bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lists with and without syntax: A new approach to measuring the neural processing of syntax
Authors: Law Ryan , Pylkkänen Liina 
Published: May 2020

ABSTRACTIn the neurobiology of language, a fundamental challenge is deconfounding syntax from semantics. Changes in syntactic structure usually correlate with changes in meaning. We approached this challenge from a new angle. We deployed word lists, which are usually the unstructured control in studies of syntax, as both the test and the control stimulus. Three-noun lists (lamps, dolls, guitars) were embedded in sentences (The eccentric man hoarded lamps, dolls, guitars…) and in longer lists (forks, pen, toilet, rodeo, graves, drums, mulch, lamps, dolls, guitars…). This allowed us to perfectly control both lexical characteristics and local combinatorics: the same words occurred in both conditions and in neither case did the list items locally compose into phrases (e.g. ‘lamps’ and ‘dolls’ do not form a phrase). But in one case, the list partakes in a syntactic tree, while in the other, it does not. Being embedded inside a syntactic tree increased source-localized MEG activity at ~250-300ms from word onset in the left inferior frontal cortex, at ~300-350ms in the left anterior temporal lobe and, most reliably, at ~330-400ms in left posterior temporal cortex. In contrast, effects of semantic association strength, which we also varied, localized in left temporo-parietal cortex, with high associations increasing activity at around 400ms. This dissociation offers a novel characterization of the structure vs. meaning contrast in the brain: The fronto-temporal network that is familiar from studies of sentence processing can be driven by the sheer presence of global sentence structure, while associative semantics has a more posterior neural signature.SIGNIFICANCE STATEMENTHuman languages all have a syntax, which both enables the infinitude of linguistic creativity and determines what is grammatical in a language. The neurobiology of syntactic processing has, however, been challenging to characterize despite decades of study. One reason is pure manipulations of syntax are difficult to design. The approach here offers a perfect control of two variables that are notoriously hard to keep constant when syntax is manipulated: word meaning and phrasal combinatorics. The same noun lists occurred inside longer lists and sentences, while semantic associations also varied. Our MEG results show that classic fronto-temporal language regions can be driven by sentence structure even when local semantic contributions are absent. In contrast, the left temporo-parietal junction tracks associative relationships.
OTTER, a new method quantifying absolute amounts of tRNAs
Authors: Nagai Akihisa , Mori Kohei , Shiomi Yuma , Yoshihisa Tohru 
Published: May 2020

ABSTRACTTo maintain optimal proteome, both codon choice of each mRNA and supply of aminoacyl-tRNAs are two principal factors in translation. Recent reports revealed that tRNAs are more dynamic in amount than we had expected. High-throughput methods such as RNA-Seq or microarray are versatile for comprehensive analyses of changes in individual tRNA amounts, but they suffer from lack of assessment of signal production efficiency of individual tRNA species. Thus, they are not the perfect choice to measure absolute amounts of tRNA. Here, we introduce a novel method for this purpose, oligonucleotide-directed three-primer terminal extension of RNA (OTTER), which employs fluorescence labeling at the 3’-terminus of a specific tRNA by optimized reverse primer extension and an assessment step of each labeling efficiency by Northern blotting. We quantified absolute amounts of 34 individual and 4 pairs of isoacceptor tRNAs out of the total 42 nuclear-encoded isoacceptors in the yeastSaccharomyces cerevisiae. We revealed that the amounts of tRNAs are in the range of 0.030–0.73 pmol/μg RNA in the yeast cells logarithmically grown in a rich glucose medium. The tRNA amounts seem to be regulated at the isoacceptor level by a few folds according to physiological growing conditions. Data obtained by OTTER are poorly correlated with those by simple RNA-Seq and only marginally with those by microarray. However, the OTTER data are good agreement with those by 2D-gel analysis ofin vivoradiolabeled RNA samples. Thus, OTTER is a suitable method for quantifying absolute amounts of tRNAs in the isoacceptor resolution.
Infrared fiber optic spectroscopy detects bovine articular cartilage degeneration
Authors: Virtanen Vesa , Nippolainen Ervin , Shaikh Rubina , Afara Isaac , Töyräs Juha , Solheim Johanne , Tafintseva Valeria , Zimmermann Boris , Kohler Achim , Saarakkala Simo , Rieppo Lassi 
Published: May 2020

AbstractArticular cartilage (AC) is a soft connective tissue that covers the ends of articulating bones. Joint injuries may lead to degeneration of cartilage tissue and initiate development of post-traumatic osteoarthritis (OA). Arthroscopic surgeries can be used to treat joint injuries, but arthroscopic evaluation of cartilage quality is subjective. Therefore, new methods are needed for objective assessment of cartilage degeneration. Fourier transform infrared (FTIR) spectroscopy can be used to assess tissue composition based on the fundamental molecular vibrations. When combined with fiber optics and attenuated total reflectance (ATR) crystal, the measurements can be done flexibly without any sample processing. We hypothesize that Fourier transform infrared attenuated total reflection (FTIR-ATR) spectroscopy can detect enzymatically and mechanically induced changes similar to changes occurring during progression of OA. Fresh bovine patellar cartilage plugs (n= 60) were extracted and degraded enzymatically and mechanically. Adjacent untreated control samples (n= 60) were utilized as controls. Enzymatic degradation was implemented by 90-min and 24-hour collagenase as well as 30-min trypsin treatments. Mechanical damage was induced by: 1) dropping a weight impactor on the cartilage plugs, and 2) abrading the cartilage surface with a rotating sandpaper. Fiber optic FTIR-ATR spectroscopic measurements were conducted for control and degraded samples, and spectral changes were assessed with random forest (RF), partial least squares discriminant analysis (PLS-DA), and support vector machine (SVM) classifiers. RF (accuracy 93.1 % to 79.2 %), PLS-DA (accuracy 95.8% to 81.9%), and SVM (accuracy 91.7% to 80.6%) all had excellent classification performance for detecting the different enzymatic and mechanical damage on cartilage matrix. The results suggest that fiber optic FTIR-ATR spectroscopy is a viable way to detect minor degeneration of AC.
Molecular Mechanism for Rotational Switching of the Bacterial Flagellar Motor
Authors: Chang Yunjie , Zhang Kai , Carroll Brittany L. , Zhao Xiaowei , Charon Nyles W. , Norris Steven J. , Motaleb Md A , Li Chunhao , Liu Jun 
Published: May 2020

AbstractThe bacterial flagellar motor is a remarkable nanomachine that can rapidly rotate in both counter-clockwise (CCW) and clockwise (CW) senses. The transitions between CCW and CW rotation are critical for chemotaxis, and they are controlled by a signaling protein (CheY-P) that interacts with a switch complex at the cytoplasmic side of the flagellar motor. However, the exact molecular mechanism by which CheY-P controls the motor rotational switch remains enigmatic. Here, we use the Lyme disease spirochete,Borrelia burgdorferi, as the model system to dissect the mechanism underlying flagellar rotational switching. We first determined high resolutionin situmotor structures in thecheXandcheY3mutants in which motors are genetically locked in CCW or CW rotation. The structures showed that the CheY3 protein ofB. burgdorferiinteracts directly with the FliM protein of the switch complex in a phosphorylation-dependent manner. The binding of CheY3-P to FliM induces a major remodeling of the switch protein FliG2 that alters its interaction with the torque generator. Because the remodeling of FliG2 is directly correlated with the rotational direction, our data lead to a model for flagellar function in which the torque generator rotates in response to an inward flow of H+driven by the proton motive force. Rapid conformational changes of FliG2 allow the switch complex to interact with opposite sides of the rotating torque generator, thereby facilitating rotational switching between CW and CCW.
Multiplex enCas12a screens show functional buffering by paralogs is systematically absent from genome-wide CRISPR/Cas9 knockout screens
Authors: Dede Merve , McLaughlin Megan , Kim Eiru , Hart Traver 
Published: May 2020

AbstractMajor efforts on pooled library CRISPR knockout screening across hundreds of cell lines have identified genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the number of essential genes detected from these monogenic knockout screens are very low compared to the number of constitutively expressed genes in a cell, raising the question of why there are so few essential genes. Through a systematic analysis of screen data in cancer cell lines generated by the Cancer Dependency Map, we observed that half of all constitutively-expressed genes are never hits in any CRISPR screen, and that these never-essentials are highly enriched for paralogs. We investigated paralog buffering through systematic dual-gene CRISPR knockout screening by testing algorithmically defined ~400 candidate paralog pairs with the enCas12a multiplex knockout system in three cell lines. We observed 24 synthetic lethal paralog pairs which have escaped detection by monogenic knockout screens at stringent thresholds. Nineteen of 24 (79%) synthetic lethal interactions were present in at least two out of three cell lines and 14 of 24 (58%) were present in all three cell lines tested, including alternate subunits of stable protein complexes as well as functionally redundant enzymes. Together these observations strongly suggest that paralogs represent a targetable set of genetic dependencies that are systematically under-represented among cell-essential genes due to genetic buffering in monogenic CRISPR-based mammalian functional genomics approaches.
Biomineral armor in leaf-cutter ants
Authors: Li Hongjie , Sun Chang-Yu , Fang Yihang , Carlson Caitlin M. , Xu Huifang , Ješovnik Ana , Sosa-Calvo Jeffrey , Zarnowski Robert , Bechtel Hans A. , Fournelle John H. , Andes David R. , Schultz Ted R. , Gilbert Pupa U. P. A. , Currie Cameron R. 
Published: May 2020

AbstractAlthough calcareous anatomical structures have evolved in diverse animal groups, such structures have been unknown in insects. Here, we report the discovery of high-magnesium calcite [CaMg(CO3)2] armor overlaying the exoskeletons of major workers of the leaf-cutter antAcromyrmex echinatior. Live-rearing andin vitrosynthesis experiments indicate that the biomineral layer accumulates rapidly as ant workers mature, that the layer is continuously distributed, covering nearly the entire integument, and that the ant epicuticle catalyzes biomineral nucleation and growth.In situnanoindentation demonstrates that the biomineral layer significantly hardens the exoskeleton. Increased survival of ant workers with biomineralized exoskeletons during aggressive encounters with other ants and reduced infection by entomopathogenic fungi demonstrate the protective role of the biomineral layer. The discovery of biosynthesized high-magnesium calcite in the relatively well-studied leaf-cutting ants suggests that calcareous biominerals enriched in magnesium may be more common in metazoans than previously recognized.
Interactions with Commensal and Pathogenic Bacteria Induce HIV-1 Latency in Macrophages through Altered Transcription Factor Recruitment to the LTR
Authors: Viglianti Gregory A. , Planelles Vicente , Hanley Timothy M. 
Published: May 2020

ABSTRACTMacrophages are infected by HIV-1in vivoand contribute to both viral spread and pathogenesis. Recent human and animal studies suggest that HIV-1-infected macrophages serve as a reservoir that contributes to HIV-1 persistence during anti-retroviral therapy. The ability of macrophages to serve as persistent viral reservoirs is likely influenced by the local tissue microenvironment, including interactions with pathogenic and commensal microbes. Here we show that the sexually transmitted pathogenNeisseria gonorrhoeae(GC) and the gut-associated microbeEscherichia coli (E. coli),which encode ligands for both Toll-like receptor 2 (TLR2) and TLR4, repressed HIV-1 replication in macrophages and thereby induced a state reminiscent of viral latency. This repression was mediated by signaling through TLR4 and the adaptor protein TRIF and was associated with increased production of type I interferons. Inhibiting TLR4 signaling, blocking type 1 interferon, or knocking-down TRIF reversed LPS- and GC-mediated repression of HIV-1. Finally, the repression of HIV-1 in macrophages was associated with the recruitment of interferon regulatory factor 8 (IRF8) to the interferon stimulated response element (ISRE) downstream of the 5′ HIV-1 long terminal repeat (LTR). Our data indicate that IRF8 is responsible for repression of HIV-1 replication in macrophages in response to TRIF-dependent signaling during GC andE. colico-infection. These findings highlight the potential role of macrophages as HIV-1 reservoirs as well as the role of the tissue microenvironment and co-infections as modulators of HIV-1 persistence.IMPORTANCEThe major barrier toward the eradication of HIV-1 infection is the presence of a small reservoir of latently infected cells, which include CD4+ T cells and macrophages that escape immune-mediated clearance and the effects of anti-retroviral therapy. There remain crucial gaps in our understanding of the molecular mechanisms that lead to transcriptionally silent or latent HIV-1 infection of macrophages. The significance of our research is in identifying microenvironmental factors, such as commensal and pathogenic microbes, that can contribute to the establishment and maintenance of latent HIV-1 infection in macrophages. It is hoped that identifying key processes contributing to HIV-1 persistence in macrophages may ultimately lead to novel therapeutics to eliminate latent HIV-1 reservoirsin vivo.
The impact of physical distancing measures against COVID-19 transmission on contacts and mixing patterns in the Netherlands: repeated cross-sectional surveys in 2016/2017, April 2020 and June 2020
Authors: Backer Jantien A. , Mollema Liesbeth , Vos R.A. Eric , Klinkenberg Don , van der Klis Fiona R.M. , de Melker Hester E. , van den Hof Susan , Wallinga Jacco 
Published: May 2020

AbstractBackgroundDuring the current COVID-19 pandemic many countries have taken drastic measures to reduce the transmission of SARS-CoV-2. These often include decreasing the number of contacts by physical distancing.AimTo measure the actual reduction of contacts when physical distancing measures are implemented.MethodsIn the Netherlands, a cross-sectional survey was carried out in 2016/2017 in which participants reported the number and age of their contacts during the previous day. The survey was repeated among a subsample of the participants in April 2020 after physical distancing measures had been implemented, and in an extended sample in June 2020 after some of these measures were relaxed.ResultsThe average number of community contacts per day was reduced from on average 14.9 (interquartile range: 4-20) in the 2016/2017 survey to 3.5 (0-4) after physical distancing measures were implemented, and rebounded to 8.8 (1-10) after some of these measures were relaxed. All age groups restricted their number of community contacts to at most 5 contacts on average after physical distancing measures were implemented. After relaxation, children reverted to baseline levels while elderly had a number of community contacts that was less than half their baseline levels.ConclusionThe physical distancing measures have greatly reduced contact numbers, which has likely been beneficial in curbing the first wave of the COVID-19 epidemic in the Netherlands. Different age groups reacted differently upon relaxation of these measures. These findings offer guidance for the deployment of age-targeted measures in the future course of the pandemic.
Population genomics and antimicrobial resistance inCorynebacterium diphtheriae
Authors: Hennart Melanie , Panunzi Leonardo G. , Rodrigues Carla , Gaday Quentin , Baines Sarah L. , Barros-Pinkelnig Marina , Carmi-Leroy Annick , Dazas Melody , Wehenkel Anne-Marie , Didelot Xavier , Toubiana Julie , Badell Edgar , Brisse Sylvain 
Published: May 2020

ABSTRACTCorynebacterium diphtheriae, the agent of diphtheria, is a genetically diverse bacterial species. Although antimicrobial resistance has emerged against several drugs including first-line penicillin, the genomic determinants and population dynamics of resistance are largely unknown for this neglected human pathogen.Here we analyzed the associations of antimicrobial susceptibility phenotypes, diphtheria toxin production and genomic features inC. diphtheriae.We used 247 strains collected over several decades in multiple world regions, including the 163 clinical isolates collected prospectively from 2008 to 2017 in France mainland and overseas territories.Phylogenetic analysis revealed multiple deep-branching sublineages, grouped into a Mitis lineage strongly associated with diphtheria toxin production, and atox-negative Gravis lineage with fewtox+exceptions including the 1990s ex-Soviet Union outbreak strain. The distribution of susceptibility phenotypes allowed proposing ecological cutoffs for most of the 19 agents tested, thereby defining acquired antimicrobial resistance. Penicillin resistance was found in 17.2% of prospective isolates. Four isolates were multidrug resistant (>8 agents), including to penicillin and macrolides. Homologous recombination was frequent (r/m = 5) and horizontal gene transfer contributed to the emergence of antimicrobial resistance in multiple sublineages. Genome-wide association mapping uncovered genetic factors of resistance, including an accessory penicillin-binding protein (PBP2m) located in diverse genomic contexts. Genepbp2mis widespread in otherCorynebacteriumspecies and its expression inC. glutamicumdemonstrated its effect against several beta-lactams. A novel 73-kbC. diphtheriaemulti-resistance plasmid was discovered.This work uncovers the dynamics of antimicrobial resistance inC. diphtheriaein the context of phylogenetic structure, biovar and diphtheria toxin production, and provides a blueprint to analyze re-emerging diphtheria.
SERINC5 potently restricts retrovirus infectionin vivo
Authors: Timilsina Uddhav , Umthong Supawadee , Lynch Brian , Stablewski Aimee , Stavrou Spyridon 
Published: May 2020

ABSTRACTThe Serine Incorporator (SERINC) proteins are multipass transmembrane proteins that affect sphingolipid and phosphatidylserine synthesis. Human SERINC5 and SERINC3 were recently shown to possess antiretroviral activity to a number of retroviruses including human immunodeficiency virus (HIV), murine leukemia virus (MLV) and equine infectious anemia virus (EIAV). In the case of MLV, the glycosylated Gag (glyco-Gag) protein was found to counteract SERINC5-mediated restriction inin vitroexperiments and that the viral envelope determines virion sensitivity or resistance to SERINC5. However, nothing is known about thein vivofunction of SERINC5. Antiretroviral function of a host factorin vitrois not always associated with antiretroviral functionin vivo. Using SERINC5-/- mice we generated, we show that mouse SERINC5 (mSERINC5) restriction of MLV infectionin vivois dependent not only on glyco-Gag, but also on the retroviral envelope. Finally, we also examined thein vivofunction of the other SERINC gene with known antiretroviral functions, SERINC3. By using SERINC3-/- mice, we found that the murine homologue, mSERINC3, had no antiretroviral role bothin vivoandin vitro. This report provides the first data showing that SERINC5 restricts retrovirus infectionin vivoand that restriction of retrovirus infectivityin vivois dependent on both the presence of glyco-Gag and the viral envelope.IMPORTANCEThis study examines for the first time thein vivofunction of theSerineIncorporator (SERINC) proteins during retrovirus infection. SERINC3/5 restrict a number of retroviruses including human immunodeficiency virus 1 (HIV-1) and murine leukemia virus (MLV) by blocking their entry into cells. Nevertheless, HIV-1 and MLV encode factors, Nef and glycosylated Gag respectively, that counteract SERINC3/5in vitro. We recently developed SERINC3 and SERINC5 knockout mice to examine thein vivofunction of these genes. We found that SERINC5 potently restricted retrovirus infection in a glycosylated Gag and envelope dependent manner. On the other hand, SERINC3 had no antiviral function. Our findings have implication in the development of therapeutics that target SERINC5 during retrovirus infection.
Non-canonical proline-tyrosine interactions with multiple host proteins regulate Ebola virus infection
Authors: Batra Jyoti , Anantpadma Manu , Small Gabriel I. , Shtanko Olena , Zhang Mengru , Liu Dandan , Williams Caroline G. , Biedenkopf Nadine , Becker Stephan , Gross Michael L. , Leung Daisy W. , Davey Robert A. , Amarasinghe Gaya K. , Krogan Nevan J. , Basler Christopher F. 
Published: May 2020

AbstractThe Ebola virus VP30 protein interacts with the viral nucleoprotein and with host protein RBBP6 via PPxPxY motifs. In these interactions the largely alpha-helical carboxy-terminal domain of the EBOV VP30 engages with the motif such that the prolines adopt non-canonical orientations, as compared to other proline-rich motifs. Affinity tag-purification mass spectrometry identified additional PPxPxY-containing host proteins, including hnRNP L, hnRNPUL1 and PEG10, as VP30 interactors. Of these, hnRNP L and PEG10, like RBBP6, inhibit viral RNA synthesis and EBOV replication, whereas hnRNPUL1 enhances. Further, double knockdown studies support additive effects of RBBP6 and hnRNP L. Binding studies demonstrate variable capacity of PPxPxY motifs to bind VP30 and the extended motif PxPPPPxY is demonstrated to confer optimal binding and to inhibit RNA synthesis, with the fifth proline and the tyrosine being most critical. Competition binding and hydrogen-deuterium exchange studies demonstrate that each protein binds a similar interface on VP30 and impacts VP30 phosphorylation. VP30 therefore represents a novel proline recognition domain that allows multiple host proteins to target a single viral protein-protein interface to modulate viral transcription.