bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep mutational scanning identifies SARS-CoV-2 Nucleocapsid escape mutations of currently available rapid antigen tests
Authors: Frank Filipp , Keen Meredith M. , Rao Anuradha , Bassit Leda , Liu Xu , Bowers Heather B. , Patel Anamika B. , Cato Michael L. , Sullivan Julie A. , Greenleaf Morgan , Piantadosi Anne , Lam Wilbur A. , Hudson William H. , Ortlund Eric A. 
Published: May 2022

AbstractWidespread and frequent testing is critical to prevent the spread of COVID-19, and rapid antigen tests are the diagnostic tool of choice in many settings. With new viral variants continuously emerging and spreading rapidly, the effect of mutations on antigen test performance is a major concern. In response to the spread of variants the National Institutes of Health’s Rapid Acceleration of Diagnostics (RADx®) initiative created a Variant Task Force to assess the impact of emerging SARS-CoV-2 variants on in vitro diagnostic testing. To evaluate the impact of mutations on rapid antigen tests we developed a lentivirus-mediated mammalian surface-display platform for the SARS-CoV-2 Nucleocapsid protein, the target of the majority of rapid antigen tests. We employed deep mutational scanning (DMS) to directly measure the effect of all possible Nucleocapsid point mutations on antibody binding by 17 diagnostic antibodies used in 11 commercially available antigen tests with FDA emergency use authorization (EUA). The results provide a complete map of the antibodies’ epitopes and their susceptibility to mutational escape. This approach identifies linear epitopes, conformational epitopes, as well as allosteric escape mutations in any region of the Nucleocapsid protein. All 17 antibodies tested exhibit distinct escape mutation profiles, even among antibodies recognizing the same folded domain. Our data predict no vulnerabilities of rapid antigen tests for detection of mutations found in currently and previously dominant variants of concern and interest. We confirm this using the commercial tests and sequence-confirmed COVID-19 patient samples. The antibody escape mutation profiles generated here serve as a valuable resource for predicting the performance of rapid antigen tests against past, current, as well as any possible future variants of SARS-CoV-2, establishing the direct clinical and public health utility of our system. Further, our mammalian surface-display platform combined with DMS is a generalizable platform for complete mapping of protein-protein interactions.
Substantial seagrass blue carbon pools in the southwestern Baltic Sea are spatially heterogeneous, mostly autochthonous, and include relics of terrestrial peatlands
Authors: Stevenson Angela , Corcora Tadhg C. Ó , Hukriede Wolfgang , Schubert Philipp R. , Reusch Thorsten B.H. 
Published: May 2022

AbstractSeagrass meadows have a disproportionally high organic carbon (Corg) storage potential (‘blue carbon’) within their sediments and thus can play an important role in climate change mitigation via their conservation and restoration. However, high spatial heterogeneity is observed in Corg, with wide differences seen globally (i.e. tropical vs temperate), regionally, and even locally (within a seagrass meadow). Consequently, it is difficult to determine their contributions to the national remaining carbon dioxide (CO2) budget without introducing a large degree of uncertainty.In order to address this spatial heterogeneity, we sampled 20 locations across the Baltic Sea coast of Germany to quantify carbon stocks and sources inZostera marinaseagrass-vegetated and adjacent unvegetated sediments. To predict and integrate the Corginventory in space, we measured the physical (seawater depth, sediment grain size, current velocity at the seafloor, anthropogenic inputs) and biological (seagrass complexity) environment to determine regional (between sites) and local (within site) drivers of Corgvariation.Here we show that seagrass meadows in the German Baltic Sea constitute a significant Corgstock, storing on average 7,785 ± 679 g C/m2, 13 times greater than meadows from other parts of the Baltic Sea (outside of Germany), and four-fold richer than adjacent unvegetated sediments. Stocks were highly heterogenous; they differed widely between (by 10-fold) and even within (by 3 to 55-fold) sites. At a regional scale (350 km), Corgwas controlled by seagrass complexity, fine sediment fraction, and seawater depth. Autochthonous material (seagrass-derived and large infauna) contributed to 78% of the total Corgin vegetated sediments and the remaining 22% originated from allochthonous sources (phytoplankton, drift algaePilayella littoralis, and other macroalgae). However, relic terrestrial peatland material, deposited during the last deglaciation 5,806 and 5,095 years BP, was an unexpected and significant source of Corg.Collectively, German seagrass meadows in the Baltic Sea are preventing 8.14 Mt of future CO2emissions. Because Corgis mostly produced on site, and not imported from outside the boundaries of the meadow, the richness of this pool may be contingent on seagrass habitat health. Disturbance of this Corgstock could act as a source of CO2emissions. However, the high spatial heterogeneity seen across the region warrant site-specific investigations to obtain accurate estimates of blue carbon, and a need to consider millennial timescale deposits of Corgbeneath seagrass meadows in Germany and potentially other parts of the southwestern Baltic Sea.
mNeonGreen-tagged fusion proteins and nanobodies reveal localization of tropomyosin to patches, cables, and contractile actomyosin rings in live yeast cells
Authors: Hatano Tomoyuki , Lim Tzer Chyn , Billault-Chaumartin Ingrid , Dhar Anubhav , Gu Ying , Massam-Wu Teresa , Adishesha Sushmitha , Springall Luke , Sivashanmugam Lavanya , Scott William , Mishima Masanori , Martin Sophie G , Oliferenko Snezhana , Palani Saravanan , Balasubramanian Mohan K. 
Published: May 2022

AbstractTropomyosins are structurally conserved α-helical coiled-coil dimeric proteins that bind along the length of filamentous actin (F-actin) in fungi and animals. Tropomyosins play essential roles in the stability of actin filaments in non-muscle cells and are essential for calcium regulation of myosin II contractility in the muscle. Despite the crucial role of tropomyosin in actin cytoskeletal regulation, in vivo investigations of tropomyosin are limited, mainly due to the suboptimal live cell imaging tools currently available in many organisms. Here, we report mNeon-Green (mNG) tagged tropomyosin, with native promoter and linker length configuration, that clearly reports tropomyosin localization and dynamics in Schizosaccharomyces pombe (Cdc8), Schizosaccharomyces japonicus (Cdc8), and Saccharomyces cerevisiae (Tpm1 and Tpm2), in vivo and in isolated S. pombe cell division apparatuses. We extended this approach to also visualize the mammalian TPM2 isoform. Finally, we generated a camelid-nanobody against S. pombe Cdc8, which mimics the localization of mNG-Cdc8 in vivo without significantly influencing cell growth and dynamics of actin cytoskeleton. Using these tools, we report the presence of tropomyosin in previously unappreciated patch-like structures in fission and budding yeasts, show flow of tropomyosin (F-actin) cables to the cytokinetic actomyosin ring, and identify rearrangements of the actin cytoskeleton during mating. These powerful tools and strategies will aid better analyses of tropomyosin and actin cables in vivo.
Computational modelling of local fluctuations causing transient solvent exposure of protein amides
Authors: Bhakat Soumendranath , Söderhjelm Pär 
Published: May 2022

AbstractHydrogen exchange (HX) between protein amides and solvent water molecules can function as a probe for protein dynamics and provide a bridge between the experimental and computational worlds. However, it is important that the underlying assumptions are tested on well-known systems. Here we perform an analysis of a long MD simulation of BPTI, which has previously been used by Persson and Halle to propose a functional definition of the exchange-competent configurations. We find support for the hypothesis that the exchange-competent configurations typically do not constitute a metastable state per se, but rather occur as the outermost tail of the water distribution around a metastable broken state directly identifiable as having a broken intermolecular hydrogen bond and increased solvent-exposure. Furthermore, we estimate the lifetime of these broken states and the probability that exchange-competent configurations occur in them. We have also tested various sampling protocols and their ability to enhance the exploration of the broken states. Computational protocol used in this study can be applied to a broad range of sys-tems to gain valuable insight into the nature of the broken state, although further development is needed to devise a generally applicable quantitative method.
Model metamers illuminate divergences between biological and artificial neural networks
Authors: Feather Jenelle , Leclerc Guillaume , Mądry Aleksander , McDermott Josh H. 
Published: May 2022

AbstractDeep neural network models of sensory systems are often proposed to learn representational transformations with invariances like those in the brain. To reveal these invariances we generated “model metamers” – stimuli whose activations within a model stage are matched to those of a natural stimulus. Metamers for state-of-the-art supervised and unsupervised neural network models of vision and audition were often completely unrecognizable to humans when generated from deep model stages, suggesting differences between model and human invariances. Targeted model changes improved human-recognizability of model metamers, but did not eliminate the overall human-model discrepancy. The human-recognizability of a model’s metamers was well predicted by their recognizability by other models, suggesting that models learn idiosyncratic invariances in addition to those required by the task. Metamer recognition dissociated from both traditional brain-based benchmarks and adversarial vulnerability, revealing a distinct failure mode of existing sensory models and providing a complementary benchmark for model assessment.
Timed Notch Inhibition drives Photoreceptor fate specification in Human Retinal Organoids
Authors: Chew Shereen H. , Martinez Cassandra , Chirco Kathleen R. , Kandoi Sangeetha , Lamba Deepak A. 
Published: May 2022

ABSTRACTPurposeTransplanting photoreceptors from human pluripotent stem cell derived retinal organoids have the potential to reverse vision loss in affected individuals. However, transplantable photoreceptors are only a subset of all cells in the organoids. Hence the goal of our current study was to accelerate and synchronize photoreceptor differentiation in retinal organoids by inhibiting the Notch signaling pathway at different developmental time-points using a small molecule, PF-03084014 (PF).MethodsHuman induced pluripotent stem cell (hiPSC)- and embryonic stem cells (hESC)-derived retinal organoids were treated with 10μM PF for three days at day 45 (D45), D60, D90 and D120 of differentiation. Organoids collected at 14-, 28-, and 42-days post-PF treatment were analyzed for progenitor and photoreceptor markers and Notch pathway inhibition by immunohistochemistry (IHC), quantitative PCR (qPCR) and bulk RNA-seq (n=3-5 organoids from 3 independent experiments).ResultsRetinal organoids collected at 14-days post-PF treatment showed a decrease in progenitor markers (KI67, VSX2, PAX6, and LHX2) and an increase in differentiated pan-photoreceptor markers (OTX2, CRX, and RCVRN) at all organoid stages except D120. PF-treated organoids at D45 and D60 exhibited an increase in cone photoreceptor markers (RXRG and ARR3). PF-treatment at D90 revealed an increase in cone and rod photoreceptors markers (ARR3, NRL, and NR2E3). Bulk RNA-seq analysis mirrored the IHC data and qPCR confirmed Notch effector inhibition.ConclusionsTiming the Notch pathway inhibition in human retinal organoids to align with progenitor competency stages can yield an enriched population of early cone or rod photoreceptors.
recountmethylation enables flexible analysis of public blood DNA methylation array data
Authors: Maden Sean K. , Walsh Brian , Ellrott Kyle , Hansen Kasper D. , Thompson Reid F. , Nellore Abhinav 
Published: May 2022

AbstractThousands of DNA methylation (DNAm) array samples from human blood are publicly available on the Gene Expression Omnibus (GEO), but they remain underutilized for experiment planning, replication, and cross-study and cross-platform analyses. To facilitate these tasks, we augmented our recountmethylation R/Bioconductor package with 12,537 uniformly processed EPIC and HM450K blood samples on GEO as well as several new features. We subsequently used our updated package in several illustrative analyses, finding (1) study ID bias adjustment increased variation explained by biological and demographic variables, (2) most variation in autosomal DNAm was explained by genetic ancestry and CD4+ T-cell fractions, and (3) the dependence of power to detect differential methylation on sample size was similar for each of peripheral blood mononuclear cells (PBMC), whole blood, and umbilical cord blood. Finally, we used PBMC and whole blood to perform independent validations, and we recovered 40-46% of differentially methylated probes (DMPs) between sexes from two previously published epigenome-wide association studies (EWAS).
Single-molecule and super-resolved imaging deciphers membrane behaviour of onco-immunogenic CCR5
Authors: Hunter Patrick , Payne-Dwyer Alex L. , Shaw Michael , Signoret Nathalie , Leake Mark C. 
Published: May 2022

SummaryThe ability of tumors to establish a pro-tumorigenic microenvironment is becoming an important point of investigation in the search for new therapeutics. Tumors form microenvironments in part by the ‘education’ of immune cells attracted via chemotactic axes such as that of CCR5-CCL5. Further, CCR5 upregulation by cancer cells, coupled with its association with pro-tumorigenic features such as drug-resistance and metastasis, has suggested CCR5 as a target for therapeutic inhibition. However, with several conformational “pools” being reported, phenotypic investigations must be capable of unveiling heterogeneity. Addressing this challenge, we performed structured illumination (SIM) and Partially TIRF coupled HILO (PaTCH) microscopy for super-resolution imaging and single-molecule imaging of CCR5 in fixed cells. Determining the positions of super-resolved CCR5 assemblies revealed a non-random spatial orientation. Further, intensity-tracking of assemblies revealed a distribution of molecular stoichiometries indicative of dimeric sub-units independent of CCL5 perturbation. These biophysical methods can provide important insights into the structure and function of onco-immunogenic receptors and a plethora of other biomolecules.HighlightsWe use SIM and novel PaTCH microscopy for precise bioimaging and single-molecule tracking of receptor protein CCR5 in model cell lineBy tracking the position of CCR5 assemblies we conclude that they are clustered in the plasma membrane beyond a level expected from a random distributionWe use these high-precision data to determine molecular stoichiometries of CCR5 assemblies
Conserved and variable responses of the HEAT SHOCK FACTOR transcription factor family in maize and Setaria viridis
Authors: Myers Zachary A. , Wootan Clair M. , Liang Zhikai , Zhou Peng , Englehorn Julia , Hartwig Thomas , Springer Nathan M. 
Published: May 2022

AbstractResponding to the environment is a core aspect of plant growth and development. Mounting an effective response is important for plants to balance growth and survival. The HEAT SHOCK FACTOR (HSF) transcription factor family is a central and required component of plant heat stress responses and acquired thermotolerance. The HSF family has dramatically expanded in plant lineages, often including a repertoire of 20 or more genes. Here we assess the composition and heat responsiveness of the HSF family in Setaria viridis (Setaria), a model C4 panicoid grass, and make targeted comparisons between the HSF families of Setaria and maize. Examples of both conserved and variable expression responses to a heat stress event were observed when comparing the two species. Novel and existing data on chromatin accessibility, histone modifications, and genome-wide DNA binding profiles were utilized to assess the chromatin of HSF family members with distinct responses to heat stress. We observed significant variability for both expression and chromatin state within syntenic and orthologous sets of HSFs between Setaria and maize, as well as between syntenic pairs of maize HSFs retained following its most recent genome duplication event. These observations collectively support a complex scenario of expansion and sub-functionalization within this transcription factor family that has significant untapped potential for better understanding the evolution of large gene families.Significance StatementA comparison of the Heat Shock Factor transcription factors in maize and Setaria reveals examples of consistent and variable expression responses to heat stress and provides insights into the role of chromatin in predicting expression responses.
JEDII: Juxtaposition Enabled DNA-binding Interface Identifier
Authors: Nair Sanjana , Madhusudhan M.S. 
Published: May 2022

AbstractThe specific recognition of small stretches of the genomic sequence by their cognate binding protein partners is crucial for various biological processes. Traditionally the prediction of DNA-protein interactions has been treated as two separate problems - one where we predict the most probable DNA sequence that a given protein would bind to and another where we determine the amino acids constituting the DNA binding pocket on a protein. In this study, we introduce JEDII, a template-based method that combines these two aspects of DNA-protein interactions and predicts the residues, nucleotides and amino acids, that would mediate the interaction. Our computational method utilises known structures of DNA-protein complexes in a protocol that superimposes amino acid-nucleotide hydrogen-bonding donor and acceptors atoms on one another to identify the protein-DNA interface. The corner stone of the method is that specificity bestowing hydrogen-bonding interactions are structurally conserved. We validated the accuracy of our procedure on a dataset of 285 DNA-protein complexes where JEDII predicted the cognate DNA sequence with a 62% accuracy. It predicted the DNA-binding amino acids on the protein with 94 % accuracy and an MCC of 0.70. JEDII was also separately compared to other popular methods that predict the cognate DNA sequence and to methods that predict the DNA binding residues. The comparisons were done over four different datasets and JEDII outperformed most methods over all these data sets. JEDII is a robust method following a simple replicable algorithm to determine the molecular basis of DNA-protein specificity and could be instrumental in predicting DNA-protein complexes that are central to key biological phenomena.
The canonical Wnt signaling pathway is not a promising therapeutic target for PNS regeneration enhancement
Authors: Mehta Nikita , Vardy Maia , Elbaz Benayahu 
Published: May 2022

AbstractPNS injury initiates transcriptional changes in Schwann cells, satellite glial cells and PNS neurons that facilitate regeneration. The signaling pathways that control these transcriptional changes are not fully understood. The canonical Wnt signaling pathway is active during early stages of PNS development, where it controls radial axonal sorting and the onset of PNS myelination. Upon PNS injury, the Wnt signaling pathway is re-activated, suggesting that Wnt signaling plays an important role in PNS regeneration. To explore the potential of the Wnt pathway as a therapeutic target for enhancement of PNS recovery, we used a combination of genetic and pharmacological approaches to either activate or inhibit the Wnt signaling pathway during PNS recovery. We found that manipulating the Wnt signaling pathway does not alter PNS regeneration. Our data suggests that the Wnt signaling pathway is not a strong therapeutic target for the enhancement of PNS regeneration.
Scent mark signal investment predicts fight dynamics in house mice
Authors: Miller Caitlin H. , Haxhillari Klaudio , Hillock Matthew F. , Reichard Tess M. , Sheehan Michael J. 
Published: May 2022

AbstractSignals mediate competitive interactions by allowing rival assessment, yet are often energetically expensive to produce. Individuals face tradeoffs when deciding when and where to signal, such that over or under-investing in signaling effort can be costly. One of the key mechanisms maintaining signal reliability is via social costs. While the social costs of over-signaling are well-known, the social costs of under-signaling are underexplored, particularly for dynamic signals. In this study we investigate a dynamic and olfactory-mediated signaling system that is ubiquitous among mammals: scent marking. Male house mice territorially scent mark their environment with metabolically costly urine marks. While competitive male mice are thought to deposit abundant scent marks in the environment, we recently identified a cohort of low-marking males that win fights. Whereas there are clear energetic costs to investing in urine signals in mice, we hypothesized that there may be social costs imposed on individuals who under-invest in signaling. Here we find that scent mark investment predicts fight dynamics. Despite fight outcome being unambiguous, aggressive intensity varies considerably across trials. Males that produce fewer scent marks engage in more intense fights that take longer to resolve. This effect appears to be driven by an unwillingness among losers to acquiesce to weakly signaling winners. We therefore find evidence for rival assessment of scent marks as well as social costs to under-signaling, which supports existing hypotheses for the importance of social punishment in maintaining optimal signaling equilibria. Our results further highlight the possibility of diverse signaling strategies in house mice.
Interpreting the fossil record and the origination of birds
Authors: Crouch Nicholas M. A. 
Published: May 2022

AbstractThe fossil record is essential for understanding when lineages originate and their pace of diversification. However, numerous taphonomic biases in the fossil record can hinder interpretation, creating discord between palaeontological and phylogenetic estimates of clade origination dates. Here, I use the recently published Bayesian Brownian Bridge method to infer the age of birds using occurrence data from the Paleobiology Database. I also estimate the age of the speciose sub-clade Telluraves to compare age estimates with previous tip-dating analyses of the same group. Analyses of all birds show place the root age approximately 100 Ma, approximately 26 Myr before the oldest fossil occurrences. Increasing the time bin size from 2.5 to 5 Myr produced significantly older and less precise estimates. Divergence estimates for Telluraves were strikingly consistent with tip-dating analyses, placing origination of the group in the latest Cretaceous. Although these dates are consistent with a hypothesis of Mesozoic origination and Cenozoic diversification, significant diversification was estimated before the end-Cretaceous mass extinction suggesting analyses using pooled species counts may produce spurious results. Overall, these analyses provide further evidence to a growing consensus that several major avian lineages survived the end-Cretaceous mass extinction before diversifying into the most speciose extant tetrapod radiation.