bluuebunny/crossref_metadata_2025 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

In 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 STATEMENT

Human 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

To 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

Articular 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

The 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

Major 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

Although 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

Macrophages 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.

IMPORTANCE

The 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

Background

During 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.

Aim

To measure the actual reduction of contacts when physical distancing measures are implemented.

Methods

In 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.

Results

The 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.

Conclusion

The 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.
Changing trends of excess self-protective behavior, and association with belief in prevention myths during the COVID-19 epidemic in China: A panel study
Authors: Yousef Yang Xiaozhao , peng Sihui , Yang Tingzhong , Rockett Ian R.H.
Published: May 2020

Abstract
Objective
This prospective observational study examined changing trends of excess self-protective behavior (EPB), and its association with perceived risk, severity and belief in prevention myths during the Chinese COVID-19 epidemic.
Methods
The study employed a longitudinal design. Participants were recruited for an online panel survey from chat groups on social media platforms. Descriptive statistics and the CATMOD program were used for data analysis.
Findings
Participants numbered 150 for the linkable baseline survey and 102 for the final survey. There were 5 waves of interviews. The prevalence of participants perceiving a personal risk of contracting COVID-19, and severe consequences of the disease, was 18.6% and 25.5%, respectively. Their prevalence had declined to 4.9% and 17.6%, respectively, by the last observation point. The 5 selected EPBs also manifested a decreasing trend. Belief in COVID-19 prevention myths trended upwards. Perceived risk was positively associated with each EPB, and perceived severity with disinfection of clothes and hoarding of products. Myth adherence was positively associated with disinfection of clothes and both hand washing and sanitization.
Conclusion
This study yielded new information about EPB among the public during the COVID-19 epidemic. Policy and health education modifications are essential for minimizing the adverse health effects of subscribing to prevention myths.
Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2
Authors: Mick Eran , Kamm Jack , Pisco Angela Oliveira , Ratnasiri Kalani , Babik Jennifer M , Calfee Carolyn S , Castaneda Gloria , DeRisi Joseph L , Detweiler Angela M , Hao Samantha , Kangelaris Kirsten N , Kumar G Renuka , Li Lucy M , Mann Sabrina A , Neff Norma , Prasad Priya A , Serpa Paula Hayakawa , Shah Sachin J , Spottiswoode Natasha , Tan Michelle , Christenson Stephanie A , Kistler Amy , Langelier Charles
Published: May 2020

We studied the host transcriptional response to SARS-CoV-2 by performing metagenomic sequencing of upper airway samples in 238 patients with COVID-19, other viral or non-viral acute respiratory illnesses (ARIs). Compared to other viral ARIs, COVID-19 was characterized by a diminished innate immune response, with reduced expression of genes involved in toll-like receptor and interleukin signaling, chemokine binding, neutrophil degranulation and interactions with lymphoid cells. Patients with COVID-19 also exhibited significantly reduced proportions of neutrophils and macrophages, and increased proportions of goblet, dendritic and B-cells, compared to other viral ARIs. Using machine learning, we built 26-, 10- and 3-gene classifiers that differentiated COVID-19 from other acute respiratory illnesses with AUCs of 0.980, 0.950 and 0.871, respectively. Classifier performance was stable at low viral loads, suggesting utility in settings where direct detection of viral nucleic acid may be unsuccessful. Taken together, our results illuminate unique aspects of the host transcriptional response to SARS-CoV-2 in comparison to other respiratory viruses and demonstrate the feasibility of COVID-19 diagnostics based on patient gene expression.
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

Corynebacterium 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

The 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.

IMPORTANCE

This 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

The 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.
Transcriptional profiling of immune and inflammatory responses in the context of SARS-CoV-2 fungal superinfection in a human airway epithelial model
Authors: de Lamballerie Claire Nicolas , Pizzorno Andrés , Fouret Julien , Szpiro Lea , Padey Blandine , Dubois Julia , Julien Thomas , Traversier Aurélien , Dulière Victoria , Brun Pauline , Lina Bruno , Rosa-Calatrava Manuel , Terrier Olivier
Published: May 2020

Superinfections of bacterial/fungal origin are known to affect the course and severity of respiratory viral infections. An increasing number of evidence indicate a relatively high prevalence of superinfections associated with COVID-19, including invasive aspergillosis, but the underlying mechanisms remain to be characterized. In the present study, to better understand the biological impact of superinfection we sought to determine and compare the host transcriptional response to SARS-CoV-2 versusAspergillussuperinfection, using a model of reconstituted humain airway epithelium. Our analyses reveal that both simple infection and superinfection induce a strong deregulation of core components of innate immune and inflammatory responses, with a stronger response to superinfection in the bronchial epithelial model compared to its nasal counterpart. Our results also highlight unique transcriptional footprints of SARS-CoV-2Aspergillussuperinfection, such as an imbalanced type I/type III IFN, and an induction of several monocyte- and neutrophil associated chemokines, that could be useful for the understanding ofAspergillus-associated COVID-19 and but also management of severe forms of aspergillosis in this specific context.
AnAms1.0: A high-quality chromosome-scale assembly of a domestic catFelis catusof American Shorthair breed
Authors: Isobe Sachiko , Matsumoto Yuki , Chung Claire , Sakamoto Mika , Chan Ting-Fung , Hirakawa Hideki , Ishihara Genki , Lam Hon-Ming , Nakayama Shinobu , Sasamoto Shigemi , Tanizawa Yasuhiro , Watanabe Akiko , Watanabe Kei , Yagura Masaru , Nakamura Yasukazu
Published: May 2020

The domestic cat (Felis catus) is one of the most popular companion animals in the world. Comprehensive genomic resources will aid the development and application of veterinary medicine including to improve feline health, in particular, to enable precision medicine which is promising in human application. However, currently available cat genome assemblies were mostly built based on the Abyssinian cat breed which is highly inbred and has limited power in representing the vast diversity of the cat population. Moreover, the current reference assembly remains fragmented with sequences contained in thousands of scaffolds. We constructed a reference-grade chromosome-scale genome assembly of a domestic cat,Felis catusgenome of American Shorthair breed, Anicom American shorthair 1.0 (AnAms1.0) with high contiguity (scaffold N50 > 120 Mb), by combining multiple advanced genomic technologies, including PacBio long-read sequencing as well as sequence scaffolding by long-range genomic information obtained from Hi-C and optical mapping data. Homology-based andab initiogene annotation was performed with the Iso-Seq data. Analyzed data is be publicly accessible on Cats genome informatics (Cats-I,https://cat.annotation.jp/), a cat genome database established as a platform to facilitate the accumulation and sharing of genomic resources to improve veterinary care.
Emerging phylogenetic structure of the SARS-CoV-2 pandemic
Authors: Fountain-Jones Nicholas M. , Appaw Raima Carol , Carver Scott , Didelot Xavier , Volz Erik , Charleston Michael
Published: May 2020

Since spilling over into humans, SARS-CoV-2 has rapidly spread across the globe, accumulating significant genetic diversity. The structure of this genetic diversity, and whether it reveals epidemiological insights, are fundamental questions for understanding the evolutionary trajectory of this virus. Here we use a recently developed phylodynamic approach to uncover phylogenetic structures underlying the SARS-CoV-2 pandemic. We find support for three SARS-CoV-2 lineages co-circulating, each with significantly different demographic dynamics concordant with known epidemiological factors. For example, Lineage C emerged in Europe with a high growth rate in late February, just prior to the exponential increase in cases in several European countries. Mutations that characterize Lineage C in particular are non-synonymous and occur in functionally important gene regions responsible for viral replication and cell entry. Even though Lineages A and B had distinct demographic patterns, they were much more difficult to distinguish. Continuous application of phylogenetic approaches to track the evolutionary epidemiology of SARS-CoV-2 lineages will be increasingly important to validate the efficacy of control efforts and monitor significant evolutionary events in the future.
A ChIC solution for ChIP-seq quality assessment
Authors: Livi Carmen Maria , Tagliaferri Ilario , Pal Koustav , Sebestyén Endre , Lucini Federica , Bianchi Andrea , Valsoni Sara , Lanzuolo Chiara , Ferrari Francesco
Published: May 2020

Despite the widespread adoption of the ChIP-seq technique, there is still no consensus on quality assessment procedures. Quantitative metrics previously proposed in literature are not always effective in discriminating the success or failure of an experiment, thus hampering objectivity and reproducibility of quality control. Here we introduce ChIC, a new framework for ChIP-seq data quality assessment that overcomes the limitations of previous solutions. ChIC is the first method for ChIP-seq quality control directly considering the enrichment profile shape, thus achieving good performances on ChIP targets yielding sharp and broad peaks alike. We integrate a comprehensive set of quality control metrics into one single score reliably summarizing the sample quality. The ChIC score is based on a machine learning classifier trained on a compendium with thousands of ChIP-seq profiles, which can also be used as a reference for easier evaluation of new datasets. ChIC is implemented as a user-friendly R/Bioconductor package.
Genetic Analysis of The Endangered Cleveland Bay Horse: A Century of Breeding Characterised by Pedigree and Microsatellite Data
Authors: Dell Andrew , Curry Mark , Yarnell Kelly , Starbuck Gareth , Wilson Philippe B.
Published: May 2020

The Cleveland Bay horse is one of the oldest equines in the United Kingdom, with pedigree data going back almost 300 years. The studbook is essentially closed and because of this, there are concerns about loss of genetic variation across generations. The breed is one of five equine breeds listed as “critical” (<300 registered adult breeding females) by the UK Rare Breeds Survival Trust in their annual Watchlist. Due to their critically endangered status, the current breadth of their genetic diversity is of concern, and assessment of this can lead to improved breed management strategies. Herein, both genealogical and molecular methods are combined in order to assess founder representation, lineage, and allelic diversity. Data from 16 microsatellite loci from a reference population of 402 individuals determined a loss of 91% and 48% of stallion and dam lines, respectively in the reference population. Only 3 ancestors determine 50% of the genome in the living population, with 70% of maternal lineage being derived from 3 founder females, and all paternal lineages traced back to a single founder stallion. Methods and theory are described in detail in order to demonstrate the scope of this analysis for wider conservation strategies. We quantitatively demonstrate the critical nature of the genetic resources within the breed, and offer a perspective on implementing this data in considered breed management strategies.
Actin-binding compounds, discovered by FRET-based high-throughput screening, differentially affect skeletal and cardiac muscle
Authors: Guhathakurta Piyali , Phung Lien A. , Prochniewicz Ewa , Lichtenberger Sarah , Wilson Anna , Thomas David D.
Published: May 2020

We have used spectroscopic and functional assays to evaluate the effects of a group of actin-binding compounds on striated muscle protein structure and function. Actin is present in every human cell, and its interaction with multiple myosin isoforms and multiple actin-binding proteins is essential for cellular viability. A previous high-throughput time-resolved fluorescence resonance energy transfer (TR-FRET) assay from our group identified a class of compounds that bind to actin and affect actomyosin structure and function. In the current study, we tested their effects on the two isoforms of striated muscle α-actins, skeletal and cardiac. We found that a majority of these compounds affected the transition of monomeric G-actin to filamentous F-actin, and that these effects were different for the two actin isoforms, suggesting a different mode of action. To determine the effects of these compounds on sarcomeric function, we further tested their activity on skeletal and cardiac myofibrils. We found that several compounds affected ATPase activity of skeletal and cardiac myofibrils differently, suggesting different mechanisms of action of these compounds for the two muscle types. We conclude that these structural and biochemical assays can be used to identify actin-binding compounds that differentially affect skeletal and cardiac muscles. The results of this study set the stage for screening of large chemical libraries for discovery of novel compounds that act therapeutically and specifically on cardiac or skeletal muscle.
A role for neutral variation in the evolution of C4photosynthesis
Authors: Karki Shanta , Lin HsiangChun , Danila Florence R , Abu-Jamous Basel , Giuliani Rita , Emms David M , Coe Robert A , Covshoff Sarah , Woodfield Helen , Bagunu Efren , Thakur Vivek , Wanchana Samart , Slamet-Loedin Inez , Cousins Asaph B. , Hibberd Julian M , Kelly Steven , Quick W Paul
Published: May 2020

Convergent trait evolution is a recurrent phenomenon in all domains of the tree of life. While some convergent traits are caused by simple sequence changes, many are associated with extensive changes to the sequence and regulation of large cohorts of genes. It is unknown how organisms traverse this expansive genotype space to assemble such complex convergent phenotypes. C4photosynthesis is a paradigm of large-scale phenotypic convergence. Conceptual and mathematical models propose that C4photosynthesis evolved from ancestral C3photosynthesis through sequential adaptive changes. These adaptive changes could have been rapidly assembled if modifications to the activity and abundance of enzymes of the C4cycle was neutral in C3plants. This neutrality would enable populations of C3plants to maintain genotypes with expression levels of C4enzymes analogous to those in C4species and thus enable rapid assembly of a functional C4cycle from naturally occurring genotypes given shared environmental selection. Here we show that there is substantial natural variation in expression of genes encoding C4cycle enzymes between natural accessions of the C3plantArabidopsis thaliana. We further show through targeted transgenic experiments in the C3cropOryza sativa, that high expression of the majority of C4cycle enzymes in rice is neutral with respect to growth, development, biomass and photosynthesis. Thus, substantial variation in the abundance and activity of C4cycle enzymes is permissible within the limits of operation of C3photosynthesis and the emergence of component parts of this complex convergent trait can be facilitated by neutral variation.
Are flowers tuned to buzzing pollinators? Variation in the natural frequency of stamens with different morphologies and its relationship to bee vibrations
Authors: Nunes Carlos Eduardo Pereira , Nevard Lucy , Montealegre-Zapata Fernando , Vallejo-Marin Mario
Published: May 2020

During buzz pollination, bees use vibrations to remove pollen from flowers. Vibrations at the natural frequency of pollen-carrying stamens are amplified through resonance, resulting in higher-amplitude vibrations. Because pollen release depends on vibration amplitude, bees could increase pollen removal by vibrating at the natural frequency of stamens. Yet, few studies have characterized the natural frequencies of stamens and compared them to frequencies of buzz-pollinating bees. Here we use laser Doppler vibrometry to characterise natural frequencies of stamens of six buzz-pollinatedSolanumtaxa of contrasting stamen morphology. We also compare the fundamental frequency of bumblebee buzzes produced on twoSolanumspecies with different natural frequencies. We found that stamen morphology and plant identity explain variation in natural frequency of stamens. Our results show that medium-sized pollinators, such as bumblebees, produce buzzes of frequencies higher than the natural frequency of most (5/6) of theSolanumspecies we studied. However, the observed natural frequency ofSolanumstamens is at the low end of the range of frequencies produced by other buzz-pollinating bees. Thus, our findings suggest that in some buzz pollination interactions, but not others, stamen resonance may play a role in mediating pollen release.
Interplay between bacterial deubiquitinase and ubiquitin E3 ligase regulates ubiquitin dynamics onLegionellaphagosomes
Authors: Liu Shuxin , Luo Jiwei , Zhen Xiangkai , Qiu Jiazhang , Ouyang Songying , Luo Zhao-Qing
Published: May 2020

Legionella pneumophilaextensively modulates the host ubiquitin network to create theLegionella-containing vacuole (LCV) for its replication. Many of its virulence factors function as ubiquitin ligases or deubiquitinases (DUBs). Here we identified Lem27 as a DUB that displays a preference for diubiquitin formed by K6, K11 or K48. Lem27 is associated with the LCV where it regulates Rab10 ubiquitination in concert with SidC and SdcA, two bacterial E3 ubiquitin ligases. Structural analysis of the complex formed by an active fragment of Lem27 and the substrate-based suicide inhibitor ubiquitin-propargylamide (PA) reveals that it harbors a fold resembling those in the OTU1 DUB subfamily with a Cys-His catalytic dyad and that it recognizes ubiquitin via extensive hydrogen bonding at six contact sites. Our results establish Lem27 as a deubiquitinase that functions to regulate protein ubiquitination on L. pneumophila phagosomes by counteracting the activity of bacterial ubiquitin E3 ligases.
Fungi are more dispersal limited than bacteria among flowers
Authors: Vannette Rachel L. , McMunn Marshall S. , Hall Griffin W. , Mueller Tobias G. , Munkres Ivan , Perry Douglas
Published: May 2020

Variation in dispersal ability among taxa affects community assembly and biodiversity maintenance within metacommunities. Although fungi and bacteria frequently coexist, their relative dispersal abilities are poorly understood. Nectar-inhabiting microbial communities affect plant reproduction and pollinator behavior, and are excellent models for studying dispersal of bacteria and fungi in a metacommunity framework. Here, we assay dispersal ability of common nectar bacteria and fungi in an insect-based dispersal experiment. We then compare these results to the incidence and abundance of culturable flower-inhabiting bacteria and fungi within naturally occurring flowers across two coflowering communities in California across two flowering seasons. Our microbial dispersal experiment demonstrates that bacteria disperse among habitat patches more readily than fungi via thrips. Across all flowers, bacterial and fungal incidence and abundance were positively correlated but bacteria were much more widespread, suggesting shared dispersal routes or habitat requirements but differences in dispersal and colonization frequency. The finding that bacteria are more common among flowers sampled here, in part due to superior insect-mediated dispersal, may have broad relevance for microbial life-history, community assembly of microbes and plant-pollinator interactions.
Glycans function as a Golgi export signal to promote the constitutive exocytic trafficking
Authors: Sun Xiuping , Tie Hieng Chiong , Chen Bing , Lu Lei
Published: May 2020

Most proteins in the secretory pathway are glycosylated. However, the role of glycans in the membrane trafficking is still unclear. Here, we discovered that transmembrane secretory cargos, such as interleukin 2 receptor α subunit or Tac, transferrin receptor and cluster of differentiation 8a, unexpectedly displayed substantial Golgi localization when their O-glycosylation was compromised. By quantitatively measuring their Golgi residence times, we found that the apparent Golgi localization of these O-glycan deficient cargos is due to their slow Golgi export. The super-resolution microscopy method that we previously developed revealed that O-glycan deficient Tac chimeras localize at the interior of thetrans-Golgi cisternae. The O-glycan was observed to be both necessary and sufficient for the efficient Golgi export of Tac chimeras. By sequentially introducing O-glycosylation sites to β-galactoside α-2,6-sialyltransferase1, we demonstrated that the O-glycan’s effect on the Golgi export is probably additive. Finally, the finding that N-glycosylated GFP substantially reduces the Golgi residence time of Tac chimera suggests that the N-glycan might have a similar effect. Therefore, both O- and N-glycan might function as a generic Golgi export signal at thetrans-Golgi to promote the constitutive exocytic trafficking.
Demonstration of a ring-FEL as an EUV lithography tool
Authors: Lee Jaeyu , Jang G. , Kim J. , Oh B. , Kim D.-E. , Lee S. , Kim J.-H. , Ko J. , Min C. , Shin S.
Published: May 2020

This paper presents the required structure and function of a ring-FEL as a radiation source for extreme ultraviolet radiation lithography (EUVL). A 100 m-long straight section that conducts an extremely low emittance beam from a fourth-generation storage ring can increase the average power at 13.5 nm wavelength to up to 1 kW without degrading the beam in the rest of the ring. Here, simulation results for a ring-FEL as a EUVL source are described.
Can we trust the experiment? Anisotropic displacement parameters in 1-(halomethyl)-3-nitrobenzene (halogen = Cl or Br)
Authors: Mroz Damian , Wang Ruimin , Englert Ulli , Dronskowski Richard
Published: May 2020

1-(Chloromethyl)-3-nitrobenzene, C7H6NClO2, and 1-(bromomethyl)-3-nitrobenzene, C7H6NBrO2, were chosen as test compounds for benchmarking anisotropic displacement parameters (ADPs) calculated from first principles in the harmonic approximation. Crystals of these compounds are isomorphous, and theory predicted similar ADPs for both. In-house diffraction experiments with Mo Kα radiation were in apparent contradiction to this theoretical result, with experimentally observed ADPs significantly larger for the bromo derivative. In contrast, the experimental and theoretical ADPs for the lighter congener matched reasonably well. As all usual quality indicators for both sets of experimental data were satisfactory, complementary diffraction experiments were performed at a synchrotron beamline with shorter wavelength. Refinements based on these intensity data gave very similar ADPs for both compounds and were thus in agreement with the earlier in-house results for the chloro derivative and the predictions of theory. We speculate that strong absorption by the heavy halogen may be the reason for the observed discrepancy.
Extending the Debye scattering equation for diffraction from a cylindrically averaged group of atoms: detecting molecular orientation at an interface
Authors: Ross A. E. , McCulloch D. G. , McKenzie D. R.
Published: May 2020

The Debye scattering equation is now over 100 years old and has been widely used to interpret diffraction patterns from randomly oriented groups of atoms. The present work develops and applies a related equation that calculates diffraction intensity from groups of atoms randomly oriented about a fixed axis, a scenario that occurs when molecules are oriented at an interface by the presentation of a binding motif as in antibody binding. Using an example biomolecule, the high level of sensitivity of the diffraction pattern to the orientation of the molecule and to the direction of the incident beam is shown. The use of the method is proposed not only for determining the orientation of molecules in biosensors and at membrane interfaces, but also for determining molecular conformation without the need for crystallization.
Influence of heat treatment on corrosion behavior of laser welded Mg-Gd-Y fusion zones
Authors: Wang Lyuyuan , Huang Jian , Peng Yong , Jia Yang , Ni Rong
Published: May 2020

Purpose

This paper aims to evaluate the corrosion resistance of fusion zones in different heat treated condition from laser welded Mg-Gd-Y alloys and analyze their intrinsic corrosion mechanism.

Design/methodology/approach

The corrosion behavior of fusion zone from laser-welded Mg-Gd-Y alloy joints in the as-welded, ageing and solution + ageing conditions was investigated in the 3.5 wt.% NaCl solution by immersion tests.

Findings

The corroded surface of as-welded fusion zone consists of dark and bright regions, and the bright regions were composed of high-density needle-like products, whereas some different extended direction of the cracks with lots of long ultrafine needle-shaped corrosion products appeared in the dark regions. The corrosion resistance of the fusion zone is slightly decreased after the ageing treatment.

Originality/value

The solution + ageing treated fusion zone exhibits the highest corrosion resistance than that of the as-welded and ageing treated state because of the full dissolution of the cathodic coarse eutectic compound, grains growth and relatively compact protective films. The inhomogeneous distribution of the β′ can somewhat improve the corrosion rate of solution + ageing treated fusion zone when compared with base metal.