bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated Medical Chart Review for Breast Cancer: A Novel Natural Language Processing Software System
Authors: Chen Yifu , Hao Lucy , Zou Vito Z , Hollander Zsuzsanna , Ng Raymond T , Isaac Kathryn V
Published: May 2021

The incoming health records to the BC Cancer Registry are processed between two to three years behind real-time. In response, we developed a Natural Language Processing (NLP) software to automate the electronic chart review workflow. For the same task that costs hundreds of hours of trained labour, our pipeline extracts data within minutes. During preliminary evaluation, an MD student yielded 93.0% and 98.2% accuracies on a sample of operative and pathology breast cancer documents (for a total number of 2,563 data points processed). In comparison, our prototype achieved 89.6% and 91.4% accuracies, respectively. Future plans include improving the performance of the pipeline and eventually adapt it to accepting a more comprehensive range of electronic health records across cancer types and diseases. In the context of BC’s digital healthcare transformation initiatives, this customized software may provide time and cost savings for both the Registry and cancer researchers.
Clinical evaluation of BD Veritor™ SARS-CoV-2 and Flu A+B Assay for point-of-care (POC) System
Authors: Christensen Katherine , Ren Huimiao , Chen Shirley , Cooper Charles K. , Young Stephen
Published: May 2021

Differential diagnosis of COVID-19 and/or influenza (flu) at point of care is critical for efficient patient management and treatment for either of these diseases. Clinical performance of the BD Veritor™ System for Rapid Detection of SARS-CoV-2 & FluA+B (“Veritor SARS-CoV-2/Flu”) triplex assay was characterized. The performance for SARS-CoV-2 detection was determined using two hundred and ninety-eight (298) specimens from patients reporting COVID-19 symptoms within 7 days from symptom onset (DSO) in comparison with Lyra® SARS-CoV-2 RT-PCR Assay (“Lyra SARS-CoV-2”). The Veritor SARS-CoV-2/Flu Assay met the FDA EUA acceptance criterion with 95% overall agreement for SARS-CoV-2 test when compared to Lyra SARS-CoV-2. The performance for Flu A and Flu B detection was determined using 75 influenza-positive and 40 influenza-negative retrospective specimens in comparison with the previously FDA cleared BD Veritor™ System for Rapid Detection of Flu A+B (“Veritor Flu”). The Veritor SARS-CoV-2/Flu also demonstrated 100% agreement with the Veritor Flu.
Elevated preoperative suPAR is a strong and independent risk marker for postoperative complications in high-risk patients undergoing major non-cardiac surgery (SPARSE)
Authors: Chalkias Athanasios , Laou Eleni , Kolonia Konstantina , Ragias Dimitrios , Angelopoulou Zacharoula , Mitsiouli Eleni , Kallemose Thomas , Smith-Hansen Lars , Eugen-Olsen Jesper , Arnaoutoglou Eleni
Published: May 2021

Background

Patients undergoing major surgery are often at risk of developing postoperative complications. We investigated whether the inflammatory biomarker suPAR can aid in identifying patients at high risk for postoperative complications, morbidity, and mortality.

Methods

In this prospective observational study (ClinicalTrials.gov identifier: NCT03851965), peripheral venous blood was collected from consecutive adult patients scheduled for major non-cardiac surgery with expected duration ≥2 hours under general anesthesia. Patients fulfilling the following inclusion criteria were included: age ≥18 years and American Society of Anesthesiologists’ physical status I to IV. Plasma suPAR levels were determined using the suPARnostic® quick triage lateral flow assay. The primary endpoint was post-operative complications defined as presence of any complication and/or admission to intensive care unit and/or mortality within the first 90 postoperative days.

Results

Preoperative suPAR had an OR of 1.50 (95%CI 1.24-1.82) for every ng/ml increase (AUC 0.82, 95%CI: 0.72-0.91). When including age, sex, ASA score, CRP, and grouped suPAR in multivariate analysis, patients with suPAR between 5.5 and 10 ng/ml had an OR of 12.7 (CI: 3.6-45.5) and patients with suPAR>10 ng/ml had an OR of 20.7 (CI: 4.5-95.4) compared to patients with suPAR≤5.5 ng/ml, respectively. ROC analysis including age, sex, CRP levels, and ASA score and had an AUC of 0.69 (95%CI: 0.58-0.80). When suPAR was added to this Model, the AUC increased to 0.84 (0.74-0.93) (p=0.009).

Conclusions

Preoperative suPAR provided strong and independent predictive value on postoperative complications in high-risk patients undergoing major non-cardiac surgery.
Cryo-EM single particle structure refinement and map calculation usingServalcat
Authors: Yamashita Keitaro , Palmer Colin M. , Burnley Tom , Murshudov Garib N.
Published: May 2021

In 2020, cryo-EM single particle analysis achieved true atomic resolution, thanks to technological developments in hardware and software. The number of high resolution reconstructions continues to grow, increasing the importance of accurate determination of atomic coordinates. Here, a new Python package and program calledServalcatis presented that is designed to facilitate atomic model refinement.Servalcatimplements a refinement pipeline, using the programREFMAC5 from theCCP4package. After the refinement,Servalcatcalculates a weightedFo−Fcdifference map, which was derived from Bayesian statistics. This map helps manual and automatic model building in real space, as is common practice in crystallography. TheFo−Fcmap helps visualisation of weak features including hydrogen densities. Although hydrogen densities are weak, they are stronger than in electron density maps produced by X-ray crystallography, and some hydrogen atoms are even visible at ∼ 1.8 Å resolution.Servalcatalso facilitates atomic model refinement under symmetry constraints. If a point group symmetry has been applied to the map during reconstruction, the asymmetric unit model is refined with appropriate symmetry constraints.
The central nucleus of the amygdala and gustatory cortex assess affective valence during CTA learning and expression in male and female rats
Authors: Bernanke Alyssa , Burnette Elizabeth , Murphy Justine , Hernandez Nathaniel , Zimmerman Sara , David Walker Q. , Wander Rylee , Sette Samantha , Reavis Zackery , Francis Reynold , Armstrong Christopher , Risher Mary-Louise , Kuhn Cynthia
Published: May 2021

This study evaluated behavior (Boost® intake, LiCl-induced behaviors, ultrasonic vocalizations (USVs), task performance) and c-Fos activation during conditioned taste aversion (CTA), the reinforced task (Boost® task) and control task (cage only) to understand how male and female rats balance the relative danger or safety of a stimulus in learning and performing a task. Females drank more Boost® than males but showed similar aversive behaviors after LiCl treatment. Males produced 55 kHz USVs (indicating positive valence) when anticipating Boost® and inhibited these calls after pairing with LiCl. Females produced 55 kHz USVs based on their estrous cycle but were more likely to make 22 kHz USVs than males (indicating negative valence) after pairing with LiCl. c-Fos responses were similar in males and females after Boost® or LiCl. Females engaged the gustatory cortex and ventral tegmental area more than males during the Boost® task and males engaged the amygdala more than females in both the reinforcing and devalued tasks. Network analysis of correlated c-Fos responses across brain regions identified two unique networks characterizing the Boost® and LiCl (CTA) tasks, in both of which the VTA played a central role. RNAscope identified a population of D1-receptor expressing cells in the CeA that responded to Boost® and D2 receptor-expressing cells that responded to LiCl. The present study suggests that males and females differentially process the affective valence of a stimulus to produce the same goal-directed behavior.
The role of elections as drivers of tropical deforestation
Authors: Morpurgo Joeri , Kissling W. Daniel , Tyrrell Peter , Negret Pablo J. , Allan James R.
Published: May 2021

Tropical forests support immense biodiversity and provide essential ecosystem services for billions of people. Despite this value, tropical deforestation continues at a high rate. Emerging evidence suggests that elections can play an important role in shaping deforestation, for instance by incentivising politicians to allow increased utilisation of tropical forests in return for political support and votes. Nevertheless, the role of elections as a driver of deforestation has not been comprehensively tested at broad geographic scales. Here, we created an annual database from 2001 to 2018 on political elections and forest loss for 55 tropical nations and modelled the effect of elections on deforestation. In total, 1.5 million km2of forest was lost during this time period, and the rate of deforestation increased in 37 (67%) of the analysed countries. Deforestation was significantly lower in years with presidential or lower chamber elections compared to non-election years, which is in contrast to previous local-scale studies. Moreover, deforestation was significantly higher in presidential or lower chamber elections that are competitive (i.e. when the opposition can participate in elections and has a legitimate chance to gain governmental power) compared to uncompetitive elections. Our results document a pervasive loss of tropical forests and suggest that competitive elections are potential drivers of deforestation. We recommned that organisations monitoring election transparency and fairness should also monitor environmental impacts such as forest loss, habitat destruction and resource exploitation. This would benefit the tracking of potential illegal vote buying with natural resources.
Metabarcoding and ecological interaction networks for selecting candidate biological control agents
Authors: Ollivier Mélodie , Lesieur Vincent , Tavoillot Johannes , Bénetière Fanny , Tixier Marie-Stéphane , Martin Jean-François
Published: May 2021

Classical biological control can be used to decrease the density of invasive species to below an acceptable ecological and economic threshold. Natural enemies specific to the invasive species are selected from its native range and released into the invaded range. This approach has drawbacks, despite the performance of specificity tests to ensure its safety, because the fundamental host range defined under controlled conditions does not represent the actual host rangein natura, and these tests omit indirect interactions within community.

We focus onSonchus oleraceus(Asteraceae), a weed species originating from Western Palearctic that is invasive worldwide and notably in Australia. We explore how analyses of interaction network within its native range can be used to 1) inventory herbivores associated to the target plant, 2) characterize their ecological host ranges, and 3) guide the selection of candidate biocontrol agents considering interactions with species from higher trophic levels. Arthropods were collected from plant community sympatric toS. oleraceus, in three bioclimatic regions, and interactions were inferred by a combination of molecular and morphological approaches.

The networks reconstructed were structured in several trophic levels from basal species (diversified plant community), to intermediate and top species (herbivorous arthropods and their natural enemies). The subnetwork centered onS. oleraceusrelated interactions contained 116 taxa and 213 interactions. We identified 47 herbivores feeding onS. oleraceus, 15 of which were specific to the target species (i.e. Generality value equal to 1). Some discrepancies with respect to published findings or conventional specificity tests suggested possible insufficient sampling effort for the recording of interactions or the existence of cryptic species. Among potential candidate agents, 6 exhibited interactions with natural enemies.

Synthesis and applications:Adopting a network approach as prerequisite step of the CBC program can provide a rapid screening of potential agents to be tested in priority. Once ecological host range defined, we suggest that priority should be given to agent predated by a minimum species, and, when they exist, to an agent that possesses enemies from the most distant taxonomical group from those occurring in the range of introduction.
Bacteriostatic antibiotics promote the evolution of CRISPR-Cas immunity
Authors: Dimitriu Tatiana , Kurilovich Elena , Lapinska Urszula , Severinov Konstantin , Pagliara Stefano , Szczelkun Mark D. , Westra Edze R.
Published: May 2021

Phage therapy can be used in combination with antibiotics to combat infections with bacterial pathogens1–3. However, bacteria can rapidly evolve phage resistance via receptor mutation, or using their CRISPR-Cas adaptive immune systems4, which insert short phage-derived sequences into CRISPR loci in the bacterial genome5to guide sequence-specific cleavage of cognate sequences6. Unlike CRISPR-Cas immunity, mutation of the phage receptor leads to attenuated virulence when the opportunistic pathogenPseudomonas aeruginosais infected with its phage DMS3vir7, which underscores the need to predict how phage resistance evolves under clinically relevant conditions. Here, using eight antibiotics with various modes of action, we show that bacteriostatic antibiotics (which inhibit cell growth without killing) specifically promote evolution of CRISPR-Cas immunity inP. aeruginosaby slowing down phage development and providing more time for cells to acquire phage-derived sequences and mount an immune response. Our data show that some antimicrobial treatments can contribute to the evolution of phage-resistant pathogens with high virulence.
Population structure and association mapping for hundred seed weight in mungbean minicore
Authors: Akhtar Muhammad Arslan , Aslam Muhammad , Schafleitner Roland , Ahsan Muhammad , Murtaza Ghulam
Published: May 2021

Mungbean is an important legume rich in protein and carbohydrates. It is cultivated mostly in south to south east Asia and east Africa. One of the important yield contributing traits in mungbean is 100 seed weight. Variation for this trait is available in the mungbean germplasm, and to facilitate improvement of this trait through breeding, genome-wide association mapping for 100 seed weight was carried out in the World Vegetable Center mungbean minicore collection. A total of 24,870 single nucleotide polymorphic markers were tested for association with 100 see weight in plants grown in Pakistan, Bangladesh, Myanmar and Taiwan and candidate loci associated with seed weight on chromosomes 1, 4, 6, 8 and 9 were identified. None of the QTLs was stable across all environments, but loci on chromosomes 4 and 8 were significant in Pakistan and Bangladesh and other loci on chromosome 8 were significantly associated in plants grown in Myanmar and Taiwan.
Immunomodulatory Therapy with Glatiramer Acetate Reduces Endoplasmic Reticulum Stress and Mitochondrial Dysfunction in Experimental Autoimmune Encephalomyelitis
Authors: Makar Tapas K. , Guda Poornachander R , Ray Sugata , Andhavarapu Sanketh , Nimmagadda Vamshi KC , Gerzanich Volodymyr , Simard Marc J , Bever Christopher T.
Published: May 2021

Endoplasmic reticulum (ER) stress and mitochondrial dysfunction are found in lesions of multiple sclerosis (MS) and of experimental autoimmune encephalomyelitis (EAE), an animal model of MS, and may contribute to the neuronal loss that underlies permanent impairment. These pathological changes are due to the neuroinflammation that characterizes MS and the strong interplay between the ER and mitochondria. We investigated whether immunomodulatory drug glatiramer acetate (GA) can reduce these changes in the spinal cords of chronic EAE mice by using routine histology, immunostaining, and electron microscopy. EAE spinal cord tissue exhibited increased infiltration/inflammation (upregulation of proinflammatory cytokines), demyelination, mitochondrial dysfunction (increased fission, decreased fusion, and increased biogenesis), ER stress, downregulation of NAD+ dependent pathways, and increased neuronal death. GA reversed these pathological changes, suggesting that immunomodulating therapy can attenuate ER stress, mitochondrial dysfunction, apoptotic cell death, and demyelination in the CNS and increase NAD+ utilizing activities by suppressing neuroinflammation.
The Mediator tail module cooperates with proneural factors to determine fate identity in Glioblastoma
Authors: Ahmadi Moloud , MacLeod Graham , Rajakulendran Nishani , Kosic Milena , Yang Andy , Molaei Fatemeh , Lin Sichun , Steinhart Zachary , Park Nicole I. , Dirks Peter B. , Angers Stephane
Published: May 2021

Glioblastoma stem cells (GSCs) exhibit latent neuronal lineage differentiation potential governed by the proneural transcription factor Achaete-scute homolog 1 (ASCL1) and harnessing and promoting terminal neuronal differentiation has been proposed as a novel therapeutic strategy. Here, using a genome-wide CRISPR suppressor screen we identified genes required for ASCL1-mediated neuronal differentiation. This approach revealed a specialized function of the Mediator complex tail module and of its subunits MED24 and MED25 for this process in GSCs, human fetal neural stem cells and pluripotent stem cells. We show that upon induction of neuronal differentiation MED25 is recruited to genomic loci co-occupied by ASCL1 to regulate neurogenic gene expression programs. MED24 and MED25 are sufficient to induce neuronal differentiation in GSC cultures and to mediate neuronal differentiation in multiple contexts. Collectively our data expand our understanding of the mechanisms underlying directed terminal neuronal differentiation in brain tumor stem cells and point to a unique function of the Mediator tail in neuronal reprogramming.
Same role but different actors: genetic regulation of post-translational modification of two distinct proteins
Authors: Landini Arianna , Trbojević-Akmačić Irena , Navarro Pau , Tsepilov Yakov A. , Sharapov Sodbo Z. , Vučković Frano , Polašek Ozren , Hayward Caroline , Petrovic Tea , Vilaj Marija , Aulchenko Yurii S. , Lauc Gordan , Wilson James F. , Klarić Lucija
Published: May 2021

Post-translational modifications (PTMs) diversify protein functions and dynamically coordinate their signalling networks, influencing most aspects of cell physiology. Nevertheless, their genetic regulation or influence on complex traits is not fully understood. Here, we compare for the first time the genetic regulation of the same PTM of two proteins – glycosylation of transferrin and immunoglobulin G (IgG). By performing genome-wide association analysis of transferrin glycosylation, we identified 10 significantly associated loci, all novel. Comparing these with IgG glycosylation-associated genes, we note protein-specific associations with genes encoding glycosylation enzymes (transferrin -MGAT5, ST3GAL4, B3GAT1; IgG -MGAT3, ST6GAL1) as well as shared associations (FUT6, FUT8). Colocalisation analyses of the latter suggest that different causal variants in the FUT genes regulate fucosylation of the two proteins. We propose that they affect the binding of different transcription factors in different tissues, with fucosylation of IgG being regulated by IKZF1 in B-cells and of transferrin by HNF1A in liver.
Haploinsufficiency of the essential gene RpS12 causes defects in erythropoiesis and hematopoietic stem cell maintenance
Authors: Folgado-Marco Virginia , Ames Kristina , Chuen Jacky , Gritsman Kira , Baker Nicholas E.
Published: May 2021

Ribosomal protein (Rp) gene haploinsufficiency can result in Diamond-Blackfan Anemia (DBA), characterized by defective erythropoiesis and skeletal defects. Some mouse Rp mutations recapitulate DBA phenotypes, although others lack erythropoietic or skeletal defects. We generated a conditional knockout mouse to partially deleteRpS12, which results in homozygous embryonic lethality.Rps12+/-mice have growth and morphological defects, pancytopenia and impaired erythropoiesis. A striking reduction in hematopoietic stem cells (HSCs) and progenitors in the bone marrow (BM) was associated with decreased ability to repopulate the blood system after competitive and non-competitive BM transplantation. The mutants exhibited loss of HSC quiescence, which was associated with ERK and MTOR activation and increased global translation in HSC and progenitors. Thus, RpS12 has a very strong requirement in maintaining HSC quiescence and function, in addition to erythropoiesis that is affected in DBA patients.
Convergence Assessment for Bayesian Phylogenetic Analysis using MCMC simulation
Authors: Fabreti Luiza Guimarães , Höhna Sebastian
Published: May 2021

Posterior distributions are commonly approximated by samples produced from a Markov chain Monte Carlo (MCMC) simulation. Every MCMC simulation has to be checked for convergence, i.e., that sufficiently many samples have been obtained and that these samples indeed represent the true posterior distribution.

Here we develop and test different approaches for convergence assessment in phylogenetics. We analytically derive a threshold for a minimum effective sample size (ESS) of 625. We observe that only the initial sequence estimator provides robust ESS estimates for common types of MCMC simulations (autocorrelated samples, adaptive MCMC, Metropolis-Coupled MCMC). We show that standard ESS computation can be applied to phylogenetic trees if the tree samples are converted into traces of absence/presence of splits.

Convergence in distribution between replicated MCMC runs can be assessed with the Kolmogorov-Smirnov test. The commonly used potential scale reduction factor (PSRF) is biased when applied to skewed posterior distribution. Additionally, we analytically derive the expected difference between split frequencies (EDSF) and show that it depends on the true frequency of a split. Hence, the average standard deviation of split frequencies is too simplistic and the EDSF should be used instead to check for convergence in split frequencies.

We implemented the methods described here in the open-source R package Convenience (https://github.com/lfabreti/convenience), which allows users to easily test for convergence using output from standard phylogenetic inference software.
Comparative meta-proteomic analysis for the identification of novel plasmodesmata proteins and regulatory cues
Authors: Kirk Philip , Amsbury Sam , German Liam , Gaudioso-Pedraza Rocio , Benitez-Alfonso Yoselin
Published: May 2021

A major route for cell-to-cell signaling is via cell wall-embedded pores termed plasmodesmata (PD) forming the symplasm. PD regulate many aspects of plant development and responses to the environment however, our understanding of what factors affect their structure and permeability is limited. In this paper, a meta-analysis is presented as a tool for the identification of conditions affecting PD transport and in silico generation of PD proteomes for species of interest. The custom-built pipeline searches the whole genome for protein structural features and conserved domains identified on experimental proteomes and use it to predict PD candidates in 22 compatible plant species. Using the in silico proteome and microarray analysis, interactions between PD genes and conditions affecting PD function are identified. High salinity and osmotic stress affect a significant number of PD candidate genes and we provide evidence that these conditions regulate symplasmic transport of GFP. Using the pipeline, the in silico PD proteome for Medicago truncatula was generated, as an example of a plant in which experimental data is not available. The identification of a candidate receptor like protein was experimentally validated in M. truncatula transgenic roots expressing fluorescently tagged protein fusion. Together the results highlight the power of our newly designed tool in the identification of new factors and proteins influencing PD in diverse plant species.
Hierarchical Bayesian Integrated Model for Estimating Migratory Bird Harvest in Canada
Authors: Smith Adam C. , Villeneuve Thomas , Gendron Michel
Published: May 2021

The Canadian Wildlife Service (CWS) requires reliable estimates of the harvest of migratory game birds, including waterfowl, to effectively manage populations of these hunted species. The National Harvest Survey is an annual survey of hunters who purchase Canada’s mandatory migratory game bird hunting permit, integrating information from a survey of hunting activity with information from a separate survey of species composition in the harvest. We use these survey data to estimate the number of birds harvested for each species, as well as hunting activity metrics such as the number of active hunters and days spent hunting. The analytical methods used to generate these estimates have not changed since the survey was first designed in the early 1970s. Here we describe a new hierarchical Bayesian integrated model, which replaces the series of ratio estimators that comprised the old model. We are now using this new model to generate estimates for migratory bird harvests as of the 2019-2020 hunting season, and to generate updated estimates for all earlier years. The hierarchical Bayesian model uses over-dispersed Poisson distributions to model mean hunter activity and harvest (zero inflated Poisson and zero truncated Poisson, respectively). It also includes multinomial distributions to model some key components including, variation in total harvest across periods of the hunting season, the species composition of the harvest within each of those periods, and the age and sex composition in the harvests of a given species. We estimated the parameters of the Poisson and the multinomial distributions for each year as random effects using first-difference time-series. This time-series component allows the model to share information across years and reduces the sensitivity of the estimates to annual sampling noise. The new model estimates are generally very similar to those from the old model, particularly for the species that occur most commonly in the harvest, and so the results do not suggest any major changes to harvest management decisions and regulations. However, estimates for all species from the new model are more precise and less susceptible to annual sampling error, particularly for species that occur less commonly in the harvest (e.g., sea ducks and other species of conservation concern). This new model, with its hierarchical Bayesian framework, will also facilitate future improvements and elaborations, allowing the incorporation of prior information from the rich literature and knowledge in game bird management and biology.
Reorganization of molecular networks associated with DNA methylation and changes in the rearing environments of the house wren (Troglodytes aedon)
Authors: vonHoldt Bridgett M. , Kartzinel Rebecca Y. , van Oers Kees , Verhoeven Koen J.F. , Ouyang Jenny
Published: May 2021

Environmental change, such as increased rates of urbanization, can induce shifts in phenotypic plasticity with some individuals adapting to city life while others are displaced. A key trait that can facilitate adaptation is the degree at which animals respond to stress. This stress response has a heritable component and exhibits intra- and inter-individual variation. However, the mechanisms behind this variability and whether they might be responsible for adaptation to different environments are not known. Variation in DNA methylation can be a potential mechanism that mediates environmental effects on the stress response. We used an inter- and intra-environmental cross-foster experiment to analyze the contribution of DNA methylation to early-life phenotypic variation. We found that at hatching, urban house wren (Troglodytes aedon) offspring had increased methylation as compared to their rural counterparts, and observed plasticity in methylation as offspring aged, indicating developmental effects of the rearing environment on methylation. Differential methylation analyses showed that cellular respiration genes were differentially expressed at hatching and behavioral and metabolism genes were differentially expressed at fledgling. Lastly, hyper-methylation of a single gene (CNTNAP2) is associated with increased glucocorticoid levels. These differential methylation patterns linked to a specific physiological phenotype suggest that DNA methylation may be a mechanism by which individuals adapt to novel environments. Characterizing genetic and environmental influences on methylation is critical for understanding the role of epigenetic mechanisms in evolutionary adaptation.
Probing pathophysiology of extracellular cGAMP with substrate-selective ENPP1
Authors: Carozza Jacqueline A. , Cordova Anthony F. , AlSaif Yasmeen , Böhnert Volker , Skariah Gemini , Li Lingyin
Published: May 2021

The biology of the immune second messenger cGAMP depends on its cellular localization. cGAMP, which is synthesized in response to cytosolic double-stranded DNA, also exists in the extracellular space as a paracrine immunotransmitter that enhances the anticancer immune response. However, the role of extracellular cGAMP is unexplored outside of cancer due to a lack of tools to systemically manipulate it. The extracellular enzyme ENPP1, the only known hydrolase of cGAMP, is a promising target. However, because ENPP1 also degrades extracellular ATP, using genetic knockouts of ENPP1 to study extracellular cGAMP leads to confounding effects. Here we report the H362A point mutation in ENPP1, the dominant cGAMP hydrolase, which selectively abolishes ENPP1’s ability to degrade cGAMP, while retaining activity toward other substrates. H362 is not necessary for binding cGAMP or the catalytically-essential zinc atoms but instead supports the in-line reaction geometry. H362 is evolutionarily conserved down to bacteria, suggesting an ancient origin for extracellular cGAMP biology. Enpp1H362A mice do not display the systemic calcification seen in Enpp1-/- mice, highlighting the substrate-specific phenotype of ENPP1. Remarkably, Enpp1H362A mice were resistant to HSV-1 infection, demonstrating the antiviral role of endogenous extracellular cGAMP. The ENPP1H362A mutation is the first genetic tool to enable exploration of extracellular cGAMP biology in a wide range of tissues and diseases.
The conserved zinc-finger protein GTSF1 helps PIWI proteins achieve their full catalytic potential
Authors: Arif Amena , Bailey Shannon , Izumi Natsuko , Anzelon Todd A. , Ozata Deniz M. , Andersson Cecilia , Gainetdinov Ildar , MacRae Ian J. , Tomari Yukihide , Zamore Phillip D.
Published: May 2021

Argonaute proteins use nucleic acid guides to find and bind specific DNA or RNA target sequences. Argonaute proteins can be found in all kingdoms of life, and play diverse biological functions including genome defense, gene regulation, and chromosome partitioning. Many Argonautes retain their ancestral endoribonuclease activity, cleaving the phosphodiester bond between target nucleotides t10 and t11. In animals, a specialized class of Argonautes, the PIWI proteins, use 21–35 nt PIWI-interacting RNAs (piRNAs) to direct transposon silencing, protect the germline genome, and regulate gene expression during gametogenesis1. The piRNA pathway is required for fertility in one or both sexes of nearly all animals. Both piRNA production and function require RNA cleavage catalyzed by PIWI proteins. Spermatogenesis in mice and other placental mammals requires three distinct, developmentally regulated PIWI proteins: MIWI (PIWIL1), MILI (PIWIL2), and MIWI2 (PIWIL4)2–4. The piRNA-guided endoribonuclease activities of MIWI and MILI are essential to produce functional sperm5, 6. piRNA-directed silencing in mice and insects also requires Gametocyte-Specific Factor 1 (GTSF1), a PIWI-associated protein of unknown function7–12. Here, we report that GTSF1 potentiates the weak, intrinsic, piRNA-directed RNA cleavage activities of PIWI proteins, transforming them into efficient endoribonucleases. GTSF1 represents the first example of an auxiliary protein that potentiates the catalytic activity of an Argonaute protein.
Fertility costs of cryptic viral infections in a model social insect
Authors: Chapman Abigail , Amiri Esmaeil , Han Bin , McDermott Erin , Rueppell Olav , Tarpy David R , Foster Leonard J , McAfee Alison
Published: May 2021

Declining insect populations emphasize the importance of understanding the drivers underlying reductions in insect fitness. Here, we investigated viruses as a threat to social insect reproduction, using honey bees as a model species. We report that in a sample of N = 93 honey bee (Apis mellifera) queens from nine beekeeping operations across a wide geographic range, high levels of natural viral infection are associated with decreased ovary mass. We confirmed this finding in an independent sample of N = 54 queens. Failed (poor quality) queens displayed higher levels of viral infection, reduced sperm viability, smaller ovaries, and altered ovary protein composition compared to healthy queens. We experimentally infected queens with Israeli acute paralysis virus (IAPV) and found that the ovary masses of IAPV-injected queens were significantly smaller than control queens, demonstrating a causal relationship between viral infection and ovary size. Queens injected with IAPV also had significantly lower expression of vitellogenin, the main source of nutrition deposited into developing oocytes, and higher levels of heat-shock proteins (HSPs), which are part of the honey bee’s antiviral response. This work together shows that viral infections occurring naturally in the field are compromising queen reproductive success.
Durable antibody responses in staff at two long-term care facilities, during and post SARS-CoV-2 outbreaks
Authors: Gallichotte Emily N. , Nehring Mary , Young Michael C. , Pugh Sierra , Sexton Nicole R. , Fitzmeyer Emily , Quicke Kendra M. , Richardson Megan , Pabilonia Kristy L. , Ehrhart Nicole , Fosdick Bailey K. , VandeWoude Sue , Ebel Gregory D.
Published: May 2021

SARS-CoV-2 has had a disproportionate impact on non-hospital healthcare settings such as long-term care facilities (LTCFs). The communal nature of these facilities, paired with the high-risk profile of residents, has resulted in thousands of infections and deaths and a high case fatality rate. To detect pre-symptomatic infections and identify infected workers, we performed weekly surveillance testing of staff at two LTCFs which revealed a large outbreak at one of the sites. We collected serum from staff members throughout the study and evaluated it for binding and neutralization to measure seroprevalence, seroconversion, and type and functionality of antibodies. At the site with very few incident infections, we detected that over 40% of the staff had preexisting SARS-CoV-2 neutralizing antibodies, suggesting prior exposure. At the outbreak site, we saw rapid seroconversion following infection. Neutralizing antibody levels were stable for many weeks following infection, suggesting a durable, long-lived response. Receptor-binding domain antibodies and neutralizing antibodies were strongly correlated. The site with high seroprevalence among staff had two unique introductions of SARS-CoV-2 into the facility through seronegative infected staff during the period of study but these did not result in workplace spread or outbreaks. Together our results reveal that high seroprevalence rate among staff can contribute to herd immunity within a workplace and protect against subsequent infection and spread within a facility.
Breaking the fibrinolytic speed limit with microwheel co-delivery of tissue plasminogen activator and plasminogen
Authors: Disharoon Dante , Trewyn Brian G. , Herson Paco S. , Marr David W.M. , Neeves Keith B.
Published: May 2021

Fibrinolysis is the enzymatic degradation of fibrin, the biopolymer that gives blood clots their mechanical integrity. To reestablish blood flow in vessels occluded by clots, tissue plasminogen activator (tPA) can be used; however, its efficacy is limited by transport to and into a clot and by the depletion of its substrate, plasminogen. To overcome these rate limitations, we design a platform to co-deliver tPA and plasminogen based on microwheels (μwheels), wheel-like assemblies of superparamagnetic colloidal beads that roll along surfaces at high speeds and carry therapeutic payloads in applied magnetic fields. By experimentally measuring fibrinolysis of plasma clots at varying concentrations of tPA and plasminogen, the biochemical speed limit was first determined. These data, in conjunction with measurements of μwheel translation, activity of immobilized tPA on beads, and plasminogen release kinetics from magnetic mesoporous silica nanoparticles (mMSN), were used in a mathematical model to identify the optimal tPA:plasminogen ratio and guide the coupling of plasminogen-loaded mMSN to tPA functionalized superparamagnetic beads. Once coupled, particle-bead assemblies form into a co-delivery vehicle that rolls to plasma clot interfaces and lyses them at rates comparable to the biochemical speed limit. With the addition of mechanical action provided by rotating μwheels to penetrate clots, this barrier was exceeded by rates 40-fold higher lysis by 50 nM tPA. This co-delivery of an immobilized enzyme and its substrate via a microbot capable of mechanical work has the potential to target and rapidly lyse clots that are inaccessible by mechanical thrombectomy devices or recalcitrant to systemic tPA delivery.
Strategic infarct locations for post-stroke depressive symptoms: a lesion- and disconnection-symptom mapping study
Authors: Weaver Nick A. , Lim Jae-Sung , Schilderinck Janniek , Biessels Geert Jan , Kang Yeonwook , Kim Beom Joon , Kuijf Hugo J. , Lee Byung-Chul , Lee Keon-Joo , Yu Kyung-Ho , Bae Hee-Joon , Biesbroek J. Matthijs
Published: May 2021

Background

Depression is the most common neuropsychiatric complication after stroke. Infarct location is associated with post-stroke depressive symptoms (PSDS), but it remains debated which brain structures are critically involved. We performed a large-scale lesion-symptom mapping study to identify infarct locations, and white matter disconnections, associated with PSDS.

Methods

We included 553 patients (age 69±11 years, 42% female) with acute ischemic stroke. PSDS were measured using the 30-item Geriatric Depression Scale (GDS-30). Multivariable support vector regression (SVR)-based analyses were performed both at the level of individual voxels (SVR-VLSM) and predefined regions of interest (SVR-ROI) to relate infarct location to PSDS. We externally validated our findings in an independent stroke cohort (N=459). Finally, disconnectome-based analyses were performed using SVR-VLSM, in which white matter fibers disconnected by the infarct were analyzed instead of the infarct itself.Results:Infarcts in the right amygdala, right hippocampus and right pallidum were consistently associated with PSDS (permutation-based p<0.05) in SVR-VLSM and SVR-ROI. External validation (N=459) confirmed the association between infarcts in the right amygdala and pallidum, but not the right hippocampus, and PSDS. Disconnectome-based analyses revealed that disconnections in the right parahippocampal white matter, right thalamus and pallidum, and right anterior thalamic radiation were significantly associated (permutation-based p<0.05) with PSDS.

Conclusions

Infarcts in the right amygdala and pallidum, and disconnections of right limbic and frontal cortico-basal ganglia-thalamic circuits, are associated with PSDS. Our findings provide a comprehensive and integrative picture of strategic infarct locations for PSDS, and shed new light on pathophysiological mechanisms of depression after stroke.
Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein
Authors: Zuzic Lorena , Samsudin Firdaus , Shivgan Aishwary T. , Raghuvamsi Palur V. , Marzinek Jan K , Boags Alister , Pedebos Conrado , Tulsian Nikhil Kumar , Warwicker Jim , MacAry Paul , Crispin Max , Khalid Syma , Anand Ganesh S. , Bond Peter J
Published: May 2021

The recent global COVID-19 pandemic has prompted a rapid response in terms of vaccine and drug development targeting the viral pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this work, we modelled a complete membrane-embedded SARS-CoV-2 spike (S) protein, the primary target of vaccine and therapeutics development, based on available structural data and known glycan content. We then used molecular dynamics (MD) simulations to study the system in the presence of benzene probes designed to enhance discovery of cryptic, potentially druggable pockets on the S protein surface. We uncovered a novel cryptic pocket with promising druggable properties located underneath the 617-628 loop, which was shown to be involved in the formation of S protein multimers on the viral surface. A marked multi-conformational behaviour of this loop in simulations was validated using hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments, supportive of opening and closing dynamics. Interestingly, the pocket is also the site of the D614G mutation, known to be important for SARS-CoV-2 fitness, and within close proximity to mutations in the novel SARS-CoV-2 strains B.1.1.7 and B.1.1.28, both of which are associated with increased transmissibility and severity of infection. The pocket was present in systems emulating both immature and mature glycosylation states, suggesting its druggability may not be dependent upon the stage of virus maturation. Overall, the predominantly hydrophobic nature of the cryptic pocket, its well conserved surface, and proximity to regions of functional relevance in viral assembly and fitness are all promising indicators of its potential for therapeutic targeting. Our method also successfully recapitulated hydrophobic pockets in the receptor binding domain and N-terminal domain associated with detergent or lipid binding in prior cryo-electron microscopy (cryo-EM) studies. Collectively, this work highlights the utility of the benzene mapping approach in uncovering potential druggable sites on the surface of SARS-CoV-2 targets.
Evidence for high intergenic sequence variation in heterozygous Italian ryegrass (Lolium multiflorumLam.) genome revealed by a high-quality draft diploid genome assembly
Authors: Copetti Dario , Yates Steven A. , Vogt Maximilian M. , Russo Giancarlo , Grieder Christoph , Kölliker Roland , Studer Bruno
Published: May 2021

Background

Over the last decade, progress in DNA sequencing technologies and assembly methods allowed plant scientists to move beyond the use of model organisms and work directly on the genomes of the major crops. Forage grass research can also benefit from this revolution, enabling progress in population genetic studies, functional biology, and genomics-assisted breeding. Due to its large genome size and high repeat content, so far only incomplete and fragmented assemblies are available for the grasses of theLoliumandFestucaspecies complex.

Findings

Here, we report a highly contiguous draft assembly of Italian ryegrass (L. multiflorumLam.), spanning 4.5 Gb and with a N50 of 3 Mb, containing ~70,000 gene models. Thanks to its relatedness to barley, 78% of the assembly was anchored on seven pseudomolecules. The high heterozygosity of the plant allowed obtaining a diploid assembly – i.e. across 95% of the assembly, both alleles were assembled on separate sequences. This feature allowed unraveling a very high amount of intergenic sequence variation between allelic sequences.

Conclusions

We present a nearly complete genome assembly of a genotype used in contemporary Swiss forage grass breeding programs. This work shows how genomic research has improved, allowing to decode the genetic code of large, complex, and heterozygous plants. It also allows the functional characterization of the ryegrass gene repertoire and the large-scale development of molecular markers. Furthermore, it paves the road for a reference-based characterization and exploitation of the genetic variation within theLoliumandFestucaspecies complex.
Affective contagion: how attitudes expressed by others influence our perception of actions
Authors: Di Cesare G. , Pelosi A. , Aresta S. , Lombardi G. , Sciutti A.
Published: May 2021

Vitality forms represent a fundamental aspect of social interactions, characterizinghowactions are performed andhowwords are pronounced, on the basis of the agent’s attitude. The same action, such as a handshake, has a different impact on the receiver when it is performed kindly or vigorously, and the same happens with a gentle or rude tone of voice. In the present study, we carried out two experiments which aimed to investigate whether and how vocal requests conveying different vitality forms can influence the perception of goal-directed actions and to measure the duration of this effect over time. More specifically, participants listened to an actor voice pronouncing “give me” in a rude or gentle way, and then they were asked to observe the initial part of a rude or gentle passing action, continue it mentally and estimate its conclusion. Results showed that the perception of different vitality forms expressed by vocal requests influenced the estimated action duration. Moreover, we found that this effect was limited to a certain time interval, after which it started to decay.
Probing the biogenesis pathway and dynamics of thylakoid membranes
Authors: Huokko Tuomas , Ni Tao , Dykes Gregory F. , Simpson Deborah M. , Brownridge Philip , Conradi Fabian D. , Beynon Robert J. , Nixon Peter J. , Mullineaux Conrad W. , Zhang Peijun , Liu Lu-Ning
Published: May 2021

How thylakoid membranes are generated to form the metabolically active membrane network and how thylakoid membranes orchestrate the insertion and localization of protein complexes for efficient electron flux remain elusive. Here, we develop a method to modulate thylakoid biogenesis in the rod-shaped cyanobacteriumSynechococcus elongatusPCC 7942 by modulating light intensity during cell growth, and probe the spatial-temporal stepwise biogenesis process of thylakoid membranes in cells. Our results reveal that the plasma membrane and regularly arranged concentric thylakoid layers have no physical connections. The newly synthesized thylakoid membrane fragments emerge between the plasma membrane and pre-existing thylakoids. Photosystem I monomers appear in the thylakoid membranes earlier than other mature photosystem assemblies, followed by generation of Photosystem I trimers and Photosystem II complexes. Redistribution of photosynthetic complexes during thylakoid biogenesis ensures establishment of the spatial organization of the functional thylakoid network. This study provides insights into the dynamic biogenesis process and maturation of the functional photosynthetic machinery.