bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-molecule view of coordination in a multi-functional DNA polymerase
Authors: Pauszek Raymond F. , Lamichhane Rajan , Singh Arishma Rajkarnikar , Millar David P. 
Published: August 2020

AbstractReplication and repair of genomic DNA requires the action of multiple enzymatic functions that must be coordinated in order to ensure efficient and accurate product formation. Here we have used single-molecule FRET microscopy to investigate the physical basis of functional coordination in DNA polymerase I (Pol I) fromE. coli, a key enzyme involved in lagging-strand replication and base excision repair. Pol I contains active sites for template-directed DNA polymerization and 5’ flap processing in separate domains. We show that a DNA substrate can spontaneously transfer between polymerase (pol) and 5’ nuclease (5’ nuc) domains during a single encounter with Pol I. Additionally, we show that the flexibly tethered5’ nucdomain adopts different positions within Pol I-DNA complexes, depending on the nature of the DNA substrate. Our results reveal the structural dynamics that underlie functional coordination in Pol I and are likely relevant to other multi-functional DNA polymerases.
Attenuated influenza virions expressing the SARS-CoV-2 receptor-binding domain induce neutralizing antibodies in mice
Authors: Loes Andrea N. , Gentles Lauren E. , Greaney Allison J. , Crawford Katharine H. D. , Bloom Jesse D. 
Published: August 2020

AbstractAn effective vaccine is essential to controlling the spread of SARS-CoV-2 virus. Here, we describe an influenza-virus-based vaccine for SARS-CoV-2. We incorporated a membrane-anchored form of the SARS-CoV-2 Spike receptor binding domain (RBD) in place of the neuraminidase (NA) coding sequence in an influenza virus also possessing a mutation that reduces the affinity of hemagglutinin for its sialic acid receptor. The resulting ΔNA(RBD)-Flu virus can be generated by reverse genetics and grown to high titers in cell culture. A single-dose intranasal inoculation of mice with ΔNA(RBD)-Flu elicits serum neutralizing antibody titers against SAR-CoV-2 comparable to those observed in humans following natural infection (∼1:200). Furthermore, ΔNA(RBD)-Flu itself causes no apparent disease in mice. It might be possible to produce a vaccine similar to ΔNA(RBD)-Flu at scale by leveraging existing platforms for production of influenza vaccines.
An antiviral self-replicating molecular heterotroph
Authors: Shapiro Anastasia , Rosenberg Alexander , Levy-Zamir Adva , Bassali Liron , Ittah Shmulik , Abu-Horowitz Almogit , Bachelet Ido 
Published: August 2020

AbstractWe report the synthesis of a molecular machine, fabricated from nucleic acids, which is capable of digesting viral RNA and utilizing it to assemble additional copies of itself inside living cells. The machine’s body plan combines several parts that build upon the target RNA, assembling an immobile, DNA:RNA 4-way junction, which contains a single gene encoding a hammerhead ribozyme (HHR). Full assembly of the machine’s body from its parts enables the subsequent elongation of the gene and transcription of HHR molecules, followed by HHR-mediated digestion of the target molecule. This digestion converts the target to a building block suitable for participation in the assembly of more copies of the machine, mimicking biological heterotrophy. In this work we describe the general design of a prototypical machine, characterize its activity cycle and kinetics, and show that it can be efficiently and safely delivered into live cells. As a proof of principle, we constructed a machine that targets theAutographa californicamulticapsid nucleopolyhedrovirus (AcMNPV) GP64 gene, and show that it effectively suppresses viral propagation in a cell population, exhibiting predator/prey-like dynamics with the infecting virus. In addition, the machine significantly reduced viral infection, stress signaling, and innate immune activation inside virus-infected animals. This preliminary design could control the behavior of antisense therapies for a range of applications, particularly against dynamic targets such as viruses and cancer.
Microbial community shifts reflect losses of native soil carbon with pyrogenic and fresh organic matter additions and are greatest in low-carbon soils
Authors: Whitman Thea , DeCiucies Silene , Hanley Kelly , Enders Akio , Woolet Jamie , Lehmann Johannes 
Published: August 2020

AbstractSoil organic carbon (SOC) plays an important role in regulating global climate change, carbon and nutrient cycling in soils, and soil moisture. Organic matter (OM) additions to soils can affect the rate at which SOC is mineralized by microbes, with potentially important effects on SOC stocks. Understanding how pyrogenic organic matter (PyOM) affects the cycling of native SOC (nSOC) and the soil microbes responsible for these effects is important for fire-affected ecosystems as well as for biochar-amended systems. We used an incubation trial with five different soils from National Ecological Observatory Network sites across the US and13C-labelled 350°C corn stover PyOM and fresh corn stover OM to trace nSOC-derived CO2emissions with and without PyOM and OM amendments. We used high-throughput sequencing of rRNA genes to characterize bacterial, archaeal, and fungal communities and their response to PyOM and OM. We found that the effects of amendments on nSOC-derived CO2reflected the unamended soil C status, where amendments increased C mineralization the most in low-C soils. OM additions produced much greater effects on nSOC-CO2emissions than PyOM additions. Furthermore, the magnitude of microbial community composition change mirrored the magnitude of increases in nSOC-CO2, indicating a specific subset of microbes were likely responsible for the observed changes in nSOC mineralization. However, PyOM responders differed across soils and did not necessarily reflect a common “charosphere”. Overall, this study suggests that soils that already have low SOC may be particularly vulnerable to short-term increases in SOC loss with OM or PyOM additions.ImportanceSoil organic matter (SOM) has an important role in global climate change, carbon and nutrient cycling in soils, and soil moisture dynamics. Understanding the processes that affect SOM stocks is important for managing these functions. Recently, understanding how fire-affected, or “pyrogenic” organic matter (PyOM) affects existing SOM stocks has become increasingly important, both due to changing fire regimes, and to interest in “biochar” – pyrogenic organic matter that is produced intentionally for carbon management or as an agricultural soil amendment. We found that soils with less SOM were more prone to increased losses with PyOM (and fresh organic matter) additions, and that soil microbial communities changed more in soils that also had greater SOM losses with PyOM additions. This suggests that soils that already have low SOM content may be particularly vulnerable to short-term increases in SOM loss, and that a subset of the soil microbial community is likely responsible for these effects.
Association between the Mediterranean diet and prostate cancer risk in a Greek population
Authors: Vaioulis Alexandros , Yiannis Kiouvrekis , Perivoliotis Konstantinos , Stavros Gravas , Vasilios Tzortzis , Anastasios Karatzas 
Published: August 2020

ABSTRACTPurposeDietary modifications have been correlated with survival in several neoplasia, such as prostate cancer. The present study was designed to investigate the association between the Mediterranean diet and prostate cancer risk.MethodsA retrospective analysis of patients with a high suspicion of suffering from prostate cancer (PCa) who underwent prostate biopsy was performed. According to histopathology, two groups were generated, the PCa group and the Healthy group. The dietary profile of our study population was implemented, based on a modified MDS (Mediterranean Diet Score) questionnaire. A logistic regression model was used for the interpretation of our data.ResultsIn total, 431 patients with prostate cancer and 279 healthy men were included in our study. The demographic characteristics of the patients were comparable. Daily consumption of white meat (OR: 0.59), dairy products (OR: 0.64), nuts (OR: 0.63) and whole grains (OR: 0.55) was higher in healthy males. Infrequent consumption of vegetables was linked with an increased rate of PCa (OR: 2.55). Interestingly daily consumption of processed meat rates was higher in healthy men. However, a significant correlation between specific intake products or frequency and the incidence of PCa was not established.ConclusionsAlthough, an association between the dietary patterns and PCa was not determined, components consumption patterns displayed a higher daily intake rate of white meat, dairy products, nuts and whole grains. Further prospective trials are required to validate the effect of Mediterranean diet in the incidence and mortality of PCa patients.
Validation of Saliva and Self-Administered Nasal Swabs for COVID-19 Testing
Authors: Teo Alvin Kuo Jing , Choudhury Yukti , Tan Iain Beehuat , Cher Chae Yin , Chew Shi Hao , Wan Zi Yi , Cheng Lionel Tim Ee , Oon Lynette Lin Ean , Tan Min Han , Chan Kian Sing , Hsu Li Yang 
Published: August 2020

AbstractBackgroundActive cases of COVID-19 has primarily been diagnosed via RT-PCR of nasopharyngeal (NP) swabs. Saliva and self-administered nasal (SN) swabs can be collected safely without trained staff.We aimed to test the sensitivity of “naso-oropharyngeal” saliva and SN swabs compared to NP swabs in a large cohort of migrant workers in Singapore.MethodsWe recruited 200 male adult subjects: 45 with acute respiratory infection, 104 asymptomatic close contacts, and 51 confirmed COVID-19 cases. Each subject underwent NP swab, SN swab and saliva collection for RT-PCR testing at 1 to 3 timepoints. We additionally used a direct-from-sample amplicon-based next-generation sequencing (NGS) workflow to establish phylogeny.ResultsOf 200 subjects, 91 and 46 completed second and third rounds of testing, respectively. Of 337 sets of tests, there were 150 (44.5%) positive NP swabs, 127 (37.7%) positive SN swabs, and 209 (62.0%) positive saliva.Test concordance between different sample sites was good, with a kappa statistic of 0.616 for NP and SN swabs, and 0.537 for NP and saliva. In confirmed symptomatic COVID-19 subjects, the likelihood of a positive test from any sample fell beyond 14 days of symptom onset.NGS was conducted on 18 SN and saliva samples, with phylogenetic analyses demonstrating lineages for all samples tested were Clade O (GISAID nomenclature) and lineage B.6 (PANGOLIN nomenclature).ConclusionThis study supports saliva as a sensitive and less intrusive sample for COVID-19 diagnosis and further delineates the role of oropharyngeal secretions in increasing the sensitivity of testing. However, SN swabs were inferior as an alternate sample type. Our study also provides evidence that a straightforward next-generation sequencing workflow can provide direct-from-sample phylogenetic analysis for public health decision-making.
Fezf2transient expression via modRNA with concurrent SIRT1 inhibition enhances differentiation of cortical subcerebral / corticospinal neuron identity from mES cells
Authors: Sadegh Cameron , Ebina Wataru , Arvanites Anthony C. , Davidow Lance S. , Rubin Lee L. , Macklis Jeffrey D. 
Published: August 2020

AbstractDuring late embryonic development of the cerebral cortex, the major class of cortical output neurons termed subcerebral projection neurons (SCPN; including the predominant population of corticospinal neurons, CSN) and the class of interhemispheric callosal projection neurons (CPN) initially express overlapping molecular controls that later undergo subtype-specific refinements. Such molecular refinements are largely absent in heterogeneous, maturation-stalled, neocortical-like neurons (termed “cortical” here) spontaneously generated by established embryonic stem cell (ES) and induced pluripotent stem cell (iPSC) differentiation. Building on recently identified central molecular controls over SCPN development, we used a combination of synthetic modified mRNA (modRNA) forFezf2, the central transcription factor controlling SCPN specification, and small molecule screening to investigate whether distinct chromatin modifiers might complementFezf2functions to promote SCPN-specific differentiation by mouse ES (mES)-derived cortical-like neurons. We find that the inhibition of a specific histone deacetylase, Sirtuin 1 (SIRT1), enhances refinement of SCPN subtype molecular identity by both mES-derived cortical-like neurons and primary dissociated E12.5 mouse cortical neurons.In vivo, we identify that SIRT1 is specifically expressed by CPN, but not SCPN, during late embryonic and postnatal differentiation. Together, these data indicate that SIRT1 has neuronal subtype-specific expression in the mouse cortexin vivo, and its inhibition enhances subtype-specific differentiation of highly clinically relevant SCPN / CSN cortical neuronsin vitro.
A Wnt-specific astacin proteinase controls head formation inHydra
Authors: Ziegler Berenice , Yiallouros Irene , Trageser Benjamin , Kumar Sumit , Mercker Moritz , Kling Svenja , Fath Maike , Warnken Uwe , Schnölzer Martina , Holstein Thomas W. , Hartl Markus , Marciniak-Czochra Anna , Stetefeld Jörg , Stöcker Walter , Özbek Suat 
Published: August 2020

AbstractTheHydrahead organizer acts as a signaling center that initiates and maintains the primary body axis in steady state polyps and during budding or regeneration. Wnt/beta-Catenin signaling functions as a primary cue controlling this process, but how Wnt ligand activity is locally restricted at the protein level is poorly understood.Here we report the identification of an astacin family proteinase as a Wnt processing factor.Hydraastacin-7 (HAS-7) is expressed from gland cells as an apical-distal gradient in the body column, peaking close beneath the tentacle zone.HAS-7siRNA knockdown abrogates HyWnt3 proteolysis in the head tissue and induces a robust double axis phenotype, which is rescued by simultaneousHyWnt3knockdown. Accordingly, double axes are also observed in conditions of increased Wnt levels as in transgenic actin::HyWnt3 and HyDkk1/2/4 siRNA treated animals.HyWnt3-induced double axes inXenopusembryos could be rescued by co-injection ofHAS-7mRNA. Mathematical modelling combined with experimental promotor analysis indicate an indirect regulation ofHAS-7by beta-Catenin, expanding the classical Turing-type activator-inhibitor model.Our data suggest a negative regulatory function of Wnt processing astacin proteinases in the global patterning of the oral-aboral axis inHydra.
Metaviromic identification of genetic hotspots of coronavirus pathogenicity using machine learning
Authors: Park Jonathan J. , Chen Sidi 
Published: August 2020

AbstractThe COVID-19 pandemic caused by SARS-CoV-2 has become a major threat across the globe. Here, we developed machine learning approaches to identify key pathogenic regions in coronavirus genomes. We trained and evaluated 7,562,625 models on 3,665 genomes including SARS-CoV-2, MERS-CoV, SARS-CoV and other coronaviruses of human and animal origins to return quantitative and biologically interpretable signatures at nucleotide and amino acid resolutions. We identified hotspots across the SARS-CoV-2 genome including previously unappreciated features in spike, RdRp and other proteins. Finally, we integrated pathogenicity genomic profiles with B cell and T cell epitope predictions for enrichment of sequence targets to help guide vaccine development. These results provide a systematic map of predicted pathogenicity in SARS-CoV-2 that incorporates sequence, structural and immunological features, providing an unbiased collection of genetic elements for functional studies. This metavirome-based framework can also be applied for rapid characterization of new coronavirus strains or emerging pathogenic viruses.
Forage stoichiometry predicts the home range size of a small terrestrial herbivore
Authors: Rizzuto Matteo , Leroux Shawn J. , Vander Wal Eric , Richmond Isabella C. , Heckford Travis R. , Balluffi-Fry Juliana , Wiersma Yolanda F. 
Published: August 2020

AbstractConsumers make space use decisions based on resource quality. Most studies that investigate the influence of resource quality on the spatial ecology of consumers use diverse proxies for quality including measures based on habitat classification, forage species diversity and abundance, and nutritional indicators, e.g., protein. Ecological stoichiometry measures resource quality in terms of elemental ratios, e.g., carbon (C):nitrogen (N) ratio, but rarely have these currencies been used to study consumer space use decisions. Yet, elemental ratios provide a uniquely quantitative way to assess resource quality. Consequently, ecological stoichiometry allows for investigation of how consumers respond to spatial heterogeneity in resource quality by changing their space use, e.g. their home range size, and how this may influence ecosystem dynamics and trophic interactions. Here, we test whether the home range size of a keystone boreal herbivore, the snowshoe hare (Lepus americanus), varies with differences in the C:N, C:phosphorus (P), and N:P ratios of two preferred forage species, lowland blueberry (Vaccinium angustifolium) and red maple (Acer rubrum). We consider forage resources with higher C content relative to N and P to be lower quality than resources with lower relative C content. We use a novel approach, combining elemental distribution models with herbivore home range size estimates to test our hypothesis that hare home range size will be smaller in areas with access to high, homogeneous resource quality compared to areas with access to low, heterogeneous resource quality during summer months. Our results support our prediction for lowland blueberry, but not for red maple. Herbivore home range size decreased with increasing blueberry foliage quality, but also with decreasing spatial heterogeneity in blueberry foliage quality, i.e. N or P content. Herbivores in the boreal forest face strong nutritional constraints due to the paucity of N and P. Access to areas of high, homogeneous resource quality is paramount to meeting their dietary requirements with low effort. In turn, this may influence community (e.g., trophic interactions) and ecosystem (e.g., nutrient cycling) processes. Paradoxically, our study shows that taking a reductionist approach of viewing resources through a biochemical lens can lead to holistic insights of consumer spatial ecology.
Functional shifts of soil microbial communities associated withAlliaria petiolatainvasion
Authors: Duchesneau Katherine , Golemiec Anneke , Colautti Robert I. , Antunes Pedro M. 
Published: August 2020

AbstractSoil feedback is thought to be an important contributor to the success of invasive plants. Despite evidence that invasive plants change soil microbial diversity, the functional roles of microbes impacted by invasion are still unclear. This knowledge is a critical component of our understanding of ecological mechanisms of plant invasion. Mounting evidence suggestsAlliaria petiolatacan suppress arbuscular mycorrhizal fungi (AMF) to disrupt native plant communities in controlled laboratory and greenhouse experiments, though it is less clear if allelochemicals persist under natural field conditions. Alternatively, invasive plants may accumulate pathogens that are more harmful to competitors as predicted by the Enemy of my Enemy Hypothesis (EEH). We examined changes in functional groups of soil bacteria and fungi associated with ten naturally occurring populations ofA. petiolatausing amplicon sequences (16S and ITS rRNA). To relate soil microbial communities to impacts on co-occurring plants, we measured root infections and AMF colonization. We found no changes in the diversity and abundance of AMF in plants co-occurring withA. petiolata, suggesting that mycorrhizal suppression in the field may not be as critical to the invasion ofA. petiolataas implied by more controlled experiments. Instead, we found changes in pathogen community composition and marginal evidence of increase in root lesions of plants growing withA. petiolata, lending support to the EEH. In addition to these impacts on plant health, changes in ectomycorrhiza, and other nutrient cycling microbes may be important forces underlying the invasion ofA. petiolataand its impact on ecosystem function.
Suv39h-catalysed H3K9me3 is critical for euchromatic genome organisation and the maintenance of gene transcription
Authors: Keenan Christine R. , Coughlan Hannah D. , Iannarella Nadia , Johanson Timothy M. , Chan Wing Fuk , Garnham Alexandra L. , Smyth Gordon K. , Allan Rhys S. 
Published: August 2020

SummaryH3K9me3-dependent heterochromatin is critical for the silencing of repeat-rich pericentromeric regions and also has key roles in repressing lineage-inappropriate protein-coding genes in differentiation and development. Here, we investigate the molecular consequences of heterochromatin loss in cells deficient in both Suv39h1 and Suv39h2 (Suv39DKO), the major mammalian histone methyltransferase enzymes that catalyse heterochromatic H3K9me3 deposition. Unexpectedly, we reveal a predominant repression of protein-coding genes in Suv39DKO cells, with these differentially expressed genes principally in euchromatic (DNaseI-accessible, H3K27ac-marked) rather than heterochromatic (H3K9me3-marked) regions. Examination of the 3D nucleome reveals that transcriptomic dysregulation occurs in euchromatic regions close to the nuclear periphery in 3-dimensional space. Moreover, this transcriptomic dysregulation is highly correlated with altered 3-dimensional genome organization in Suv39DKO cells. Together, our results suggest that the nuclear lamina-tethering of Suv39-dependent H3K9me3 domains provides an essential scaffold to support euchromatic genome organisation and the maintenance of gene transcription for healthy cellular function.
circHiC: circular visualization of Hi-C data and integration of genomic data
Authors: Junier Ivan , Varoquaux Nelle 
Published: August 2020

SummaryGenome wide contact frequencies obtained using Hi-C-like experiments have raised novel challenges in terms of visualization and rationalization of chromosome structuring phenomena. In bacteria, display of Hi-C data should be congruent with the circularity of chromosomes. However, standard representations under the form of square matrices or horizontal bands are not adapted to periodic conditions as those imposed by (most) bacterial chromosomes. Here, we fill this gap and propose a Python library, built upon the widely used Matplotlib library, to display Hi-C data in circular strips, together with the possibility to overlay genomic data. The proposed tools are light and fast, aiming to facilitate the exploration and understanding of bacterial chromosome structuring data. The library further includes the possibility to handle linear chromosomes, providing a fresh way to display and explore eukaryotic data.Availability and implementationThe package runs under Python 3 and is freely available at https://github.com/TrEE-TIMC/circHiC. The documentation can be found at https://tree-timc.github.io/circhic/; images obtained in different organisms are provided in the gallery section and are accompanied with codes.Contactivan.junier@univ-grenoble-alpes.fr, nelle.varoquaux@univ-grenoble-alpes.fr