bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation of ELISA based with random access serologic immunoassays for identifying adaptive immune response to SARS-CoV-2
Authors: Nguyen Nguyen N. , Mutnal Manohar B. , Gomez Richard R. , Pham Huy N. , Nguyen Lam T. , Koss William , Rao Arundhati , Arroliga Alejandro C. , Wang Liping , Wang Dapeng , Hua Yinan , Powell Priscilla R. , Chen Li , McCormack Colin C. , Linz Walter J. , Mohammad Amin A. 
Published: July 2020

AbstractPublic health emergency of SARS-CoV-2 has facilitated diagnostic testing as a related medical countermeasure against COVID-19 outbreak. Numerous serologic antibody tests have become available through an expedited federal emergency use only process. This paper highlights the analytical characteristic of an ELISA based assay by AnshLabs and three random access immunoassay (RAIA) by DiaSorin, Roche, and Abbott that have been approved for emergency use authorization (EUA), at a tertiary academic center in a low disease-prevalence area. The AnshLabs gave higher estimates of sero-prevalence, over the three RAIA methods. For positive results, AnshLabs had 93.3% and 100% concordance with DiaSorin or Abbott and Roche respectively. For negative results, AnshLabs had 69.7% and 73.0% concordance with DiaSorin and Roche or Abbott respectively. All discrepant samples that were positive by AnshLabs and negative by RAIA tested positive by all-in-one step SARS-CoV-2 Total (COV2T) assay performed on the automated Siemens Advia Centaur XPT analyzer. None of these methods, however, are useful in early diagnosis of SARS-CoV-2.
Forcing Seasonality of influenza-like epidemics with daily Solar resonance
Authors: Nicastro Fabrizio , Sironi Giorgia , Antonello Elio , Bianco Andrea , Biasin Mara , Brucato John R. , Ermolli Ilaria , Pareschi Giovanni , Salvati Marta , Tozzi Paolo , Trabattoni Daria , Clerici Mario 
Published: July 2020

SummarySeasonality of acute viral respiratory diseases is a well-known and yet not fully understood phenomenon. Several models have been proposed to explain the regularity of yearly recurring outbreaks and the phase-differences observed at different latitudes on Earth. Such models take into account known internal causes, primarily the periodic emergence of new virus variants that evade the host immune response. Yet, this alone, is generally unable to explain the regularity of recurrences and the observed phase-differences.Here we show that seasonality of viral respiratory diseases, as well as its distribution with latitude on Earth, can be fully explained by the virucidal properties of UV-B and A Solar photons through a daily, minute-scale, resonant forcing mechanism. Such an induced periodicity can last, virtually unperturbed, from tens to hundreds of cycles, and even in presence of internal dynamics (host’s loss of immunity) much slower than seasonal will, on a long period, generate seasonal oscillations.
The benefits of peer transparency in safe workplace operation post pandemic lockdown
Authors: Wey Arkady , Champneys Alan , Dyson Rosemary J. , Alwan Nisreen A. , Barker Mary 
Published: July 2020

AbstractThe benefits, both in terms of productivity and public health, are investigated for different levels of engagement with the test, trace and isolate procedures in the context of a pandemic in which there is little or no herd immunity. Simple mathematical modelling is used in the context of a single, relatively closed workplace such as a factory or back-office where, in normal operation, each worker has lengthy interactions with a fixed set of colleagues.A discrete-time SEIR model on a fixed interaction graph is simulated with parameters that are motivated by the recent COVID-19 pandemic in the UK during a post-peak phase, including a small risk of viral infection from outside the working environment. Two kinds of worker are assumed,transparentswho regularly test, share their results with colleagues and isolate as soon as a contact tests positive for the disease, andopaqueswho do none of these. Moreover, the simulations are constructed as a “playable model” in which the transparency level, disease parameters and mean interaction degree can be varied by the user. The model is analysed in the continuum limit.All simulations point to the double benefit of transparency in maximising productivity and minimising overall infection rates. Based on these findings, public policy implications are discussed on how to incentivise this mutually beneficial behaviour in different kinds of workplace, and simple recommendations are made.
Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning
Authors: Ing-Simmons Elizabeth , Vaid Roshan , Mannervik Mattias , Vaquerizas Juan M. 
Published: July 2020

ABSTRACTThe relationship between the 3D organisation of chromatin inside the nucleus and the regulation of gene expression remains unclear. While disruption of domains and domain boundaries can lead to mis-expression of developmental genes, acute depletion of key regulators of genome organisation, such as CTCF and cohesin, and major reorganisation of genomic regions have relatively small effects on gene expression. Therefore, it is unclear whether changes in gene expression and chromatin state drive chromatin reorganisation, or whether changes in chromatin organisation facilitate cell type-specific activation of genes and their regulatory elements. Here, using the Drosophila melanogaster dorsoventral patterning system as a model, we demonstrate the independence of 3D chromatin organisation and developmental gene regulation. We define tissue-specific enhancers and link them to expression patterns at the single-cell level using single cell RNA-seq. Surprisingly, despite tissue-specific differences in chromatin state and gene expression, 3D chromatin organisation is maintained across tissues. Our results provide strong evidence that tissue-specific chromatin conformation is not required for tissue-specific gene expression, but rather acts as an architectural framework to facilitate proper gene regulation during development.
The evolutionary history of ACE2 usage within the coronavirus subgenusSarbecovirus
Authors: Wells H.L , Letko M , Lasso G , Ssebide B , Nziza J , Byarugaba D.K , Navarrete-Macias I , Liang E , Cranfield M , Han B.A , Tingley M.W , Diuk-Wasser M , Goldstein T , Johnson C.K , Mazet J , Chandran K , Munster V.J , Gilardi K , Anthony S.J 
Published: July 2020

AbstractSARS-CoV-1 and SARS-CoV-2 are not phylogenetically closely related; however, both use the ACE2 receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda which are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario; and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2, and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.
Adenoviral chromatin organization primes for early gene activation
Authors: Schwartz Uwe , Komatsu Tetsuro , Huber Claudia , Lagadec Floriane , Baumgartl Conradin , Silberhorn Elisabeth , Nuetzel Margit , Rayne Fabienne , Basyuk Eugenia , Bertrand Edouard , Rehli Michael , Wodrich Harald , Laengst Gernot 
Published: July 2020

SUMMARYWithin the virion, adenovirus DNA associates with the virus-encoded, protamine-like structural protein pVII. Whether this association is organized, and how genome packaging changes during infection and subsequent transcriptional activation is currently unknown. Here, we combined RNA-seq, MNase-seq, ChIP-seq and single genome imaging during early adenovirus infection to unveil the structure- and time-resolved dynamics of viral chromatin changes as well as their correlation with gene transcription. Our MNase mapping data indicates that the viral genome is arranged in precisely positioned nucleoprotein particles (Adenosomes), like nucleosomes. We identified 238 Adenosomes, being positioned by a DNA sequence code and protecting about 60 to 70bp of DNA. The incoming genome is more accessible at early gene loci that undergo additional chromatin de-condensation upon infection. Histone H3.3 containing nucleosomes specifically replace pVII at distinct genomic sites and at the transcription start sites of early genes. Acetylation of H3.3 is predominant at the transcription start sites, preceding transcriptional activation. Based on our results we propose a central role for the viral pVII nucleoprotein-architecture, which is required for the dynamic structural changes during early infection, including the regulation of nucleosome assembly prior to transcription initiation. Our study thus may aid the rational development of recombinant adenoviral vectors exhibiting sustained expression in gene therapy.
Anoxygenic phototrophicChloroflexotamember uses a Type I reaction center
Authors: Tsuji JM , Shaw NA , Nagashima S , Venkiteswaran JJ , Schiff SL , Watanabe T , Fukui M , Hanada S , Tank M , Neufeld JD 
Published: July 2020

AbstractScientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified. Through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within theChloroflexotaphylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a Type I reaction center (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a Type II reaction center (RCII) for phototrophy. Using physiological, phylogenomic, and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes and bacteriochlorophylls related to those of RCII-utilizingChloroflexotamembers. Despite using different reaction centers, our phylogenomic data provide strong evidence that RCI- and RCII-utilizingChloroflexiamembers inherited phototrophy from a most recent common phototrophic ancestor that used RCI, RCII, or both reaction center classes, substantially revising our view of the diversity and evolution of phototrophic life. TheChloroflexotaphylum preserves an evolutionary record of interaction between RCI and RCII among anoxygenic phototrophs that gives new context for exploring the origins of phototrophy on Earth.
Noncanonical targeting contributes significantly to miRNA-mediated regulation
Authors: Tan Jennifer Y. , Abdulkarim Baroj , Marques Ana C. 
Published: July 2020

ABSTRACTDetermining which genes are targeted by miRNAs is crucial to elucidate their contributions to diverse biological processes in health and disease. Most miRNA target prediction tools rely on the identification of complementary regions between transcripts and miRNAs. Whereas important for target recognition, the presence of complementary sites is not sufficient to identify transcripts targeted by miRNAs.Here, we describe an unbiased statistical genomics approach that explores genetically driven changes in gene expression between human individuals. Using this approach, we identified transcripts that respond to physiological changes in miRNA levels. We found that a much smaller fraction of mRNAs expressed in lymphoblastoid cell lines (LCLs) than what is predicted by other tools is targeted by miRNAs. We estimate that each miRNA has a relatively small number of targets. The transcripts we predict to be miRNA targets are enriched in AGO-binding and previously validated miRNAs target interactions, supporting the reliability of our predictions. Consistent with previous analysis, these targets are also enriched among dosage sensitive and highly controlled genes.Almost a third of genes we predict to be miRNA targets lack sequence complementarity to the miRNA seed region (noncanonical targets). These noncanonical targets have higher complementary with the miRNA 3’ end. The impact of miRNAs on the levels of their canonical or noncanonical targets is identical supporting the relevance of this poorly explored mechanism of targeting.
Alignment of virus-host protein-protein interaction networks by integer linear programming: SARS-CoV-2
Authors: Llabrés Mercè , Valiente Gabriel 
Published: July 2020

AbstractBeside socio-economic issues, coronavirus pandemic COVID-19, the infectious disease caused by the newly discovered coronavirus SARS-CoV-2, has caused a deep impact in the scientific community, that has considerably increased its effort to discover the infection strategies of the new virus. Among the extensive and crucial research that has been carried out in the last few months, the analysis of the virus-host relationship plays an important role in drug discovery. Virus-host protein-protein interactions are the active agents in virus replication, and the analysis of virus-host protein-protein interaction networks is fundamental to the study of the virus-host relationship. We have adapted and implemented a recent integer linear programming model for protein-protein interaction network alignment to virus-host networks, and obtained a consensus alignment of the SARS-CoV-1 and SARS-CoV-2 virus-host protein-protein interaction networks. Despite the lack of shared human proteins in these virus-host networks and the low number of preserved virus-host interactions, the consensus alignment revealed aligned human proteins that share a function related to viral infection, as well as human proteins of high functional similarity that interact with SARS-CoV-1 and SARS-CoV-2 proteins, whose alignment would preserve these virus-host interactions.
Defining the sediment microbiome of the Indian River Lagoon, FL, USA, an Estuary of National Significance
Authors: Bradshaw David J. , Dickens Nicholas J. , Trefry John H. , McCarthy Peter J. 
Published: July 2020

AbstractThe Indian River Lagoon, located on the east coast of Florida, USA, is an Estuary of National Significance and an important economic and ecological resource. The Indian River Lagoon faces several environmental pressures, including freshwater discharges through the St. Lucie Estuary; accumulation of a anoxic, fine-grained, organic-rich sediment; and metal contamination from agriculture and marinas. Although the Indian River Lagoon has been well-studied, little is known about its microbial communities; thus, a two-year 16S amplicon sequencing study was conducted to assess the spatiotemporal changes of the sediment microbiome. In general, the Indian River Lagoon exhibited a microbiome that was consistent with other estuarine studies. Statistically different microbiomes were found between the Indian River Lagoon and St. Lucie Estuary due to changes in porewater salinity causing microbes that require salts for growth to be higher in the Indian River Lagoon. The St. Lucie Estuary exhibited more obvious microbial seasonality, such as higher Betaproteobacteriales, a freshwater associated organism, in wet season and higher Flavobacteriales in dry season samples. Distance-based linear models revealed these microbiomes were more affected by changes in total organic matter and copper than changes in temperature. Anaerobic organisms, such as Campylobacterales, were more associated with high total organic matter and copper samples while aerobic organisms, such as Nitrosopumilales, were more associated with low total organic matter and copper samples. This initial study fills the knowledge gap on the Indian River Lagoon microbiome and serves as an important baseline for possible future changes due to human impacts or environmental changes.
TheVibrio choleraecytotoxin MakA induces noncanonical autophagy resulting in the spatial inhibition of canonical autophagy
Authors: Corkery Dale P. , Nadeem Aftab , Aung Kyaw Min , Hassan Ahmed , Liu Tao , Cervantes-Rivera Ramón , Lystad Alf Håkon , Wang Hui , Persson Karina , Puhar Andrea , Simonsen Anne , Uhlin Bernt Eric , Wai Sun Nyunt , Wu Yao-Wen 
Published: July 2020

AbstractAutophagy plays an essential role in the defence against many microbial pathogens as a regulator of both innate and adaptive immunity. Among some pathogens, sophisticated mechanisms have evolved that promote their ability to evade or subvert host autophagy. Here, we describe a novel mechanism of autophagy subversion mediated by the recently discoveredVibrio choleraecytotoxin, MakA. pH-dependent endocytosis of MakA by host cells resulted in the formation of a cholesterol-rich endolysosomal membrane aggregate in the perinuclear region. Aggregate formation induced the noncanonical autophagy pathway driving unconventional LC3 lipidation on endolysosomal membranes. Subsequent sequestration of the ATG12-ATG5-ATG16L1 E3-like enzyme complex required for LC3 lipidation at the membranous aggregate resulted in an inhibition of both canonical autophagy and autophagy-related processes including the unconventional secretion of IL-1β. These findings identify a novel mechanism of host autophagy subversion and immune modulation employed byV. choleraeduring bacterial infection.
Nonsense-mediated mRNA decay relies on “two-factor authentication” by SMG5-SMG7
Authors: Boehm Volker , Kueckelmann Sabrina , Gerbracht Jennifer V. , Britto-Borges Thiago , Altmüller Janine , Dieterich Christoph , Gehring Niels H. 
Published: July 2020

AbstractEukaryotic gene expression is constantly regulated and controlled by the translation-coupled nonsense-mediated mRNA decay (NMD) pathway. Aberrant translation termination leads to NMD activation and robust clearance of NMD targets via two seemingly independent and redundant mRNA degradation branches. Here, we uncover that the loss of the first SMG5-SMG7-dependent pathway also inactivates the second SMG6-dependent branch, indicating an unexpected functional hierarchy of the final NMD steps. Transcriptome-wide analyses of SMG5-SMG7-depleted cells confirm complete NMD inhibition resulting in massive transcriptomic alterations. The NMD activity conferred by SMG5-SMG7 is determined to varying degrees by their interaction with the central NMD factor UPF1, heterodimer formation and the initiation of deadenylation. Surprisingly, we find that SMG5 functionally substitutes SMG7 and vice versa. Our data support an improved model for NMD execution that requires two-factor authentication involving UPF1 phosphorylation and SMG5-SMG7 recruitment to access SMG6 activity.
SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation
Authors: Schubert Katharina , Karousis Evangelos D. , Jomaa Ahmad , Scaiola Alain , Echeverria Blanca , Gurzeler Lukas-Adrian , Leibundgut Marc , Thiel Volker , Mühlemann Oliver , Ban Nenad 
Published: July 2020

AbstractThe non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, is the first viral protein that is synthesized in SARS-CoV-2 infected human cells to suppress host innate immune functions1,2. By combining cryo-electron microscopy and biochemical experiments, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes including the 43S pre-initiation complex. The protein inserts its C-terminal domain at the entrance to the mRNA channel where it interferes with mRNA binding. We observe potent translation inhibition in the presence of Nsp1 in lysates from human cells. Based on the high-resolution structure of the 40S-Nsp1 complex, we identify residues of Nsp1 crucial for mediating translation inhibition. We further show that the full-length 5’ untranslated region of the genomic viral mRNA stimulates translationin vitro, suggesting that SARS-CoV-2 combines inhibition of translation by Nsp1 with efficient translation of the viral mRNA to achieve expression of viral genes3.
Occipital Intralobar fasciculi and a novel description of three forgotten tracts
Authors: Bugain Maeva , Dimech Yana , Torzhenskaya Natalia , de Schotten Michel Thiebaut , Caspers Svenja , Muscat Richard , Bajada Claude J 
Published: July 2020

ABSTRACTThe continuously developing field of magnetic resonance imaging (MRI) has made a considerable contribution to the knowledge of brain architecture. It has given shape to a desire to construct a complete map of functional and structural connections. In particular, diffusion MRI paired with tractography has facilitated a non-invasive exploration of structural brain anatomy, which has helped build evidence for the existence of many association, projection and commissural fiber tracts. However, there is still a scarcity in research studies related to intralobar association fibers. The Dejerines’ (two of the most notable neurologists of 19thcentury France) gave an in-depth description of the intralobar fibers of the occipital lobe. Unfortunately, their exquisite work has since been sparsely referred to in the modern literature. This work gives the first modern description of many of the occipital intralobar lobe fibers described by the Dejerines. We perform a virtual dissection and reconstruct the tracts using diffusion MRI tractography. The virtual dissection is guided by the Dejerines’ treatise,Anatomie des Centres Nerveux.As an accompaniment to this article, the authors provided a French-to-English translation of the treatise portion concerning intra-occipital fiber bundles. This text provides the original description of five intralober occipital tracts, namely: the stratum calcarinum, the stratum proprium cunei, the vertical occipital fasciculus of Wernicke, the transverse fasciculus of the cuneus (TFC) and the transverse fasciculus of the lingual lobe of Vialet. It was possible to reconstruct all these tracts except for the TFC – possibly because its trajectory intermingles with a large amount of other fiber bundles. For completeness, the recently described sledge runner fasciculus, although not one of the Dejerine tracts, was identified and successfully reconstructed.