bluuebunny/crossref_metadata_2025 huggingface dataset:
Immunophenotyping and machine learning identify distinct immunotypes that predict COVID-19 clinical severity
Authors: Mueller Yvonne M. , Schrama Thijs J. , Ruijten Rik , Schreurs Marco W.J. , Grashof Dwin G.B. , van de Werken Harmen J. G. , de la Sierra Daniel Alvarez , Kiernan Caoimhe H. , Eiro Melisa D. Castro , van Meurs Marjan , Brouwers-Haspels Inge , Zhao Manzhi , Li Ling , de Wit Harm , Ouzounis Christos A. , Wilmsen Merel E. P. , Alofs Tessa , Laport Danique A. , van Wees Tamara , Kraker Geoffrey , Jaimes Maria C. , Van Bockstael Sebastiaan , Hernández-González Manuel , Rokx Casper , Rijnders Bart J.A. , Pujol-Borrell Ricardo , Katsikis Peter D.
Published: May 2021

Quantitative or qualitative differences in immunity may drive and predict clinical severity in COVID-19. We therefore measured modules of serum pro-inflammatory, anti-inflammatory and anti-viral cytokines in combination with the anti-SARS-CoV-2 antibody response in COVID-19 patients admitted to tertiary care. Using machine learning and employing unsupervised hierarchical clustering, agnostic to severity, we identified three distinct immunotypes that were shown post-clustering to predict very different clinical courses such as clinical improvement or clinical deterioration. Immunotypes did not associate chronologically with disease duration but rather reflect variations in the nature and kinetics of individual patient’s immune response. Here we demonstrate that immunophenotyping can stratify patients to high and low risk clinical subtypes, with distinct cytokine and antibody profiles, that can predict severity progression and guide personalized therapy.
Immune profile of children with post-acute sequelae of SARS-CoV-2 infection (Long Covid)
Authors: Sante Gabriele Di , Buonsenso Danilo , De Rose Cristina , Valentini Piero , Ria Francesco , Sanguinetti Maurizio , Sali Michela
Published: May 2021

There is increasing reporting by patients’ organization and researchers of long covid (or post-acute sequelae of SARS-CoV-2 - PASC), characterized by symptoms such as fatigue, dyspnea, chest pain, cognitive and sleeping disturbances, arthralgia and decline in quality of life. Immune system dysregulation with a hyperinflammatory state, direct viral toxicity, endothelial damage and microvascular injury have been proposed as pathologenic mechanisms. Recently, cohorts of children with PASC have been reported in Italy, Sweden and Russia. However, immunological studies of children with PASC have never been performed.

In this study, we documented significant immunologic differences between children that completely recovered from acute infection and those with PASC, providing the first objective laboratory sign of the existence of PASC in children.
Effect of using personal protective equipment during the COVID-19 pandemic on the quality indicators of screening colonoscopies
Authors: Chirayath Subin , Bahirwani Janak , Kaur Parampreet , Martins Noel , Modi Ronak
Published: May 2021

Background

Coronavirus Disease 2019 (COVID-19) has affected many facets of the practice of medicine including screening colonoscopies.

Aims

Our study looks to observe if there has been an effect on the quality of colonoscopies, as indicated by quality measures such as cecal intubation rate (CIR), cecal intubation time (CIT), scope withdrawal time (SWT) and adenoma detection rate (ADR) with the adoption of standard COVID-19 precautions.

Methods

We conducted a retrospective chart review to analyze the effects of the COVID-19 pandemic on screening colonoscopies. The study utilized data on CIR, CIT, SWT and ADR from outpatient, non-emergent procedures conducted at 3 endoscopy suites of St Luke’s University Health Network. All inpatient and emergent procedures were excluded.

Results

Our study demonstrated that the total number of screening colonoscopies was decreased between 2019 to 2020 (318 in 2019 vs 157 in 2020, p= 0.005). CIT (320±105 seconds in 2019 vs 392±107 seconds in 2020, p=0.001) and SWT (706±232 seconds in 2019 vs 830±241 seconds in 2020, p=0.001) were increased while CIR (98.2% in 2019 vs 96.6% in 2020, p=0.04) was decreased between 2019 and 2020 likely due to PPE introduction. ADR was similar between the two groups (38.23 (12.50-66.66) in 2019 vs 38.18(16.66-66.00) in 2020, p=0.8).

Conclusion

Our study showed that quality indices for screening colonoscopies like CIR, CIT, and SWT were negatively impacted during the COVID-19 time period. ADR, however, were similar. Thus, the efficiency of the procedures was affected by the use of PPE but it did not affect the colonoscopy’s clinical benefit.
Cross-sectional study of the association between perceived organizational support and COVID-19 vaccine intention
Authors: Kobayashi Yuichi , Nagata Tomohisa , Fujino Yoshihisa , Hino Ayako , Tateishi Seiichiro , Ogami Akira , Tsuji Mayumi , Matsuda Shinya , Mori Koji ,   CORoNaWork project
Published: May 2021

Objectives

This study examined the association between perceived organizational support (POS) and COVID-19 vaccine intention and the influence of the implementation of workplace infection prevention measures.

Methods

We analyzed 23,846 workers using data from an Internet survey of workers aged 20–65 years conducted in December 2020, during a period of widespread COVID-19 infection in Japan.

Results

A higher POS was associated with a higher intention to vaccinate. The relationship between POS and vaccine intention was attenuated when adjusted for infection prevention measures in the workplace.

Conclusions

In workplaces where POS is present, a sense of responsibility to the group and altruistic behavior may arise. This means employees act to acquire herd immunity to protect others, which may result in increased vaccine intention. The association between POS and vaccination intention was attenuated by adjusting for workplace infection prevention measures, which suggested that infection prevention measures may be a confounding factor or that POS created a health climate that promoted infection prevention measures. The results suggest that working to improve employee well-being and implementing appropriate workplace infection prevention measures during infectious disease outbreaks may promote vaccination behavior and contribute to the acquisition of herd immunity in the community.
Bayesian Additive Regression Trees for Genotype by Environment Interaction Models
Authors: Sarti Danilo A. , Prado Estevão B. , Inglis Alan N. , dos Santos Antônia A. L. , Hurley Catherine B. , Moral Rafael A. , Parnell Andrew C.
Published: May 2021

We propose a new class of models for the estimation of genotype by environment (GxE) interactions in plant-based genetics. Our approach, named AMBARTI, uses semi-parametric Bayesian additive regression trees to accurately capture marginal genotypic and environment effects along with their interaction in a cut Bayesian framework. We demonstrate that our approach is competitive or superior to similar models widely used in the literature via both simulation and a real world dataset. Furthermore, we introduce new types of visualisation to properly assess both the marginal and interactive predictions from the model. An R package that implements our approach is available athttps://github.com/ebprado/ambarti.
Benchmarking 50 classification algorithms on 50 gene-expression datasets
Authors: Piccolo Stephen R. , Mecham Avery , Golightly Nathan P. , Johnson Jérémie L. , Miller Dustin B.
Published: May 2021

By classifying patients into subgroups, clinicians can provide more effective care than using a uniform approach for all patients. Such subgroups might include patients with a particular disease subtype, patients with a good (or poor) prognosis, or patients most (or least) likely to respond to a particular therapy. Diverse types of biomarkers have been proposed for assigning patients to subgroups. For example, DNA variants in tumors show promise as biomarkers; however, tumors exhibit considerable genomic heterogeneity. As an alternative, transcriptomic measurements reflect the downstream effects of genomic and epigenomic variations. However, high-throughput technologies generate thousands of measurements per patient, and complex dependencies exist among genes, so it may be infeasible to classify patients using traditional statistical models. Machine-learning classification algorithms can help with this problem. However, hundreds of classification algorithms exist—and most support diverse hyperparameters—so it is difficult for researchers to know which are optimal for gene-expression biomarkers. We performed a benchmark comparison, applying 50 classification algorithms to 50 gene-expression datasets (143 class variables). We evaluated algorithms that represent diverse machine-learning methodologies and have been implemented in general-purpose, open-source, machine-learning libraries. When available, we combined clinical predictors with gene-expression data. Additionally, we evaluated the effects of performing hyperparameter optimization and feature selection in nested cross-validation folds. Kernel- and ensemble-based algorithms consistently outperformed other types of classification algorithms; however, even the top-performing algorithms performed poorly in some cases. Hyperparameter optimization and feature selection typically improved predictive performance, and univariate feature-selection algorithms outperformed more sophisticated methods. Together, our findings illustrate that algorithm performance varies considerably when other factors are held constant and thus that algorithm selection is a critical step in biomarker studies.

Author Summary
Re-evaluating rhythmic attentional switching: Spurious oscillations from shuffling-in-time
Authors: Brookshire Geoffrey
Published: May 2021

How does attention help to focus perceptual processing on the important parts of a visual scene? Although the neural and perceptual effects of attention were traditionally assumed to be sustained over time, the field is converging on a dramatically different view: that covert attention rhythmically switches between objects at 3-8 Hz. Here I demonstrate that ubiquitous analyses in this literature conflate rhythmic oscillations with aperiodic temporal structure. Using computational simulations, I show that the behavioral oscillations reported in this literature could reflect aperiodic dynamics in attention, rather than periodic rhythms. I then propose two analyses (one novel and one widely used in climate science) that discriminate between periodic and aperiodic structure in behavioral time-series. Finally, I apply these alternative analyses to published data-sets, and find no evidence for rhythms in attentional switching after accounting for aperiodic temporal structure. Attention shows rich temporal structure. The techniques presented here will help to clarify the periodic and aperiodic dynamics of perception and cognition.
“Destructive fishing” – a ubiquitously used but vague term? Usage and impacts across academic research, media, and policy
Authors: Willer David F. , Brian Joshua I. , Derrick Christina J. , Hicks Marcus , Pacay Alerick , McCarthy Arlie H. , Benbow Sophie , Brooks Holly , Hazin Carolina , Mukherjee Nibedita , McOwen Chris J , Walker Jessica , Steadman Daniel
Published: May 2021

The term “destructive fishing” appears in multiple international policy instruments intended to improve outcomes for marine biodiversity, coastal communities and sustainable fisheries. However, the meaning of “destructive fishing” is often vague, limiting effectiveness in policy. Therefore, in this study we systematically reviewed the use of “destructive fishing” in three record types: academic literature, media articles, and policy documents between 1976-2020. A more detailed analysis was performed on sub-sets of these records, considering the extent to which the term is characterised, geographic distribution of use, and specific impacts and practices associated with the term. We found that use of “destructive fishing” relative to the generic term ‘fisheries’ has increased since the 1990s. Records focused predominantly on fishing practices in South-eastern Asia, followed by Southern Asia and Europe. The term was characterised in detail in only 15% of records. Habitat damage and blast/poison fishing were the most associated ecological impacts and gear/practices, respectively. Bottom trawling and unspecified net fishing were regularly linked to destructive fishing. Importantly, the three record types use the term differently. Academic literature tends to specifically articulate the negative impacts, while media articles focus generally on associated gears/practices. Significant regional variation also exists in how the term is used and what phenomena it is applied to. This study provides evidence and recommendations to inform stakeholders in any future pursuit of a unified definition of “destructive fishing” to support more meaningful implementation of global sustainability goals.
The effects of predator odor (TMT) exposure and mGlu3NAM pretreatment on lasting behavioral and molecular adaptations in the insular cortex and BNST
Authors: Tyler Ryan E. , Bluitt Maya N. , Engers Julie L. , Lindsley Craig W. , Besheer Joyce
Published: May 2021

A stressor can trigger adaptations that contribute to neuropsychiatric disorders. Predator odor (TMT) exposure is an innate stressor that produces lasting adaptations. TMT exposure may activate metabotropic glutamate receptor 3 (mGlu3), triggering excitatory corticolimbic adaptations that underlie behavioral changes. To evaluate functional involvement, the mGlu3negative allosteric modulator (NAM, VU6010572; 3 mg/kg, i.p.) was administered before TMT exposure in male, Long Evans rats. Two weeks after stressor, rats underwent behavioral testing (context re-exposure, zero maze and acoustic startle response) followed by RT-PCR gene expression in the insular cortex and BNST. During the TMT exposure, rats displayed stress-reactive behaviors that were not affected by the VU6010572. During the context re-exposure, prior TMT exposure and VU6010572 pretreatment both produced a hyperactive response. TMT exposure did not affect zero maze or ASR measures, but VU6010572 increased time spent in the open arms and habituation to ASR, indicating anxiolytic-like effects. In the insular cortex, TMT exposure resulted in excitatory adaptations as shown by increased expression of mGlu (Grm3, Grm5), NMDA (GriN2A, GriN2B, GriN2C, GriN3A, GriN3B) and AMPA (GriA3) receptor transcripts. Interestingly, mGlu3signaling during stressor mediatedGriN3Bupregulation. Stress reactivity during TMT exposure was associated withGrm5, GriN2A, GriN2C, andGriA3upregulation in the insular cortex and context re-exposure reactivity in the TMT/vehicle, but not the TMT/mGlu3NAM group. In the BNST,GriN2A, GriN2BandGriN3Bwere increased by VU6010572, but TMT prevented these effects. These data demonstrate that mGlu3signaling contributes to the lasting behavioral and molecular adaptations of predator odor stressor.
Tree diversity effects on forest productivity: disentangling the effects of tree species addition vs. substitution
Authors: Maude Toïgo , Bastien Castagneyrol , Hervé Jactel , Xavier Morin , Celine Meredieu
Published: May 2021

Mixture effect on stand productivity is usually apprehended through a substitutive approach, whereby productivity in mixed stands is compared to productivity in monocultures, at equivalent stand density. This approach has proved that in many cases mixed stands perform better than monospecific forests, however, we do not yet have a solid theory about species behaviour in the mixture or even guidelines for combining species. The addition of a second tree species to an existing mono-specific stand has received much less consideration. Yet, this approach has the potential to separate the facilitation effect from the complementarity effect.

We compared the effect of tree species substitution vs. addition on the productivity of maritime pine and silver birch in a young tree diversity experiment implemented in 2008 in SW France.

Substituting pines with birches to create two-species mixtures resulted in an increase of tree productivity at stand level beyond what was expected from monocultures (i.e., overyielding). In contrast, creating mixture through the addition of birches to pine stands had no effect on the maritime pine stand productivity (transgressive mixture effect not significant). This absence of effect is produced by two distinct density-dependence responses at an individual level.

Our results allow clarifying the cases in which a mixed stand can be considered as an alternative to a monoculture of a productive species. In particular, the addition of a pioneer and soil low-demanding species during young developmental stages is a possibility to diversify the stand and potentially to increase ecosystem services without altering the productivity of the target species.
Genetic variation associated with plastic and homeostatic growth responses to drought in Arabidopsis
Authors: Ferrero-Serrano Ángel , Assmann Sarah M.
Published: May 2021

Natural genetic variation influences plant responses to environmental stressors. However, the extent to which such variation underlies plastic versus homeostatic response phenotypes deserves more attention. We quantified the extent of drought-induced changes in leaf area in a set of Iberian Arabidopsis accessions and then performed association studies correlating plasticity and homeostasis in this phenotype with genomic and transcriptomic variation. Drought-induced plastic reductions in relative leaf area typified accessions originating from productive environments. In contrast, homeostasis in relative leaf area typified accessions originating from unproductive environments. Genome-Wide Association Studies (GWAS), Transcriptome Wide Association Studies (TWAS), and expression GWAS (eGWAS) highlighted the importance of auxin-related processes in conferring leaf area plasticity. Homeostatic responses in relative leaf area were associated with a diverse gene set and positively associated with a higher intrinsic water use efficiency (WUEi), as confirmed in a TWAS metanalysis of previously published δ13C measurements. Thus, we have identified not only candidate “plasticity genes” but also candidate “homeostasis genes” controlling leaf area. Our results exemplify the value of a combined GWAS, TWAS, and eGWAS approach to identify mechanisms underlying phenotypic responses to stress.

Highlight

Information on phenotype, genotype, and transcript abundance is integrated to identify candidate plasticity and homeostasis genes and processes associated with local adaptation to drought stress in Arabidopsis accessions of the Iberian Peninsula.
White matter microstructure characterisation in temporal lobe epilepsy
Authors: Rolandi Nicolò , Palesi Fulvia , Padelli Francesco , Giachetti Isabella , Aquino Domenico , Summers Paul , Tartara Elena , Germani Giancarlo , Mariani Valeria , D’Angelo Egidio , Tassi Laura , Wheeler-Kingshott Claudia AM Gandini , Vitali Paolo
Published: May 2021

Temporal lobe epilepsy (TLE) is the most common form of focal epilepsy. Parameters of microstructural abnormalities derived from diffusion tensor imaging(DTI) have been reported to be helpful in differentiating between Left and Right TLE (L-TLE and R-TLE) but few of them compared L-TLE and R-TLE with a voxelwise approach. In this study, a whole brain tract based spatial statistical analysis was performed on DTI, diffusion kurtosis and NODDI derived parameters of 88 subjects to identify specific white matter patterns of alteration in patient affected by L-TLE and R-TLE with respect to healthy controls. Our findings demonstrated the presence of specific patterns of white matter alterations, with L-TLE more widely affected both in cerebral and cerebellar regions. This result supports the need to consider patients separately, according to the side of their pathology.
Increasing phagocytosis of microglia through targeting CD33 with liposomes displaying glycan ligands
Authors: Bhattacherjee Abhishek , Daskhan Gour Chand , Bains Arjun , Watson Adrianne E. S. , Eskandari-Sedighi Ghazaleh , St. Laurent Chris D. , Voronova Anastassia , Macauley Matthew S.
Published: May 2021

CD33 is an immunomodulatory receptor expressed on microglia and genetically linked to Alzheimer’s disease (AD) susceptibility. While antibodies targeting CD33 have entered clinical trials to treat neurodegeneration, it is unknown whether the glycan-binding properties of CD33 can be exploited to modulate microglia. Here, we use liposomes that multivalently display glycan ligands of CD33 (CD33L liposomes) to engage CD33. We find that CD33L liposomes increase phagocytosis of cultured monocytic cells and microglia in a CD33-dependent manner. Enhanced phagocytosis strongly correlates with loss of CD33 from the cell surface and internalization of liposomes. Increased phagocytosis by treatment with CD33L liposomes is dependent on a key intracellular signaling motif on CD33 as well as the glycan-binding ability of CD33. These effects are specific totransengagement of CD33 by CD33L liposomes, ascisengagement through insertion of lipid-linked CD33L into cells produces the opposite effect on phagocytosis. Moreover, intracerebroventricular injection of CD33L liposomes in mice enhances phagocytosis of microglia in a CD33-dependent manner. These results demonstrate that multivalent engagement of CD33 with glycan ligands can modulate microglial cell function.
Resource Profile and User Guide of the Polygenic Index Repository
Authors: Becker Joel , Burik Casper A.P. , Goldman Grant , Wang Nancy , Jayashankar Hariharan , Bennett Michael , Belsky Daniel W. , Linnér Richard Karlsson , Ahlskog Rafael , Kleinman Aaron , Hinds David A. ,   23andMe Research Group, Caspi Avshalom , Corcoran David L. , Moffitt Terrie E. , Poulton Richie , Sugden Karen , Williams Benjamin S. , Harris Kathleen Mullan , Steptoe Andrew , Ajnakina Olesya , Milani Lili , Esko Tõnu , Iacono William G. , McGue Matt , Magnusson Patrik K.E. , Mallard Travis T. , Harden K. Paige , Tucker-Drob Elliot M. , Herd Pamela , Freese Jeremy , Young Alexander , Beauchamp Jonathan P. , Koellinger Philipp , Oskarsson Sven , Johannesson Magnus , Visscher Peter M. , Meyer Michelle N. , Laibson David , Cesarini David , Benjamin Daniel J. , Turley Patrick , Okbay Aysu
Published: May 2021

Polygenic indexes (PGIs) are DNA-based predictors. Their value for research in many scientific disciplines is rapidly growing. As a resource for researchers, we used a consistent methodology to construct PGIs for 47 phenotypes in 11 datasets. To maximize the PGIs’ prediction accuracies, we constructed them using genome-wide association studies—some of which are novel—from multiple data sources, including 23andMe and UK Biobank. We present a theoretical framework to help interpret analyses involving PGIs. A key insight is that a PGI can be understood as an unbiased but noisy measure of a latent variable we call the “additive SNP factor.” Regressions in which the true regressor is the additive SNP factor but the PGI is used as its proxy therefore suffer from errors-in-variables bias. We derive an estimator that corrects for the bias, illustrate the correction, and make a Python tool for implementing it publicly available.
Emerged human-like facial expression representation in a deep convolutional neural network
Authors: Zhou Liqin , Meng Ming , Zhou Ke
Published: May 2021

Face identity and expression play critical roles in social communication. Recent research found that the deep convolutional neural networks (DCNNs) trained to recognize facial identities spontaneously learn features that support facial expression recognition, and vice versa, suggesting an integrated representation of facial identity and expression. In the present study, we found that the expression-selective units spontaneously emerged in a VGG-Face trained for facial identity recognition and tuned to distinct basic expressions. Importantly, they exhibited typical hallmarks of human expression perception, i.e., the facial expression confusion effect and categorical perception effect. We then investigated whether the emergence of expression-selective units is attributed to either face-specific experience or domain-general processing, by carrying out the same analysis on a VGG-16 trained for object classification and an untrained VGG-Face without any visual experience, both of them having the identical architecture with the pretrained VGG-Face. Although Similar expression-selective units were found in both DCNNs, they did not exhibit reliable human-like characteristics of facial expression perception. Taken together, our computational findings revealed the necessity of domain-specific visual experience of face identity for the development of facial expression perception, highlighting the contribution of nurture to form human-like facial expression perception. Beyond the weak equivalence between human and DCNNS at the input-output behavior, emerging simulated algorithms between models and humans could be established through domain-specific experience.
Estimating the glutamate transporter surface density in distinct sub-cellular compartments of mouse hippocampal astrocytes
Authors: Rădulescu Anca R. , Todd Gabrielle C. , Williams Cassandra L. , Bennink Benjamin A. , Lemus Alex A. , Chesbro Haley E. , Bourgeois Justin R. , Kopec Ashley M. , Zuloaga Damian G. , Scimemi Annalisa
Published: May 2021

Glutamate transporters preserve the spatial specificity of synaptic transmission by limiting glutamate diffusion away from the synaptic cleft, and prevent excitotoxicity by keeping the extracellular concentration of glutamate at low nanomolar levels. Glutamate transporters are abundantly expressed in astrocytes, and previous estimates have been obtained about their surface expression in astrocytes of the rat hippocampus and cerebellum. Analogous estimates for the mouse hippocampus are currently not available. In this work, we derive the surface density of astrocytic glutamate transporters in mice of different ages via quantitative dot blot. We find that the surface density of glial glutamate transporters is similar in 7-8 week old mice and rats. In mice, the levels of glutamate transporters increase until about 6 months of age and then begin to decline slowly. Our data, obtained from a combination of experimental and modeling approaches, show that there are stark differences in the density of expression of glutamate transporters across different sub-cellular compartments, indicating that the extent to which astrocytes limit extrasynaptic glutamate diffusion depends not only on their level of synaptic coverage, but also on the identity of the astrocyte compartment in contact with the synapse. Together, these findings provide information on how heterogeneity in the spatial distribution of glutamate transporters in the plasma membrane of hippocampal astrocytes my alter glutamate receptor activation out of the synaptic cleft.

Author summary

In this work, we use experimental and modeling approaches to estimate the surface density of the glial glutamate transporters GLAST and GLT-1 in mouse hippocampal astrocytes. The results show that the surface density of glutamate transporters in hippocampal astrocytes is similar in 7-8 week old mice and rats. In mice, GLAST and GLT-1 reach their peak expression at ~ 6 months of age. Their expression, however, varies widely across different sub-cellular compartments. These findings indicate that the identity of the sub-cellular compartment of an astrocyte in contact with a glutamatergic synapses, in addition to the extent of its synaptic coverage, is a main factor to limit glutamate spillover and receptor activation at a distance from the release site.
Serotonin signals through postsynaptic Gαq, Trio RhoGEF, and diacylglycerol to promoteC. elegansegg-laying circuit activity and behavior
Authors: Dhakal Pravat , Chaudhry Sana I. , Signorelli Rossana , Collins Kevin M.
Published: May 2021

Activated Gαqsignals through Phospholipase-Cβ (PLCβ) and Trio, a Rho GTPase exchange factor (RhoGEF), but how these distinct effector pathways promote cellular responses to neurotransmitters like serotonin remains poorly understood. We used the egg-laying behavior circuit ofC. elegansto determine whether PLCβ and Trio mediate serotonin and Gαqsignaling through independent or related biochemical pathways. Our genetic rescue experiments suggest that PLCβ functions in neurons while Trio RhoGEF functions in both neurons and the postsynaptic vulval muscles. While Gαq, PLCβ, and Trio RhoGEF mutants all fail to lay eggs in response to serotonin, optogenetic stimulation of the serotonin-releasing HSN neurons restores egg laying only in PLCβ mutants. PLCβ mutants showed vulval muscle Ca2+transients while strong Gαqand Trio RhoGEF mutants had little or no vulval muscle Ca2+activity. Treatment with phorbol 12-myristate 13-acetate (PMA) that mimics 1,2-diacylglycerol (DAG), a product of PIP2hydrolysis, rescued egg-laying circuit activity and behavior defects of Gαqsignaling mutants, suggesting both Phospholipase-C and Rho signaling promote synaptic transmission and egg laying via modulation of DAG levels. DAG activates effectors including UNC-13, however we find that phorbol esters, but not serotonin, stimulate egg laying inunc-13and PLCβ mutants. These results support a model where serotonin signaling through Gαq, PLCβ, and UNC-13 promote neurotransmitter release, and that serotonin also signals through Gαq, Trio RhoGEF, and an unidentified, PMA-responsive effector to promote postsynaptic muscle excitability. Thus, the same neuromodulator serotonin can signal in distinct cells and effector pathways to coordinate activation of a motor behavior circuit.
Compositional Data Analysis using Kernels in Mass Cytometry Data
Authors: Rudra Pratyaydipta , Baxter Ryan , Hsieh Elena WY , Ghosh Debashis
Published: May 2021

Motivation

Cell type abundance data arising from mass cytometry experiments are compositional in nature. Classical association tests do not apply to the compositional data due to their non-Euclidean nature. Existing methods for analysis of cell type abundance data suffer from several limitations for high-dimensional mass cytometry data, especially when the sample size is small.

Results

We proposed a new multivariate statistical learning methodology, Compositional Data Analysis using Kernels (CODAK), based on the kernel distance covariance (KDC) framework to test the association of the cell type compositions with important predictors (categorical or continuous) such as disease status. CODAK scales well for high-dimensional data and provides satisfactory performance for small sample sizes (n< 25). We conducted simulation studies to compare the performance of the method with existing methods of analyzing cell type abundance data from mass cytometry studies. The method is also applied to a high-dimensional dataset containing different subgroups of populations including Systemic Lupus Erythematosus (SLE) patients and healthy control subjects.

Availability and Implementation

CODAK is implemented using R. The codes and the data used in this manuscript are available on the web athttp://github.com/GhoshLab/CODAK/.

Supplementary information

Supplementary Materials.pdf.
In situand transcriptomic identification of synapse-associated microglia in the developing zebrafish brain
Authors: Silva Nicholas J. , Dorman Leah C. , Vainchtein Ilia D. , Horneck Nadine C. , Molofsky Anna V.
Published: May 2021

Microglia are brain resident macrophages that play vital roles in central nervous system (CNS) development, homeostasis, and pathology. Microglia both remodel synapses and engulf apoptotic cell corpses during development, but whether unique molecular programs regulate these distinct phagocytic functions is unknown. Here we identify a molecularly distinct synapse-associated microglial subset in the zebrafish (Danio rerio). We found that ramified microglia populated synapse-rich regions of the midbrain and hindbrain between 7 and 28 days post fertilization. In contrast, microglia in the optic tectum were ameboid and clustered around neurogenic zones. Using single-cell mRNA sequencing combined with metadata from regional bulk sequencing, we identified synapse-associated microglia (SAMs) that were highly enriched in the hindbrain, expressed known synapse modulating genes as well as novel candidates, and engulfed synaptic proteins. In contrast, neurogenic-associated microglia (NAMs) were enriched in optic tectum, had active cathepsin activity, and preferentially engulfed neuronal corpses. These data yielded a functionally annotated atlas of zebrafish microglia (https://www.annamolofskylab.org/microglia-sequencing). Furthermore, they reveal that molecularly distinct phagocytic programs mediate synaptic remodeling and cell engulfment, and establish zebrafish hindbrain as a model circuit for investigating microglial-synapse interactions.
In-vivo Protection from SARS-CoV-2 infection by ATN-161 in k18-hACE2 transgenic mice
Authors: Amruta Narayanappa , Engler-Chiurazzi Elizabeth B. , Murray-Brown Isabel C. , Gressett Timothy E. , Biose Ifechukwude J. , Chastain Wesley H. , Bix Gregory
Published: May 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an infectious disease that has spread worldwide. Current treatments are limited in both availability and efficacy, such that improving our understanding of the factors that facilitate infection is urgently needed to more effectively treat infected individuals and to curb the pandemic. We and others have previously demonstrated the significance of interactions between the SARS-CoV-2 spike protein, integrin α5β1, and human ACE2 to facilitate viral entry into host cellsin vitro. We previously found that inhibition of integrin α5β1 by the clinically validated small peptide ATN-161 inhibits these spike protein interactions and cell infectionin vitro. In continuation with our previous findings, here we have further evaluated the therapeutic potential of ATN-161 on SARS-CoV-2 infection in k18-hACE2 transgenic (SARS-CoV-2 susceptible) micein vivo. We discovered that treatment with single- or repeated intravenous doses of ATN-161 (1 mg/kg) within 48 hours after intranasal inoculation with SARS-CoV-2 lead to a reduction of lung viral load, viral immunofluorescence and improved lung histology in a majority of mice 72 hours post-infection. Furthermore, ATN-161 reduced SARS-CoV-2-induced increased expression of lung integrin α5 and αv (an α5-related integrin that has also been implicated in SARS-CoV-2 interactions) as well as the C–X–C motif chemokine ligand 10 (Cxcl10), further supporting the potential involvement of these integrins, and the anti-inflammatory potential of ATN-161, respectively, in SARS-CoV-2 infection. To the best of our knowledge, this is the first study demonstrating the potential therapeutic efficacy of targeting integrin α5β1 in SARS-CoV-2 infectionin vivoand supports the development of ATN-161 as a novel SARS-CoV-2 therapy.
Uncovering long-term existence of a silent short-term memory trace
Authors: Wally Maha E. , Nomoto Masanori , Abdou Kareem , Inokuchi Kaoru
Published: May 2021

Active recall of short-term memory (STM) is known to last for a few hours, but whether STM has long-term functions is unknown. Here we show that, STM can be optogenetically retrieved at a time point during which natural recall is not possible, uncovering the long-term existence of a silent STM engram. Moreover, re-training within 3 days led to natural long-term recall, indicating facilitated consolidation. Calcium imaging revealed hippocampal CA1 reactivations of the STM trace during post-learning sleep. Inhibiting offline CA1 activity, N-methyl-D-aspartate receptor activity, or protein synthesis after first exposure to the STM-forming event impaired the future re-exposure-facilitated consolidation, which highlights a role of protein synthesis and sleep in storing a silent STM trace. These results provide evidence that STM is not completely lost within hours and demonstrates a possible two-step STM consolidation, first storage as a silent engram, then transformation into an active state by recurrence within 3 days.
Analogs of the Dopamine Metabolite 5,6-Dihydroxyindole Bind Directly to and Activate the Nuclear Receptor Nurr1 (NR4A2)
Authors: Kholodar Svetlana A. , Lang Geoffrey , Cortopassi Wilian A. , Iizuka Yoshie , Brah Harman S. , Jacobson Matthew P. , England Pamela M.
Published: May 2021

The nuclear receptor-related 1 protein, Nurr1, is a transcription factor critical for the development and maintenance of dopamine-producing neurons in the substantia nigra pars compacta, a cell population that progressively loses the ability to make dopamine and degenerates in Parkinson’s disease. Recently, we demonstrated that Nurr1 binds directly to and is regulated by the endogenous dopamine metabolite 5,6-dihydroxyindole (DHI). Unfortunately, DHI is an unstable compound, and thus a poor tool for studying Nurr1 function. Here we report that 5-chloroindole, an unreactive analog of DHI, binds directly to the Nurr1 ligand binding domain with micromolar affinity and stimulates the activity of Nurr1, including the transcription of genes governing the synthesis and packaging of dopamine.
Climate-change risk analysis for global urban forests
Authors: Esperon-Rodriguez Manuel , Baumgartner John B. , Beaumont Linda J. , Lenoir Jonathan , Nipperess David , Power Sally A. , Richard Benoît , Rymer Paul D. , Tjoelker Mark G. , Gallagher Rachael V.
Published: May 2021

Urban forests (i.e. all vegetation present in urban areas), provide environmental and socioeconomic benefits1to more than half of the global population2. Projected climate change threatens these benefits to society3–5. Here, we assess vulnerability to climate change of 16,006 plant species present in the urban forests of 1,010 cities within 93 countries, using three vulnerability metrics: exposure, safety margin and risk. Exposure expresses the magnitude of projected changes in climate in a given area, safety margin measures species’ sensitivity to climate change, and risk is the difference between exposure and safety margin6. We identified 9,676 (60.5%) and 8,344 (52.1%) species exceeding their current climatic tolerance (i.e. safety margin) for mean annual temperature (MAT) and annual precipitation (AP), respectively. By 2050, 13,479 (84.2%) and 9,960 (62.2%) species are predicted to be at risk from projected changes in MAT and AP, respectively, with risk increasing in cities at lower latitudes. Our results can aid evaluation of the impacts of climate change on urban forests and identify the species most at risk. Considering future climates when selecting species for urban plantings will enhance the long-term societal benefits provided by urban forests, including their contribution to mitigating the magnitude and impacts of climate change.
SCON - A Short Conditional intrON for conditional knockout with one-step zygote injection
Authors: Wu Szu-Hsien Sam , Szép-Bakonyi Réka , Lee Heetak , Colozza Gabriele , Boese Ayse , Gert Krista Rene , Hallay Natalia , Kim Jihoon , Zhu Yi , Pilat-Carotta Sandra , Theussl Hans-Christian , Pauli Andrea , Koo Bon-Kyoung
Published: May 2021

The generation of conditional alleles using CRISPR technology is still challenging. Here, we introduce a Short Conditional intrON (SCON, 189 bp) that enables rapid generation of conditional alleles via one-step zygote injection. SCON has conditional intronic function in various vertebrate species and its target insertion is as simple as CRISPR/Cas9-mediated gene tagging.
Rbfox1 is required for myofibril development and maintaining fiber-type specific isoform expression inDrosophilamuscles
Authors: Nikonova Elena , Kamble Ketaki , Mukherjee Amartya , Barz Christiane , Nongthomba Upendra , Spletter Maria L.
Published: May 2021

Protein isoform transitions confer distinct properties on muscle fibers and are regulated predominantly by differential transcription and alternative splicing. RNA-binding Fox protein 1 (Rbfox1) can affect both transcript levels and splicing, and is known to control skeletal muscle function. However, the detailed mechanisms by which Rbfox1 contributes to normal muscle development and physiology remain obscure. In this study, we report that Rbfox1 contributes to the generation of adult muscle diversity inDrosophila. Rbfox1 is differentially expressed in tubular and fibrillar muscle fiber types. RNAi knockdown of Rbfox1 leads to a loss of flight, climbing and jumping ability, as well as eclosion defects. Myofibers in knockdown muscle are frequently torn, and sarcomeres are hypercontracted. These defects arise from mis-regulation of fiber-type specific gene and splice isoform expression, notably loss of an IFM-specific isoform of Troponin-I that is critical for regulating myosin activity. We find that Rbfox1 influences mRNA transcript levels through 1) direct binding of 3’-UTRs of target transcripts as well as 2) through regulation of myogenic transcription factors, including Mef2, Exd and Salm. Moreover, Rbfox1 modulates splice isoform expression through 1) direct regulation of target splice events in structural genes and 2) regulation of the CELF-family RNA-binding protein Bruno1. Our data indicate that cross-regulatory interactions observed between FOX and CELF family RNA-binding proteins in vertebrates are conserved between their counterparts, Rbfox1 and Bruno1 in flies. Rbfox1 thus affects muscle development by regulation of both fiber-type specific gene and gene isoform expression dynamics of identity genes and structural proteins.
Glutathione regulates transcriptional activation of iron transporters via S-nitrosylation of bHLH factors to modulate subcellular iron homeostasis
Authors: Shee Ranjana , Ghosh Soumi , Khan Pinki , Sahid Salman , Roy Chandan , Shee Dibyendu , Paul Soumitra , Datta Riddhi
Published: May 2021

While glutathione (GSH) is known to regulate iron (Fe) deficiency response in plants, its involvement in modulating subcellular Fe homeostasis remained elusive. In this study, we report that the GSH depleted mutants, cad2-1 and pad2-1 displayed increased sensitivity to Fe deficiency with significant down-regulation of the vacuolar Fe exporters, AtNRAMP3 and AtNRAMP4 and the chloroplast Fe importer, AtPIC1. Moreover, the pad2-1 mutant accumulated higher Fe content in vacuoles and lower in chloroplasts compared with Col-0 under Fe limited condition. Exogenous GSH treatment could enhance the chloroplast Fe content in Col-0 plants but failed to do so in the nramp3nramp4 double mutant demonstrating the role of GSH in modulating subcellular Fe homeostasis. Pharmacological experiments, mutant analysis and promoter assay revealed that this regulation involved transcriptional activation of the transporter genes by a GSH-GSNO module. The Fe responsive bHLH transcription factors (TFs), AtbHLH29, AtbHLH38 and AtbHLH101 were identified to interact with the promoters of these genes which were in turn activated via S-nitrosylation. Together, the present study delineates the role of GSH-GSNO module in regulating subcellular Fe homeostasis by transcriptional activation of the Fe transporters AtNRAMP3, AtNRAMP4 and AtPIC1 via S-nitrosylation of the bHLH TFs during Fe deficiency.

Summary statement

Glutathione regulates subcellular iron homeostasis under iron deficiency via GSNO dependent transcriptional activation of AtNRAMP3, AtNRAMP4 and AtPIC1 genes by S-nitrosylation of the iron responsive bHLH transcription factors, AtbHLH29, AtbHLH38 and AtbHLH101.
Receptor Activity-Modifying Protein 2 (RAMP2) alters glucagon receptor trafficking in hepatocytes with functional effects on receptor signalling
Authors: McGlone Emma Rose , Manchanda Yusman , Jones Ben , Pickford Phil , Inoue Asuka , Carling David , Bloom Stephen R , Tan Tricia , Tomas Alejandra
Published: May 2021

Objectives

Receptor Activity-Modifying Protein 2 (RAMP2) is a chaperone protein which allosterically binds to and interacts with the glucagon receptor (GCGR). The aims of this study were to investigate the effects of RAMP2 on GCGR trafficking and signalling in the liver, where glucagon is important for carbohydrate and lipid metabolism.

Methods

Subcellular localisation of GCGR in the presence and absence of RAMP2 was investigated using confocal microscopy, trafficking assays and radioligand binding assays in human embryonic kidney (HEK293T) and human hepatoma (Huh7) cells. Mouse embryonic fibroblasts (MEFs) lacking Wiskott Aldrich Syndrome protein and scar homologue (WASH) complex were used to investigate the effect of a halt in recycling of internalised proteins on GCGR signalling in the absence of RAMP2. NanoBiT complementation and cyclic AMP assays were used to study the functional effect of RAMP2 on recruitment and activation of GCGR signalling mediators. Response to hepatic RAMP2 up-regulation in lean and obese adult mice using a bespoke adeno-associated viral vector was also studied.

Results

GCGR is predominantly localised at the plasma membrane in the absence of RAMP2 and exhibits remarkably slow internalisation in response to agonist stimulation. Rapid intracellular retention of glucagon-stimulated GCGR in cells lacking WASH complex indicates that activated GCGRs undergo continuous cycles of internalisation and recycling despite apparent GCGR plasma membrane localisation up to 40 minutes post-stimulation. Co-expression of RAMP2 induces GCGR internalisation both basally and in response to agonist-stimulation. The intracellular retention of GCGR in the presence of RAMP2 confers a bias away from β-arrestin-2 recruitment coupled to increased activation of Gαs proteins at endosomes. This is associated with increased short-term efficacy for glucagon-stimulated cAMP production, although long-term signalling is dampened by increased receptor lysosomal targeting for degradation. Despite these signalling effects, only minor disturbance of carbohydrate metabolism was observed in mice with up-regulated hepatic RAMP2.

Conclusions

By retaining GCGR intracellularly, RAMP2 alters the spatiotemporal pattern of GCGR signalling. Further exploration of the effects of RAMP2 on GCGR in vivo is warranted.

Graphical abstract

Icons sourced from [1]