ofDrosophila melanogaster, Mus musculusandHomo sapiens. We also show that Q-rich-motif proteins are expanded massively in ten ciliates with reassigned TAAQand TAGQcodons. Notably, the usage frequency of CAGQis much lower in ciliates with reassigned TAAQand TAGQcodons than in organisms with expanded and unstable Q runs (e.g.,D. melanogasterandH. sapiens), indicating that the use of noncanonical stop codons in ciliates may have coevolved with codon usage biases to avoid triplet repeat disorders mediated by CAG/GTC replication slippage.
Canonical and novel non-canonical activities of the Holliday junction resolvase Yen1
Authors: Aguado F. Javier , Carreira Raquel , Hurtado-Nieves Vanesa , Blanco Miguel G. 
Published: December 2020

ABSTRACTYen1 and GEN1 are members of the Rad2/XPG family of nucleases that were identified as the first canonical nuclear Holliday junction (HJ) resolvases in budding yeast and humans due to their ability to introduce two symmetric, coordinated incisions on opposite strands of the HJ, yielding nicked DNA products that could be readily ligated. While GEN1 has been extensively characterizedin vitro, much less is known about the biochemistry of Yen1. Here, we have performed the first in-depth characterization of purified Yen1. We confirmed that Yen1 resembles GEN1 in many aspects, including range of substrates targeted, position of most incisions they produce or monomeric state in solution. However, we have also observed unexpected alternative processing of substrates, such as nicked HJs and a different conformational preference on intact HJs. Moreover, we demonstrate that Yen1 is endowed with additional nuclease activities, like a nick-specific 5’-3’ exonuclease or HJ arm-chopping that could apparently blur its classification as a canonical HJ resolvase. Despite this, we show that Yen1 fulfills the requirements of a canonical HJ resolvase and hypothesize that its wider array of nuclease activities might contribute to its function in the removal of persistent recombination or replication intermediates.
Dual site-specific chemoenzymatic antibody fragment conjugation using CRISPR-based hybridoma engineering
Authors: Le Gall Camille M. , van der Schoot Johan M.S. , Ramos-Tomillero Iván , Khalily Melek Parlak , van Dalen Floris J. , Wijfjes Zacharias , Smeding Liyan , van Dalen Duco , Cammarata Anna , Bonger Kimberly M. , Figdor Carl G. , Scheeren Ferenc A. , Verdoes Martijn 
Published: December 2020

I.AbstractFunctionalized antibodies and antibody fragments have found applications in the fields of biomedical imaging, theragnostics, and antibody-drug conjugates (ADC). Antibody functionalization is classically achieved by coupling payloads onto lysine or cysteine residues. However, such stochastic strategies typically lead to heterogenous products, bearing a varying number of payloads. This affects bioconjugate efficacy and stability, as well as its in vivo biodistribution, and therapeutic index, while potentially obstructing the binding sites and leading to off-target toxicity. In addition, therapeutic and theragnostic approaches benefit from the possibility to deliver more than one type of cargo to target cells, further challenging stochastic labelling strategies. Thus, bioconjugation methods to reproducibly obtain defined homogenous conjugates bearing multiple different cargo molecules, without compromising target affinity, are in demand. Here, we describe a straightforward CRISPR/Cas9-based strategy to rapidly engineer hybridoma cells to secrete Fab’ fragments bearing two distinct site-specific labelling motifs, which can be separately modified by two different sortase A mutants. We show that sequential genetic editing of the heavy chain (HC) and light chain (LC) loci enables the generation of a stable cell line that secretes a dual tagged Fab’ molecule (DTFab’), which can be easily isolated in high yields. To demonstrate feasibility, we functionalized the DTFab’ with two distinct cargos in a site-specific manner. This technology platform will be valuable in the development of multimodal imaging agents, theragnostics, and next-generation ADCs.
Thiol drugs decrease SARS-CoV-2 lung injuryin vivoand disrupt SARS-CoV-2 spike complex binding to ACE2in vitro
Authors: Khanna Kritika , Raymond Wilfred , Jin Jing , Charbit Annabelle R. , Gitlin Irina , Tang Monica , Werts Adam D. , Barrett Edward G. , Cox Jason M. , Birch Sharla M. , Martinelli Rachel , Sperber Hannah S. , Franz Sergej , Pillai Satish , Healy Anne Marie , Duff Thomas , Oscarson Stefan , Hoffmann Markus , Pöhlmann Stefan , Simmons Graham , Fahy John V. 
Published: December 2020

AbstractNeutrophil-induced oxidative stress is a mechanism of lung injury in COVID-19, and drugs with a functional thiol group (“thiol drugs”), especially cysteamine, have anti-oxidant and anti-inflammatory properties that could limit this injury. Thiol drugs may also alter the redox status of the cysteine-rich SARS-CoV-2 spike glycoprotein (SARS-2-S) and thereby disrupt ACE2 binding. Using ACE2 binding assay, reporter virus pseudotyped with SARS-CoV-2 spikes (ancestral and variants) and authentic SARS-CoV-2 (Wuhan-1), we find that multiple thiol drugs inhibit SARS-2-S binding to ACE2 and virus entry into cells. Pseudoviruses carrying variant spikes were less efficiently inhibited as compared to pseudotypes bearing an ancestral spike, but the most potent drugs still inhibited the Delta variant in the low millimolar range. IC50 values followed the order of their cystine cleavage rates and lower thiol pKa values. In hamsters infected with SARS-CoV-2, intraperitoneal (IP) cysteamine decreased neutrophilic inflammation and alveolar hemorrhage in the lungs but did not decrease viral infection, most likely because IP delivery could not achieve millimolar concentrations in the airways. These data show that thiol drugs inhibit SARS-CoV-2 infectionin vitroand reduce SARS-CoV-2-related lung injuryin vivoand provide strong rationale for trials of systemically delivered thiol drugs as COVID-19 treatments. We propose that antiviral effects of thiol drugsin vivowill require delivery directly to the airways to ensure millimolar drug concentrations and that thiol drugs with lower thiol pKa values are most likely to be effective.One Sentence SummaryThe effect of cysteamine to decrease SARS-CoV-2 pneumoniain vivoand of multiple thiol drugs to inhibit SARS-CoV-2 infectionin vitroprovides rationale for clinical trials of thiol drugs in COVID-19.
MRSA emerges through natural transformation
Authors: Maree Mais , Nguyen Le Thuy Thi , Ohniwa Ryosuke L. , Huang Shenghe , Higashide Masato , Msadek Tarek , Morikawa Kazuya 
Published: December 2020

AbstractMethicillin-resistant Staphylococcus aureus (MRSA) carries the resistance gene mecA in the staphylococcal cassette chromosome (SCC) that disseminates among staphylococci but the cell-to-cell transmission mechanism of SCC has not been clarified for half a century1. Here, we present evidence for efficient natural transformation in Staphylococcus aureus and its relevance in SCCmec transmission. We found that growth in biofilm conditions increased the transformation efficiency in a dependent manner on two component signal transduction systems, TCS13 (AgrCA) and TCS17 (BraSR). Strikingly, we demonstrate that natural transformation mediates the transfer of SCCmec from MRSA or methicillin-resistant coagulase negative staphylococci to methicillin-sensitive S. aureus. The site-specific insertion/excision system mediated by cassette chromosome recombinases was essential for SCCmec transformation while the stability of SCCmec varied depending on SCC types and recipients. We propose that natural transformation is the key process in the emergence of MRSA.
Lexical frequency and sentence context influence the brain’s response to single words
Authors: Huizeling Eleanor , Arana Sophie , Hagoort Peter , Schoffelen Jan Mathijs 
Published: December 2020

AbstractTypical adults read remarkably quickly. Such fast reading is facilitated by brain processes that are sensitive to both word frequency and contextual constraints. It is debated as to whether these attributes have additive or interactive effects on language processing in the brain. We investigated this issue by analysing existing magnetoencephalography data from 99 participants readingintact and scrambled sentences.Using a cross-validated model comparison scheme, we found that lexical frequency predicted the word-by-word elicited MEG signal in a widespread cortical network, irrespective of sentential context. In contrast, index (ordinal word position) was more strongly encoded in sentence words, in left front-temporal areas. This confirms that frequency influences word processing independently of predictability, and that contextual constraints affect word-by-word brain responses. With a conservative multiple comparisons correction, only the interaction between lexical frequency and surprisal survived, in anterior temporal and frontal cortex, and not between lexical frequency and entropy, nor between lexical frequency and index. However, interestingly, the uncorrected index*frequency interaction revealed an effect in left frontal and temporal cortex that reversed in time and space for intact compared to scrambled sentences. Finally, we provide evidence to suggest that, in sentences, lexical frequency and predictability may independently influence early (<150ms) and late stages of word processing, but also interact during late stages of word processing (>150-250ms), thus helping to converge previous contradictory eye-tracking and electrophysiological literature. Current neuro-cognitive models of reading would benefit from accounting for these differing effects of lexical frequency and predictability on different stages of word processing.
Choline Transporter regulates olfactory habituation via a neuronal triad of excitatory, inhibitory and mushroom body neurons
Authors: Hamid Runa , Sant Hitesh Sonaram , Kulkarni Mrunal Nagaraj 
Published: December 2020

AbstractCholine is an essential component of Acetylcholine (ACh) biosynthesis pathway which requires high-affinity Choline transporter (ChT) for its uptake into the presynaptic terminals of cholinergic neurons. Previously, we reported a predominant expression of ChT in memory processing and storing region ofDrosophilabrain called mushroom bodies (MB). It is unknown how ChT contributes to the functional principles of MB operation. Here, we demonstrate the role of ChT in non-associative form of learning,Habituation. Odour driven habituation traces are laid down in ChT dependent manner in antennal lobes (AL), projection neurons (PN) and MB. We observed that reduced habituation due to knockdown of ChT in MB causes hypersensitivity towards odour, suggesting that ChT also regulates incoming stimulus suppression. Importantly, we show for the first time that ChT is not unique to cholinergic neurons but is also required in inhibitory GABAergic neurons to drive habituation behaviour. Our results support a model in which ChT regulates both habituation and incoming stimuli through multiple circuit loci via an interplay between excitatory and inhibitory neurons. Strikingly, the lack of ChT in MB recapitulates major features of Autism spectrum disorders (ASD) including attenuated habituation, sensory hypersensitivity as well as defective GABAergic signalling. Our data establish the role of ChT in habituation learning and suggest that its dysfunction may contribute to neuropsychiatric disorders like ASD.
Factors motivating destination decisions of Chinese study abroad students
Authors: Wang Zhiqi , Crawford Ian 
Published: December 2020

PurposeThe paper examines the effects of individual differences on the key motivational factors affecting Chinese study abroad students.Design/methodology/approachThe current study adopts a quantitative survey approach. Students are recruited through the largest online survey provider in China. Using 335 completed questionnaires and factor analysis, the key factors influencing Chinese students are identified. Subsequently, regressions are employed to analyse the impact of age, gender, socio-economic status, previous study or travel abroad experience, degree level and location on factor scores.FindingsThis research sheds new light on the decision-making process of Chinese study abroad students. It is found that Chinese students are influenced by three key factors, social, cultural and economic environment, non-personal and personal recommendations. The results reveal that male students from the lowest socio-economic group rely on non-personal information to decide destination where they can significantly upgrade their socio-economic status. Personal recommendations are used by young persons aged between 18 and 24 and those without previous overseas travel or study experience.Originality/valueAlthough prior studies explore the motivations of Chinese study abroad students, very few focus on a large sample of students both in China and abroad and identify key factors using the statistical tool factor analysis. No research has been carried out to understand the impact of personal characteristics such as age, gender, prior study or travel abroad experience, degree level and location on significant factor scores. Such analysis is crucial for the financial stability of the international higher education market, particularly during the current COVID-19 crisis.
Treatment Goals and Alcohol Use Outcomes in Veterans With Comorbid Alcohol Dependence and Posttraumatic Stress Disorder
Authors: Lozano Brian E. , Allan Nicholas P. , Gros Daniel F. , Jones Jennifer , Back Sudie E. 
Published: December 2020

Background and ObjectivesPrevious research demonstrates the utility of goals in attaining improved drinking outcomes. Considerably less is known about the association between substance use goals and outcomes among persons with comorbid substance use disorder (SUD) and posttraumatic stress disorder (PTSD). This secondary analysis examined the association between alcohol use outcomes and participants’ treatment entry substance use goals to either abstain or reduce substance use in the context of treatment for comorbid SUD/PTSD.MethodsParticipants (N = 39) were treatment‐seeking veterans with current alcohol dependence and PTSD. Participants completed self‐report and clinician‐rated measures of substance use and PTSD as part of a larger randomized controlled trial.ResultsParticipants in both goal groups (abstain; reduce) achieved significant reductions in the likelihood of drinking and the likelihood of exceeding low‐risk drinking levels. The primary analysis did not identify significant differences in outcome between goal groups; however, the exploratory analysis revealed that participants with reduced use goals were more likely to drink and more likely to exceed low‐risk drinking levels.Conclusion and Scientific SignificanceThe findings suggest a moderately strong association between substance use goal and drinking outcome in the current study. Although the findings did not unequivocally support abstinence as a superior treatment goal, they offer a preliminary indication that abstinence may be an overall lower‐risk option. These findings expand consideration of the utility of substance use goals and suggest that clinicians should invite consideration of abstinence but may need not limit integrated treatment for SUD/PTSD based on strict adherence to abstinence, particularly if low‐risk use goals are targeted. (Am J Addict 2021;30:131–137)
Systematic Review and Meta‐Analysis: Treatment of Substance Use Disorder in Attention Deficit Hyperactivity Disorder
Authors: Fluyau Dimy , Revadigar Neelambika , Pierre Christopher G. 
Published: December 2020

Background and ObjectivesTreating substance use disorder (SUD) in patients with co‐occurring attention deficit hyperactivity disorder (ADHD) and SUD may lower medical, psychiatric, and social complications. We conducted a systematic review with meta‐analysis to investigate the clinical benefits of pharmacological interventions to treat SUD in patients with ADHD.MethodsArticles were searched on Cochrane Central Register of Controlled Trials, PubMed, EBSCO, Google Scholar, Embase, Web of Science, and Ovid MEDLINE from 1971 to 2020. Data for SUD treatment as primary study endpoints and ADHD symptoms management as secondary outcomes were synthesized using random‐effects model meta‐analysis. Studies (N = 17) were included. The principal measure of effect size was the standardized mean difference (SMD). PROSPERO registration: CRD42020171646.ResultsThe pooled effect of pharmacological interventions compared with placebo was small for the reduction in substance use (SMD = 0.405, 95% confidence interval [CI]: [0.252, 0.557], P < .001), abstinence (SMD = 0.328, 95% CI: [0.149, 0.507], P < .001), craving (SMD = 0.274, 95% CI: [0.103, 0.446], P = .002), and the reduction in the frequency of ADHD symptoms (SMD = 0.420, 95% CI: [0.259, 0.582], P < .001). The pooled effect was moderate for the management of withdrawal symptoms (SMD = 0.577, 95% CI: [0.389, 0.764], P = .001]) and the decrease in the severity of ADHD symptoms (SMD = 0.533, 95% CI: [0.393, 0.672], P < .001).Conclusion and Scientific significanceThe magnitude of benefits for pharmacological interventions varies. Despite some limitations, it was positive. This meta‐analysis is the first to appraise the benefits of medications to treat SUD in ADHD. It is the groundwork for treatment and risk mitigation. (Am J Addict 2020;00:00–00)
Innovative features and functionalities of an artificial pancreas system: What do youth and parents want?
Authors: Commissariat Persis V. , Volkening Lisa K. , Butler Deborah A. , Dassau Eyal , Weinzimer Stuart A. , Laffel Lori M. 
Published: December 2020

AbstractAimsParticipant‐driven solutions may help youth and families better engage and maintain use of diabetes technologies. We explored innovative features and functionalities of an ideal artificial pancreas (AP) system suggested by youth with type 1 diabetes and parents.MethodsSemi‐structured interviews were conducted with 39 youth, ages 10–25 years, and 44 parents. Interviews were recorded, transcribed and coded using thematic analysis.ResultsYouth (72% female, 82% non‐Hispanic white) were (M ± SD) ages 17.0 ± 4.7 years, with diabetes for 9.4 ± 4.9 years, and HbA1c of 68 ± 11 mmol/mol (8.4 ± 1.1%); 79% were pump‐treated and 82% were continuous glucose monitor users. Of parents, 91% were mothers and 86% were non‐Hispanic white, with a child 10.6 ± 4.5 years old. Youth and parents suggested a variety of innovative features and functionalities for an ideal AP system related to (1) enhancing the appeal of user interface, (2) increasing automation of new glucose management functionalities, and (3) innovative and commercial add‐ons for greater convenience. Youth and parents offered many similar suggestions, including integration of ketone testing, voice activation, and location‐tracking into the system. Youth seemed more driven by increasing convenience and normalcy while parents expressed more concerns with safety.ConclusionsYouth and parents expressed creative solutions for an ideal AP system to increase ease of use, enhance normalcy, and reduce burden of management. Designers of AP systems will likely benefit from incorporating the desired preferences by end users to optimize acceptance and usability by young persons with diabetes.
Wnt antagonist secreted frizzled‐related protein I (sFRP1) may be involved in the osteogenic differentiation of periodontal ligament cells in chronic apical periodontitis
Authors: Yang F. , Huang D. , Xu L. , Xu W. , Yi X. , Zhou X. , Ye L. , Zhang L. 
Published: December 2020

AbstractAimTo explore the mechanism of secreted frizzled‐related protein I (sFRP1) involvement in the osteogenic differentiation of human periodontal ligament cells (hPDLCs) under inflammatory conditions.MethodologyhPDLCs were cultured in an osteogenic differentiation‐inducing medium (odi) and subjected to the stimulation of Porphyromonas gingivalis lipopolysaccharide (P. gingivalis LPS) with or without the inhibition of sFRP1. Quantitative real‐time polymerase chain reaction, Western blot and enzyme‐linked immunosorbent assay were carried out to evaluate the expression of osteogenic markers as well as the classic Wnt signalling pathway. Periapical periodontitis was induced in Wistar rats to further confirm the effect of sFRP1 inhibitor on bone loss in vivo. After the Shapiro–Wilk normality test, data were analysed by Student’s paired t‐test or one‐way Anova test with a P value less than 0.05 as the level of statistical significance.ResultsSignificantly decreased mRNA and protein expression of osteogenic markers were detected in hPDLCs treated with P. gingivalis LPS during osteogenic induction (P < 0.001). Increased expression of sFRP1 was observed (P < 0.01), whilst Wnt/β‐catenin signalling pathway was inhibited by the addition of P. gingivalis LPS (P < 0.01). After the addition of the sFRP1 inhibitor, the decrease of osteogenic markers (P < 0.05) and the inhibition of Wnt/β‐catenin signalling pathway (P < 0.05) were reversed significantly. The animal experiment further confirmed that the sFRP1 inhibitor significantly reduced bone loss of periapical lesions in vivo (P < 0.0001).ConclusionsWnt antagonist sFRP1 was involved in the osteogenic differentiation of hPDLCs under inflammation. Modulation of the Wnt/β‐catenin signalling pathway through the inhibition of sFRP1 may offer a new perspective on the treatment of chronic apical periodontitis.
The risk of under‐insurance in the Finnish statutory pension scheme for self‐employed workers: A trajectory analysis
Authors: Salonen Janne , Koskinen Lasse , Nummi Tapio 
Published: December 2020

AbstractUsing unique data on the contribution base, we investigate under‐insurance within the statutory pension scheme for self‐employed workers in Finland. Under‐insurance is defined as the difference between pension‐declared income and tax‐declared income. The trajectory modelling technique applied has allowed us to estimate the levels of under‐insurance for different subgroups and to identify possible explanatory factors. Under‐insurance is found to be persistent and large. The analysis reveals six distinctive and homogenous sub‐groups of self‐employed workers. Close to 84 per cent of these workers pay too little in contributions, often leading to inadequate protection against personal risks. Especially for lower‐income self‐employed workers, this points to myopic behaviour as regards contributing to the self‐employed statutory pension scheme and calls for fine‐tuned economic incentives.