bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity of sea star-associated densoviruses and transcribed endogenized viral elements of densovirus origin
Authors: Jackson Elliot W. , Wilhelm Roland C. , Johnson Mitchell R. , Lutz Holly L. , Danforth Isabelle , Gaydos Joseph K. , Hart Michael W. , Hewson Ian 
Published: August 2020

AbstractA viral etiology of Sea Star Wasting Syndrome (SSWS) has been largely explored using metagenomics leading to the conclusion that a densovirus is the predominant DNA virus associated with this syndrome, and, thus, the most promising viral candidate pathogen. Single-stranded DNA viruses are however highly diverse and pervasive among eukaryotic organisms which we hypothesize may confound the association between densoviruses and SSWS in sea stars. To test this hypothesis and assess the association of densoviruses to SSWS, we compiled past metagenomic data with new metagenomic-derived viral genomes from sea stars collected from Antarctica, California, Washington, and Alaska. We used 179 publicly available sea star transcriptomes to complement our approaches for densovirus discovery. Lastly, we focus the study to SSaDV, the first sea star densovirus discovered, by documenting its biogeography and putative tissue tropism. Transcriptomes contained mostly endogenized densovirus elements similar to the NS1 gene, while >30 complete and near-complete densoviral genomes were recovered from viral metagenomes. SSaDV was associated with nearly all tested species from southern California to Alaska, and in contrast to previous work, we show SSaDV is one genotype among a high diversity of densoviruses present in sea stars across the west coast of the United States and globally that are commonly associated with grossly normal (i.e. healthy or asymptomatic) animals. The diversity and ubiquity of these viruses in wild sea stars confounds the original hypothesis that one densovirus was the etiologic agent of SSWD.ImportanceThe primary interest in sea star densoviruses, specifically SSaDV, has been their association with Sea Star Wasting Syndrome (SSWS), a disease that has decimated sea star populations across the west coast of the United States since 2013. The association of SSaDV to SSWS was originally drawn from metagenomic analyses concluding that it was (1) the only densovirus present in the metagenomic data and (2) the most likely viral candidate based on representation in symptomatic sea stars. We reassessed the original metagenomic data with additional genomic datasets and found that SSaDV was one of ten densoviruses present in the original dataset and was no more represented in symptomatic sea stars than in asymptomatic sea stars. Instead, SSaDV appears to be a widespread, generalist virus that exists among a large diversity of densoviruses present in sea star populations.
The emergence of phase separation as an organizing principle in bacteria
Authors: Azaldegui C.A. , Vecchiarelli A.G. , Biteen J.S. 
Published: August 2020

AbstractRecent investigations in bacteria suggest that membraneless organelles play a crucial role in the subcellular organization of bacterial cells. However, the biochemical functions and assembly mechanisms of these compartments have not yet been completely characterized. This Review assesses the current methodologies used in the study of membraneless organelles in bacteria, highlights the limitations in determining the phase of complexes in cells that are typically an order of magnitude smaller than a eukaryotic cell, and identifies gaps in our current knowledge about the functional role of membraneless organelles in bacteria. Liquid-liquid phase separation (LLPS) is one proposed mechanism for membraneless organelle assembly. Overall, we outline the framework to evaluate LLPSin vivoin bacteria, we describe the bacterial systems with proposed LLPS activity, and we comment on the general role LLPS plays in bacteria and how it may regulate cellular function. Lastly, we provide an outlook for super-resolution microscopy and single-molecule tracking as tools to assess condensates in bacteria.Statement of SignificanceThough membraneless organelles appear to play a crucial role in the subcellular organization and regulation of bacterial cells, the biochemical functions and assembly mechanisms of these compartments have not yet been completely characterized. Furthermore, liquid-liquid phase separation (LLPS) is one proposed mechanism for membraneless organelle assembly, but it is difficult to determine subcellular phases in tiny bacterial cells. Thus, we outline the framework to evaluate LLPSin vivoin bacteria and we describe the bacterial systems with proposed LLPS activity in the context of these criteria.
The role of anionic amino acids in hydrolysis of poly-β-(1,6)-N-acetylglucosamine exopolysaccharides by the biofilm dispersing glycosidase Dispersin B
Authors: Breslawec Alexandra P. , Wang Shaochi , Li Crystal , Poulin Myles B. 
Published: August 2020

AbstractThe exopolysaccharide poly-β-(1→6)-N-acetylglucosamine (PNAG) is a major structural determinant of bacterial biofilms responsible for persistent and nosocomial infections. The enzymatic dispersal of biofilms by PNAG-hydrolyzing glycosidase enzymes, such as Dispersin B (DspB), is a possible approach to treat biofilm dependent bacterial infections. The cationic charge resulting from partial de-N-acetylation of native PNAG is critical for PNAG-dependent biofilm formation. We recently demonstrated that DspB has increased catalytic activity with de-N-acetylated PNAG oligosaccharides; however, there is still little known about the molecular interaction required for DspB to bind native de-N-acetylated PNAG polysaccharides. Here, we analyze the role of anionic amino acids surrounding the catalytic pocket of DspB in PNAG substrate recognition and hydrolysis using a combination of site directed mutagenesis, activity measurements using synthetic PNAG oligosaccharide analogs, andin vitrobiofilm dispersal assays. The results of these studies support a model in which bound PNAG is weakly associated with a shallow anionic groove on the DspB protein surface with recognition driven by interactions with the –1 GlcNAc residue in the catalytic pocket. An increased rate of hydrolysis for cationic PNAG was driven, in part, by interaction with D147 on the anionic surface. Moreover, we identified that a DspB mutant with improved hydrolysis of fully acetylated PNAG oligosaccharides correlates with improvedin vitrodispersal of PNAG dependent Staphylococcus epidermidis biofilms. These results provide insight into the mechanism of substrate recognition by DspB and suggest a method to improve DspB biofilm dispersal activity by mutation of the amino acids within the anionic binding surface.
Genomic and phenotypic diversity ofEnterococcus faecalisisolated from endophthalmitis
Authors: Chilambi Gayatri Shankar , Nordstrom Hayley R. , Evans Daniel R. , Kowalski Regis P. , Dhaliwal Deepinder K. , Jhanji Vishal , Shanks Robert MQ , Van Tyne Daria 
Published: August 2020

ABSTRACTEnterococcus faecalisare hospital-associated opportunistic pathogens and also causative agents of post-operative endophthalmitis. Patients with enterococcal endophthalmitis often have poor visual outcomes, despite appropriate antibiotic therapy. Here we investigated the genomic and phenotypic characteristics ofE. faecalisisolates collected from 13 patients treated at the University of Pittsburgh Medical Center Eye Center over 19 years. Comparative genomic analysis indicated that patients were infected withE. faecalisof diverse multi-locus sequence types (STs) previously associated with clinical, commensal, and environmental sources. We identified knownE. faecalisvirulence factors and antibiotic resistance genes in each genome, including genes conferring resistance to aminoglycosides, erythromycin, and tetracyclines. We assessed all isolates for their cytolysin production, biofilm formation, and antibiotic susceptibility, and observed phenotypic differences between isolates. Fluoroquinolone and cephalosporin susceptibilities were particularly variable, as were biofilm formation and cytolysin production. In addition, we found evidence ofE. faecalisadaptation during recurrent endophthalmitis by identifying genetic variants that arose in sequential isolates sampled over eight-months from the same patient. We identified a mutation in the DNA mismatch repair genemutSthat was associated with a hypermutator phenotype in the final isolate from the patient, which was also more resistant to ceftazidime. Overall this study documents the genomic and phenotypic variability amongE. faecaliscausing endophthalmitis, as well as possible adaptive mechanisms underlying bacterial persistence during recurrent ocular infection.IMPORTANCEBacterial endophthalmitis is a sight-threatening infection of the inside of the eye.Enterococcus faecaliscause endophthalmitis occasionally, but when they do the infections are often severe. Here we investigated the genomes, antibiotic susceptibilities, and virulence-associated traits amongE. faecaliscollected from 13 patients with post-operative endophthalmitis. We wondered whether there were common bacterial factors that might explain why enterococcal endophthalmitis is so destructive to ocular tissues. Instead we found thatE. feacalisisolated from endophthalmitis were genetically and phenotypically diverse; isolates belonged to a variety of genetic lineages and showed varying levels of antibiotic resistance and biofilm formation. We also undertook further characterization of three closely relatedE. faecalisisolates from a patient with recurrent endophthalmitis, and found that a hypermutator strain emerged during persistent infection. Hypermutators have been found in a variety of other infection contexts; here we describe what we believe is the first case of a hypermutator arising during ocular infection.
Age disaggregation of crude excess deaths during the 2020 spring COVID–19 outbreak in Spain and Netherlands
Authors: Martín-Olalla José María 
Published: August 2020

Spanish and Dutch official records of mortality and population during the 21st century are analyzed to determine the age specific crude death rate in the 2020 spring COVID–19 outbreak.Excess death rate increases exponentially with age showing a doubling time [5.0, 5.6]a (Spain) and [3.9, 6.7]a (Netherlands), roughing doubling every five years of increase in age.The effective infection fatality rate in Spain also shows this doubling time.Statistically significant mortality increase is noted above 45 a (Spain) and 60 a (Netherlands).A statistically significant increase of mortality is also noted in Spain for the youngest age group.
CoMix: comparing mixing patterns in the Belgian population during and after lockdown
Authors: Coletti Pietro , Wambua James , Gimma Amy , Willem Lander , Vercruysse Sarah , Vanhoutte Bieke , Jarvis Christofer I , Van Zandvoort Kevin , Edmunds John , Beutels Philippe , Hens Niel 
Published: August 2020

AbstractBackgroundThe COVID-19 pandemic has shown how a newly emergent communicable disease can lay considerable burden on public health. To avoid system collapse, governments have resorted to several social distancing measures. In Belgium, this included a lockdown and a following period of phased re-opening.MethodsA representative sample of Belgian adults was asked about their contact behaviour from mid-April to mid-July, during different stages of the intervention measures in Belgium. Use of personal protection equipment (face masks) and compliance to hygienic measures was also reported. We estimated the expected reproduction number computing the ratio of R0 with respect to pre-pandemic data.FindingsDuring the first two waves (the first month) of the survey, the reduction in the average number of contacts was around 80% and was quite consistent across all age-classes. The average number of contacts increased over time, particularly for the younger age classes, still remaining significantly lower than pre-pandemic values. Since the end of May, the estimated reproduction number has a median value larger than one, although with a wide dispersion.ConclusionsWe have shown how a rapidly deployed survey can measure compliance to social distancing and assess its impact on COVID-19 spread. Monitoring the effectiveness of social distancing recommendations is of paramount importance to avoid further waves of COVID-19.
The DNA mimic protein BCAS0292 is involved in the regulation of virulence ofBurkholderia cenocepacia
Authors: Dennehy Ruth , Dignam Simon , McCormack Sarah , Romano Maria , Hou Yueran , Ardill Laura , Whelan Matthew X. , Drulis-Kawa Zuzanna , Ó Cróinín Tadhg , Valvano Miguel A. , Berisio Rita , McClean Siobhán 
Published: August 2020

AbstractAdaptation of opportunistic pathogens to their host environment requires reprogramming of a vast array of genes to facilitate survival in the host.Burkholderia cenocepacia, a Gram-negative bacterium that colonizes environmental niches, is exquisitely adaptable to the hypoxic environment of the cystic fibrosis lung and survives in macrophages.B. cenocepaciapossesses a large genome encoding multiple virulence systems, stress response proteins and a large locus that responds to low oxygen. We previously identified BCAS0292, an acidic protein encoded on replicon 3. Deletion of the BCAS0292 gene resulted in altered abundance of >1000 proteins; 46 proteins became undetectable while 556 proteins showed ≥1.5-fold reduced abundance, suggesting BCAS0292 is a global regulator. Moreover, the ΔBCAS0292 mutant showed a range of pleiotropic effects: virulence, host-cell attachment and motility were reduced, antibiotic susceptibility was altered and biofilm formation enhanced. Its growth and survival were impaired in 6% oxygen. Structural analysis revealed BCAS0292 presents a dimeric β-structure with a negative electrostatic surface. Further, the ΔBCAS0292 mutant displayed altered DNA supercoiling, implicated in global regulation of gene expression. We propose that BCAS0292 acts as a DNA-mimic, altering DNA topology and regulating the expression of multiple genes, thereby enabling the adaptation ofB. cenocepaciato highly diverse environments.
The longitudinal stability of fMRI activation during reward processing in adolescents and young adults
Authors: Baranger David AA , Lindenmuth Morgan , Nance Melissa , Guyer Amanda E. , Keenan Kate , Hipwell Alison E , Shaw Daniel S , Forbes Erika E 
Published: August 2020

AbstractBackgroundThe use of functional neuroimaging has been an extremely fruitful avenue for investigating the neural basis of human reward function. This approach has included identification of potential neurobiological mechanisms of psychiatric disease and examination of environmental, experiential, and biological factors that may contribute to disease risk via effects on the reward system. However, a central and largely unexamined assumption of much of this research is that neural reward function is an individual difference characteristic that is relatively stable over time.MethodsIn two independent samples of adolescents and young adults studied longitudinally (Ns= 145 & 153, 100% female & 100% male, ages 15-21 & 20-22, 2-4 scans & 2 scans respectively), we tested within-person stability of reward-task BOLD activation, with a median of 1 and 2 years between scans. We examined multiple commonly used contrasts of active states and baseline in both the anticipation and feedback phases of a card-guessing reward task. We examined the effects of cortical parcellation resolution, contrast, network (reward regions and resting-state networks), region-size, and activation strength and variability on the stability of reward-related activation.ResultsOverall, stability (ICC; intra-class correlation) across 1-2 years was modest. In both samples, contrasts of an active state relative to a baseline were more stable (e.g., Win>Baseline; mean ICC = 0.13 – 0.33) than contrasts of two active states (e.g., Win>Loss; mean ICC = 0.048 – 0.05). Additionally, activation in reward regions was less stable than in many non-task networks (e.g., dorsal attention), and activation in regions with greater between-subject variability showed higher stability in both samples.ConclusionsThese results show that functional neuroimaging activation to reward has modest stability over 1-2 years. Notably, results suggest that contrasts intended to map cognitive function and show robust group-level effects (i.e. Win > Loss) may be less effective in studies of individual differences and disease risk. The robustness of group-level activation should be weighed against other factors when selecting regions of interest in individual difference fMRI studies.
FlyORF-TaDa allows rapid generation of new lines forin vivocell-type specific profiling of protein-DNA interactions inDrosophila melanogaster
Authors: Aughey Gabriel N , Delandre Caroline , Southall Tony D , Marshall Owen J 
Published: August 2020

AbstractTargeted DamID (TaDa) is an increasingly popular method of generating cell-type specific DNA binding profilesin vivo. Although sensitive and versatile, TaDa requires the generation of new transgenic fly lines for every protein that is profiled, which is both time-consuming and costly. Here, we describe the FlyORF-TaDa system for converting an existing FlyORF library of inducible open reading frames (ORFs) to TaDa lines via a genetic cross, with recombinant progeny easily identifiable by eye colour. Profiling the binding of the H3K36me3-associated chromatin protein MRG15 in larval neural stem cells using both FlyORF-TaDa and conventional TaDa demonstrates that new lines generated using this system provide accurate and highly-reproducible DamID binding profiles. Our data further show that MRG15 binds to a subset of active chromatin domainsin vivo. Courtesy of the large coverage of the FlyORF library, the FlyORF-TaDa system enables the easy creation of TaDa lines for 74% of all transcription factors and chromatin modifying proteins within theDrosophilagenome.
The human PDZome 2.0: characterization of a new resource to test for PDZ interactions by Yeast Two-Hybrid
Authors: Castro-Cruz Monica , Lembo Frédérique , Borg Jean-Paul , Trave Gilles , Vincentelli Renaud , Zimmermann Pascale 
Published: August 2020

AbstractPSD95-disc large-zonula occludens (PDZ) domains are globular modules of 80-90 amino acids that co-evolved with multicellularity. They commonly bind to carboxy-terminal sequences of a plethora of membrane-associated proteins and influence their trafficking and signaling. We previously built a PDZ resource (PDZome) allowing to unveil human PDZ interactions by Yeast two-hybrid. Yet, this resource is partial according to the current knowledge on the human PDZ proteome. Here we built the PDZome 2.0 library for Yeast two-hybrid, based in a PDZ library manually curated from online resources. The PDZome2.0 contains 305 individual clones (266 PDZ domains in isolation and 39 tandems), for which all boundaries have been designed based on available PDZ structures. Using as bait the E6 oncoprotein from HPV16, a known promiscuous PDZ interactor, we show that PDZome 2.0 outperforms the previous resource.
DDX50 is a viral restriction factor that enhances TRIF-dependent IRF3 activation
Authors: Pallett Mitchell A. , Lu Yongxu , Smith Geoffrey L. 
Published: August 2020

AbstractThe transcription factors IRF3 and NF-κB are crucial in innate immune signalling in response to many viral and bacterial pathogens. However, mechanisms leading to their activation remain incompletely understood. Canonical RLR signalling and detection of viral RNA is dependent upon the receptors RIG-I, MDA5 and TLR3. Alternatively, the DExD-Box RNA helicases DDX1-DDX21-DHX36 activate IRF3/NF-κB in a TRIF-dependent manner independent of RIG-I, MDA5 or TLR3. Here we describe DDX50, which shares 55.6% amino acid identity with DDX21, as a component of the dsRNA sensing machinery and signalling pathway. Deletion of DDX50 in mouse and human cells impaired activation of the IFNβ promoter, IRF3-dependent endogenous gene expression and cytokine/chemokine production in response to cytoplasmic dsRNA (polyIC transfection), and infection by RNA and DNA viruses. Mechanistically, DDX50 co-immunoprecipitated with TRIF and DDX1, promoting complex formation upon stimulation. Furthermore, whilst MAVs/TBK1 induced signalling is intact inDdx50KO cells, TRIF-dependent signalling was impaired suggesting DDX50 drives TRIF-dependentIfnβtranscription. Importantly, loss of DDX50 resulted in increased replication and dissemination of vaccinia virus, herpes simplex virus and Zika virus highlighting its important role as a viral restriction factor.Author summaryThe detection of viral RNA or DNA by host RNA or DNA sensors and the subsequent antiviral immune response are crucial for the outcome of infection and host survival in response to a multitude of viral pathogens. Detection of viral RNA or DNA culminates in the upregulation of inflammatory cytokines, chemokines and pathogen restriction factors that augment the host innate immune response, restrict viral replication and clear infection. The canonical RNA sensor RIG-I is a member of the large family of DExD/H-box helicases, however the biological role of many DExD/H-box helicases remain unknown. In this report, we describe the DExD-Box helicase DDX50 as a new component of the RNA sensing machinery. In response to DNA and RNA virus infection, DDX50 functions to enhance activation of the transcription factor IRF3, which enhances antiviral signalling. The biological importance of DDX50 is illustrated by its ability to restrict the establishment of viral infection and to diminish the yields of vaccinia virus, herpes simplex virus and Zika virus. These findings increase knowledge of the poorly characterised host protein DDX50 and add another factor to the intricate network of proteins involved in regulating antiviral signalling in response to infection.