bluuebunny/crossref_metadata_2025 huggingface dataset:
Immunoprecipitation-targeted proteomics assays facilitate rational development of SARS-CoV-2 serological diagnostics
Authors: Fu Zhiqiang , Rais Yasmine , Drabovich Andrei P.
Published: October 2021

Current design of serological tests employs conservative immunoassay approaches and is often focused on convenience, speed of manufacturing, and affordability. Limitations of such serological tests include semi-quantitative measurements, lack of standardization, potential cross-reactivity, and inability to distinguish between antibody subclasses. As a result of cross- reactivity, diagnostic specificity of serological antibody tests may not be sufficiently high to enable screening of the general asymptomatic populations for the acquired immunity against low-prevalence infectious diseases, such as COVID-19. Likewise, lack of a single standard for assay calibration limits inter-laboratory and international standardization of serological tests. In this study, we hypothesize that combination of immunoaffinity enrichments with targeted mass spectrometry measurements would enable rational design of serology diagnostics of infectious diseases, such as COVID-19. The same instrumental platform allows for sensitive and specific measurements of viral protein antigens, as wells as anti-viral antibodies circulating in human serum. Our proof-of-concept immunoprecipitation - parallel reaction monitoring (IP-PRM) assays quantified NCAP_SARS2 protein with a limit of detection of 313 pg/mL in serum. In addition, a multiplex IP-selected reaction monitoring (IP-SRM) assay facilitated differential quantification of anti-SARS-CoV-2 antibody isotypes and subclasses in patient sera. Simultaneous evaluation of numerous antigen-antibody subclass combinations revealed a receptor-binding domain (RBD)-IgG1 as a combination with the highest diagnostic specificity and sensitivity. Anti-RBD IgG1, IgG3, IgM and IgA1 subclasses, but not IgG2, IgG4 and IgA2, were found elevated in COVID-19-positive sera. Synthetic heavy isotope-labeled peptide internal standards as calibrators revealed elevated anti-RBD IgG1 in positive (510-6700 ng/mL; 0.02-0.22% of total serum IgG1) versus negative sera (60 [interquartile range 41-81] ng/mL). Likewise, anti-RBD IgM was elevated in positive (190-510 ng/mL; 0.06-0.16% of total serum IgM) versus negative sera (76 [31-108] ng/mL). Further validation of immunoprecipitation-targeted proteomics assays as a platform for serological assays will facilitate standardization and improvement of the existing serological tests, enable rational design of novel tests, and offer tools for comprehensive investigation of antibody isotype and subclass cooperation in immunity response.
Malaria parasites utilize pyrophosphate to fuel an essential proton pump in the ring stage and the transition to trophozoite stage
Authors: Solebo Omobukola , Ling Liqin , Zhou Jing , Fu Tian-Min , Ke Hangjun
Published: October 2021

The malaria parasite relies on anaerobic glycolysis for energy supply when growing inside RBCs as its mitochondrion does not produce ATP. The ring stage lasts ∼ 22 hours and is traditionally thought to be metabolically quiescent. However, recent studies show that the ring stage is active for several energy-costly processes including gene transcription/translation, protein export, and movement inside the RBC. It has remained unclear if a low glycolytic flux can meet the energy demand of the ring stage. Here we show that the metabolic by-product, pyrophosphate, is a critical energy source for the development of the ring stage and its transition to the trophozoite stage. During early phases of the asexual development, the parasite utilizes Plasmodium falciparum vacuolar pyrophosphatase 1 (PfVP1), an ancient pyrophosphate-driven proton pump, to pump protons across the parasite plasma membrane to maintain the membrane potential and cytosolic pH. Conditional deletion of PfVP1 leads to delayed ring stage development and a complete blockage of the ring-to-trophozoite transition, which can be partially rescued by Arabidopsis thaliana vacuolar pyrophosphatase 1, but not by the soluble pyrophosphatase from Saccharomyces cerevisiae. Proton-pumping pyrophosphatases are absent in humans, which highlights the possibility of developing highly selective VP1 inhibitors against the malaria parasite.
Homosalate boosts the release of tumor-derived Extracellular Vesicles with anti-anoikis properties
Authors: Grisard Eleonora , Lescure Aurianne , Nevo Nathalie , Corbé Maxime , Jouve Mabel , Lavieu Gregory , Joliot Alain , Nery Elaine Del , Martin-Jaular Lorena , Théry Clotilde
Published: October 2021

Eukaryotic cells, including cancer cells, secrete highly heterogeneous populations of extracellular vesicles (EVs). EVs could have different subcellular origin, composition and functional properties, but tools to distinguish between EV subtypes are scarce. Here, we tagged CD63- or CD9-positive EVs secreted by triple negative breast cancer cells with Nanoluciferase enzyme, to set-up a miniaturized method to quantify secretion of these two EV subtypes directly in the supernatant of cells. We performed a cell-based high-content screening to identify clinically-approved drugs able to affect EV secretion. One of the identified hits is Homosalate, an anti-inflammatory drug found in sunscreens which robustly increased EVs’ release. Comparing EVs induced by Homosalate with those induced by Bafilomycin A1, we discovered that: 1) the two drugs act on EVs generated in distinct subcellular compartments and 2) EVs released upon treatment with Homosalate, but not with Bafilomycin A1, conferred anti-anoikis properties to another recipient tumor cell line. In conclusion, we identified a new drug modifying EV release and demonstrated that under influence of different drugs, triple negative breast cancer cells release EV subpopulations from different subcellular origins harboring distinct functional properties.
Evolution of diapause in the African turquoise killifish by remodeling ancient gene regulatory landscape
Authors: Singh Param Priya , Reeves G. Adam , Contrepois Kévin , Ellenberger Mathew , Hu Chi-Kuo , Snyder Michael P. , Brunet Anne
Published: October 2021

Suspended animation states such as hibernation or diapause allow organisms to survive extreme environments. But the mechanisms underlying the evolution of these extreme survival states are unknown. The African turquoise killifish has evolved diapause as a form of suspended development to survive the complete drought that occurs every year in its habitat. Here we show that many gene duplicates – paralogs – exhibit specialized expression in diapause versus normal development in the African turquoise killifish. Surprisingly, paralogs with specialized expression in diapause are evolutionarily very ancient, and they are also present even in vertebrates that do not exhibit diapause. Profiling the chromatin accessibility landscape among different fish species reveals an evolutionarily recent increase in chromatin accessibility at these very ancient paralogs, suggesting rewiring of their regulatory landscape. The increase in chromatin accessibility in the African turquoise killifish is linked to the presence of new binding sites for transcription factors (e.g., FOXO, REST, and PPAR), due to both de novo mutations and transposable element insertion. Interestingly, accessible chromatin regions in diapause are enriched for lipid metabolism genes. By performing lipidomics in different fish species, we uncover a specific lipid profile in African turquoise killifish embryos in diapause. Notably, select very long-chain fatty acids are high in diapause, suggesting they may be used for long-term survival in this state. Together, our multi-omic analysis indicates that diapause is driven by regulatory innovation of very ancient gene programs that are critical for survival. Our work also suggests a mechanism for how complex adaptations evolve in nature and offers strategies by which a suspended animation program could be reactivated in other species for long-term preservation.
Structure, receptor recognition and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein
Authors: Tortorici M. Alejandra , Walls Alexandra C. , Joshi Anshu , Park Young-Jun , Eguia Rachel T. , Stevens-Ayers Terry , Boeckh Michael J. , Telenti Amalio , Lanzavecchia Antonio , Corti Davide , Bloom Jesse D. , Veesler David
Published: October 2021

The recent isolation of CCoV-HuPn-2018 from a child respiratory swab indicates that more coronaviruses are spilling over to humans than previously appreciated. Here, we determined cryo-electron microscopy structures of the CCoV-HuPn-2018 spike glycoprotein trimer in two distinct conformational states and identified that it binds canine, feline and porcine aminopeptidase N (APN encoded by ANPEP) orthologs which serve as entry receptors. Introduction of an oligosaccharide at position N739 of human APN renders cells susceptible to CCoV-HuPn-2018 spike-mediated entry, suggesting that single nucleotide polymorphisms could account for the detection of this virus in some individuals. Human polyclonal plasma antibodies elicited by HCoV-229E infection and a porcine coronavirus monoclonal antibody inhibit CCoV-HuPn-2018 S-mediated entry, indicating elicitation of cross-neutralizing activity among α-coronaviruses. These data provide a blueprint of the CCoV-HuPn-2018 infection machinery, unveil the viral entry receptor and pave the way for vaccine and therapeutic development targeting this zoonotic pathogen.
Disentangling single-cell omics representation with a power spectral density-based feature extraction
Authors: Zandavi Seid Miad , Koch Forrest , Vijayan Abhishek , Zanini Fabio , Mora Fa Valdes , Ortega David Gallego , Vafaee Fatemeh
Published: October 2021

Emerging single-cell technologies provide high-resolution measurements of distinct cellular modalities opening new avenues for generating detailed cellular atlases of many and diverse tissues. The high dimensionality, sparsity, and inaccuracy of single cell sequencing measurements, however, can obscure discriminatory information, mask cellular subtype variations and complicate downstream analyses which can limit our understanding of cell function and tissue heterogeneity. Here, we present a novel pre-processing method (scPSD) inspired bypower spectral densityanalysis that enhances the accuracy for cell subtype separation from large-scale single-cell omics data. We comprehensively benchmarked our method on a wide range of single-cell RNA-sequencing datasets and showed that scPSD pre-processing, while being fast and scalable, significantly reduces data complexity, enhances cell-type separation, and enables rare cell identification. Additionally, we applied scPSD to transcriptomics and chromatin accessibility cell atlases and demonstrated its capacity to discriminate over 100 cell types across the whole organism and across different modalities of single-cell omics data.
Nuclear Export of Drosophila PERIOD contributes to temperature compensation of the circadian clock
Authors: Giesecke Astrid , Johnstone Peter S , Lamaze Angelique , Landskron Johannes , Atay Ezgi , Chen Ko-Fan , Top Deniz , Stanewsky Ralf
Published: October 2021

Circadian clocks are self-sustained molecular oscillators controlling daily changes of behavioral activity and physiology. For functional reliability and precision the frequency of these molecular oscillations must be stable at different environmental temperatures, known as ‘temperature compensation’. Despite being an intrinsic property of all circadian clocks, this phenomenon is not well understood at the molecular level. Here we use behavioral and molecular approaches to characterize a novel mutation in the period (per) clock gene of Drosophila melanogaster, which alters a predicted nuclear export sequence (NES) of the PER protein. We show that this new perI530A allele leads to progressively longer behavioral periods and clock oscillations with increasing temperature in both clock neurons and peripheral clock cells. While the mutant PERI530A protein shows normal circadian fluctuations and post-translational modifications at cool temperatures, increasing temperatures lead to both, severe amplitude dampening and hypophosphorylation of PERI530A. We further show that PERI530A displays reduced repressor activity at warmer temperatures, presumably because it cannot inactivate the transcription factor CLOCK (CLK). With increasing temperatures nuclear accumulation of PERI530A within clock neurons is increased, suggesting that PER is normally exported out of the nucleus at warm temperatures. Consequently, downregulating the nuclear export factor CRM1 also leads to temperature-dependent changes of behavioral rhythms. In summary, our results suggest that the PER NES and the nuclear export of clock proteins play an important role in temperature compensation of the Drosophila circadian clock.
sumSTAAR: a flexible framework for gene-based association studies using GWAS summary statistics
Authors: Belonogova Nadezhda M. , Svishcheva Gulnara R. , Kirichenko Anatoly V. , Tsepilov Yakov A. , Axenovich Tatiana I.
Published: October 2021

Gene-based association analysis is an effective gene mapping tool. Many gene-based methods have been proposed recently. However, their power depends on the underlying genetic architecture, which is rarely known in complex traits, and so it is likely that a combination of such methods could serve as a universal approach. Several frameworks combining different gene-based methods have been developed. However, they all imply a fixed set of methods, weights and functional annotations. Moreover, most of them use individual phenotypes and genotypes as input data. Here, we introduce sumSTAAR, a framework for gene-based association analysis using summary statistics obtained from genome-wide association studies (GWAS). It is an extended and modified version of STAAR framework proposed by Li and colleagues in 2020. The sumSTAAR framework offers a wider range of gene-based methods to combine. It allows the user to arbitrarily define a set of these methods, weighting functions and probabilities of genetic variants being causal. The methods used in the framework were adapted to analyse genes with large number of SNPs to decrease the running time. The framework includes the polygene pruning procedure to guard against the influence of the strong GWAS signals outside the gene. We also present new improved matrices of correlations between the genotypes of variants within genes. These matrices estimated on a sample of 265,000 individuals are a state-of-the-art replacement of widely used matrices based on the 1000 Genomes Project data.

AUTHOR SUMMARY

Gene-based association analysis is an effective gene mapping tool. Quite a few frameworks have been proposed recently for gene-based association analysis using a combination of different methods. However, all of these frameworks have at least one of the disadvantages: they use a fixed set of methods, they cannot use functional annotations, or they use individual phenotypes and genotypes as input data. To overcome these limitations, we propose sumSTAAR, a framework for gene-based association analysis using GWAS summary statistics. Our framework allows the user to arbitrarily define a set of the methods and functional annotations. Moreover, we adopted the methods for the analysis of genes with a large number of SNPs to decrease the running time. The framework includes the polygene pruning procedure to guard against the influence of the strong GWAS signals outside the gene. We also present new improved matrices of correlations between the genotypes of variants within genes, which now allows to include ultra-rare variants in analysis.
Perception of a conserved family of plant signalling peptides by the receptor kinase HSL3
Authors: Rhodes Jack , Roman Andra-Octavia , Bjornson Marta , Brandt Benjamin , Derbyshire Paul , Wyler Michele , Schmid Marc , Menke Frank L.H. , Santiago Julia , Zipfel Cyril
Published: October 2021

Plant genomes encode hundreds of secreted peptides; however, relatively few have been characterised. We report here an uncharacterised, stress-induced family of plant signalling peptides, which we call CTNIPs. Based on the role of the common co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) in CTNIP-induced responses, we identified the orphan receptor kinase HAESA-LIKE 3 (HSL3) as the CTNIP receptor via a proteomics approach. CTNIP binding, ligand-triggered complex formation with BAK1, and induced downstream responses all involve HSL3. Notably, the HSL3-CTNIP signalling module is evolutionarily ancient, predating the divergence of extant angiosperms. The identification of this signalling module will help establish its physiological role and provides a resource to understand further receptor-ligand co-evolution.
Long-range connections mirror and link microarchitectural and cognitive hierarchies in the human brain
Authors: Wang Yezhou , Royer Jessica , Park Bo-yong , de Wael Reinder Vos , Larivière Sara , Tavakol Shahin , Rodriguez-Cruces Raul , Paquola Casey , Hong Seok-Jun , Margulies Daniel S. , Smallwood Jonathan , Valk Sofie L. , Evans Alan C. , Bernhardt Boris C.
Published: October 2021

Abstract

Core features of higher-order cognition are hypothesized to be implemented via distributed cortical networks that are linked via long-range connections. However, these connections are biologically expensive, and it is unknown how the computational advantages long-range connections provide overcome the associated wiring costs. Our study investigated this question by exploring the relationship between long-range functional connections and local cortical microarchitecture. Specifically, our work (i) profiled distant cortical connectivity using resting-state fMRI and cortico-cortical geodesic distance mapping, (ii) assessed how long-range connections reflect local brain microarchitecture, and (iii) studied the microarchitectural similarity of regions connected through long-range connections. Analysis of two independent datasets indicated that sensory and motor areas had more clustered short-range connectivity patterns, while transmodal association cortices, including regions of the default mode network, were characterized by distributed, long-range connections. Confirmatory meta-analysis suggested that this topographical difference mirrored a shift in cognitive function, from perception/action towards emotional and social cognitive processing. Analysis of myelin-sensitive in vivo MRI in the same participants as well as post mortem histology and gene expression established that gradients in functional connectivity distance are paralleled by those present in cortical microarchitecture. Moreover, long-range connections were found to link together spatially remote regions of association cortex with an unexpectedly similar microarchitecture. These findings provide novel insights into how the organization of distributed functional networks in transmodal association cortex contribute to cognition, because they suggest that long-range connections link together distant islands of association cortex with similar microstructural features.
Multi-trait and multi-environment Bayesian analysis to predict the G x E interaction in flood-irrigated rice
Authors: da Silva Júnior Antônio Carlos , de Castro Sant’Anna Isabela , Silva Michele Jorge , Cruz Cosme Damião , Azevedo Camila Ferreira , Nascimento Moyses , Soares Plínio César
Published: October 2021

The biggest challenge for the reproduction of flood-irrigated rice is to identify superior genotypes that present development of high-yielding varieties with specific grain qualities, resistance to abiotic and biotic stresses in addition to superior adaptation to the target environment.Thus, the objectives of this study were to propose a multi-trait and multi-environment Bayesian model to estimate genetic parameters for the flood-irrigated rice crop. To this end, twenty-five rice genotypes belonging to the flood-irrigated rice breeding program were evaluated. Grain yield and flowering were evaluated in the agricultural year 2017/2018. The experimental design used in all experiments was a randomized block design with three replications. The Markov Chain Monte Carlo algorithm was used to estimate genetic parameters and genetic values. The flowering is highly heritable by the Bayesian credibility interval:h2= 0.039-0.80, and 0.02-0.91, environment 1 and 2, respectively. The genetic correlation between traits was significantly different from zero in the two environments (environment 1: −0.80 to 0.74; environment 2: −0.82 to 0.86. The relationship ofCVeandCVghigher for flowering in the reduced model (CVg/CVe= 5.83 and 13.98, environments 1 and 2, respectively). For the complete model, this trait presented an estimate of the relative variation index of:CVe= 4.28 and 4.21, environments 1 and 2, respectively. In summary, the multi-trait and multi-environment Bayesian model allowed a reliable estimate of the genetic parameter of flood-irrigated rice. Bayesian analyzes provide robust inference of genetic parameters. Therefore, we recommend this model for genetic evaluation of flood-irrigated rice genotypes, and their generalization, in other crops. Precise estimates of genetic parameters bring new perspectives on the application of Bayesian methods to solve modeling problems in the genetic improvement of flood-irrigated rice.
Investigating the genetic and environmental basis of head micromovements during MRI
Authors: Beyer Frauke , Horn Katrin , Frenzel S. , Hofer Edith , Knol Maria J. , Morys Filip , Vainik Uku , Van der Auwera Sandra , Wittfeld Katharina , Saba Yasaman , Adams Hieab HH , Bülow Robin , Grabe Hans , Homuth Georg , Koini Marisa , Loeffler Markus , Schmidt Helena , Schmidt Reinhold , Teumer Alexander , Vernooij MW , Villringer Arno , Völzke Henry , Zonneveld Hazel , Dagher A. , Scholz Markus , Witte AV
Published: October 2021

Introduction

Head motion during magnetic resonance imaging is heritable. Further, it shares phenotypical and genetic variance with body mass index (BMI) and impulsivity. Yet, to what extent this trait is related to single genetic variants and physiological or behavioral features is unknown. We investigated the genetic basis of head motion in a meta-analysis of genome-wide association studies. Further, we tested whether physiological or psychological measures, such as respiratory rate or impulsivity, mediated the relationship between BMI and head motion.

Methods

We conducted a genome-wide association meta-analysis for mean and maximal framewise head displacement (FD) in seven population neuroimaging cohorts (UK Biobank, LIFE-Adult, Rotterdam Study cohort 1-3, Austrian Stroke Prevention Family Study, Study of Health in Pomerania; total N = 35.109). We performed a pre-registered analysis to test whether respiratory rate, respiratory volume, self-reported impulsivity and heart rate mediated the relationship between BMI and mean FD in LIFE-Adult.

Results

No variant reached genome-wide significance for neither mean nor maximal FD. Neither physiological nor psychological measures mediated the relationship between BMI and head motion.

Conclusion

Based on these findings from a large meta-GWAS and pre-registered follow-up study, we conclude that the previously reported genetic correlation between BMI and head motion relies on polygenic variation, and that neither psychological nor simple physiological parameters explain a substantial amount of variance in the association of BMI and head motion. Future imaging studies should thus rigorously control for head motion at acquisition and during preprocessing.
Plasmodium sporozoites require the protein B9 to invade hepatocytes
Authors: Fernandes Priyanka , Loubens Manon , Marinach Carine , Coppée Romain , Grand Morgane , Andre Thanh-Phuc , Hamada Soumia , Langlois Anne-Claire , Briquet Sylvie , Bun Philippe , Silvie Olivier
Published: October 2021

Plasmodium sporozoites are transmitted to a mammalian host during blood feeding by an infected mosquito and invade hepatocytes for initial replication of the parasite in the liver. This leads to the release of thousands of merozoites into the blood circulation and initiation of the pathogenic blood stages of malaria. Merozoite invasion of erythrocytes has been well characterized at the molecular and structural levels. In sharp contrast, the molecular mechanisms of sporozoite invasion of hepatocytes are poorly characterized. Here we report a new role during sporozoite entry for the B9 protein, a member of the 6-cysteine domain protein family. Using genetic tagging and gene deletion approaches in rodent malaria parasites, we show that B9 is secreted from sporozoite micronemes and is required for productive invasion of hepatocytes. Structural modelling indicates that the N-terminus of B9 forms a beta-propeller domain structurally related to CyRPA, a cysteine-rich protein forming an invasion complex with Rh5 and RIPR in P. falciparum merozoites. We provide evidence that the beta-propeller domain of B9 is essential for protein function during sporozoite entry and interacts with P36 and P52, both also essential for productive invasion of hepatocytes. Our results suggest that, despite using distinct sets of parasite and host entry factors, Plasmodium sporozoites and merozoites may share common structural modules to assemble protein complexes for invasion of host cells.
The Atomic-Level Physiochemical Determinants of T Cell Receptor Dissociation Kinetics
Authors: Rollins Zachary A. , Huang Jun , Tagkopoulos Ilias , Faller Roland , George Steven C.
Published: October 2021

The rational design of T Cell Receptors (TCRs) for immunotherapy has stagnated due to a limited understanding of the dynamic physiochemical features of the TCR that elicit an immunogenic response. The physiochemical features of the TCR-peptide major histocompatibility complex (pMHC) bond dictate bond lifetime which, in turn, correlates with immunogenicity. Here, we: i) characterize the force-dependent dissociation kinetics of the bond between a TCR and a set of pMHC ligands using Steered Molecular Dynamics (SMD); and ii) implement a machine learning algorithm to identify which physiochemical features of the TCR govern dissociation kinetics. Our results demonstrate that the total number of hydrogen bonds between the CDR2β-MHCα(β), CDR1α-Peptide, and CDR3β-Peptide are critical features that determine bond lifetime. We propose that amino acid substitutions to these hypervariable regions of the TCR can efficiently manipulate immunogenicity and thus be used in the rational design of TCRs for immunotherapy.
Social-affective features drive human representations of observed actions
Authors: Dima Diana C. , Tomita Tyler M. , Honey Christopher J. , Isik Leyla
Published: October 2021

Humans observe actions performed by others in many different visual and social settings. What features do we extract and attend when we view such complex scenes, and how are they processed in the brain? To answer these questions, we curated two large-scale sets of naturalistic videos of everyday actions and estimated their perceived similarity in two behavioral experiments. We normed and quantified a large range of visual, action-related and social-affective features across the stimulus sets. Using a cross-validated variance partitioning analysis, we found that social-affective features predicted similarity judgments better than, and independently of, visual and action features in both behavioral experiments. Next, we conducted an electroencephalography (EEG) experiment, which revealed a sustained correlation between neural responses to videos and their behavioral similarity. Visual, action, and social-affective features predicted neural patterns at early, intermediate and late stages respectively during this behaviorally relevant time window. Together, these findings show that social-affective features are important for perceiving naturalistic actions, and are extracted at the final stage of a temporal gradient in the brain.
Natural age-related sleep-wake alterations onset prematurely in the Tg2576 mouse model of Alzheimer’s disease
Authors: Kollarik Sedef , Moreira Carlos G. , Dias Inês , Bimbiryte Dorita , Miladinovic Djordje , Buhmann Joachim M. , Baumann Christian R. , Noain Daniela
Published: October 2021

Sleep insufficiency or decreased quality have been associated with Alzheimer’s disease (AD) already in its preclinical stages. Whether such traits are also present in rodent models of the disease has been poorly addressed, somewhat disabling the preclinical exploration of sleep-based therapeutic interventions for AD. We investigated age-dependent sleep-wake phenotype of a widely used mouse model of AD, the Tg2576 line. We implanted electroencephalography/ electromyography headpieces into 6 months old (plaque-free, n=10) and 11 months old (moderate plaque-burdened, n=10) Tg2576 and age-matched wild-type (WT) mice and recorded vigilance states for 24 hours. Tg2576 mice exhibited significantly increased wakefulness and decreased non-rapid eye movement sleep over a 24-hour period compared to WT mice at 6, but not at 11 months of age. Concomitantly, delta power appeared decreased in 6-month old Tg2576 mice in comparison to age-matched WT controls, yielding a reduced slow-wave energy phenotype in the young mutants. Lack of genotype-related differences over 24 hours in overall sleep-wake phenotype at 11 months of age appears to be the result of the natural aging of WT mice. Therefore, our results indicate that at plaque-free stages of the disease, diminished sleep quality is present in Tg2576 mice which resembles aged healthy controls, suggesting an early-onset of sleep-wake deterioration in murine AD. Whether such disturbances in the natural patterns of sleep could in turn worsen disease progression warrants further exploration.
Identification of new growth regulators using cross-species network analysis in plants
Authors: Curci Pasquale Luca , Zhang Jie , Mähler Niklas , Seyfferth Carolin , Mannapperuma Chanaka , Diels Tim , Hautegem Tom Van , Jonsen David , Street Nathaniel , Hvidsten Torgeir R. , Hertzberg Magnus , Nilsson Ove , Inze Dirk , Nelissen Hilde , Vandepoele Klaas
Published: October 2021

With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes playing a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis thaliana, maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these new growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two newly predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify new genes involved in plant growth and development.

One-sentence summary

Cross-species network analysis results in the identification and validation of new growth regulators in Arabidopsis.
Characterization of dissolved organic matter from temperate wetlands: field dynamics and photoreactivity changes driven by natural inputs and diagenesis along the hydroperiod
Authors: García Patricia E. , Ferro Carolina F. Mansilla , Diéguez María C.
Published: October 2021

Wetlands store large amounts of C in biomass, sediments and water. A major C fraction is in the dissolved organic matter (DOM) pool and has multiple regulatory functions in the ecosystem. Patagonian wetlands undergo profound changes in their water cycle due to warming and reduced precipitation, causing shorter hydroperiods and reduced landscape connectivity and overall affecting their C budgets. In this study we characterized the DOM pool of a temporary wetland of North Patagonia during a hydroperiod, using optical DOM proxies obtained by absorption and fluorescence spectroscopy. DOM components were modeled through EEM-PARAFAC. DOC varied between ∼4 and ∼9 mg L-1, displaying aromatic signals and terrestrial/sediment fingerprints. The humic components C1 (microbial and/or vegetation derived) and C2 (soil/sediment derived) prevailed in the DOM pool, whereas the non-humic component C3 (derived from aquatic production) showed lower contribution. Along the hydroperiod DOM optical proxies allowed identifying allochthonous inputs, degradation and an increasing contribution of the internal production to the DOM pool. Photodegradation experiments showed that exposure to PAR+UVR produced slight changes in the DOC concentration and a reduction in DOM molecular weight/size. The contribution of humic vs. non-humic components influenced DOM photoreactivity. The prevalence of humic components determined high DOM photorecalcitrance.
BET Inhibitors Target the SCLC-N subtype Small Cell Lung Cancer by Blocking NEUROD1 Transactivation
Authors: Chen Haobin , Gesumaria Lisa , Park Young-Kwon , Oliver Trudy G. , Singer Dinah S. , Ge Kai , Shrump David S.
Published: October 2021

Small cell lung cancer (SCLC) is a recalcitrant malignancy that urgently needs new therapies. Four master transcription factors (ASCL1, NEUROD1, POU2F3, and YAP1) are identified in SCLC, and each defines the transcriptome landscape of one molecular subtype. These master factors have not been directly druggable, and targeting their transcriptional coactivator(s) could provide an alternative approach. Here, we identify that BET bromodomain proteins physically interact with NEUROD1 and function as its transcriptional coactivators. Using CRISPR knockout and ChIP-seq, we demonstrate that NEUROD1 plays a critical role in defining the landscapes of BET bromodomain proteins in the SCLC genome. Targeting BET bromodomain proteins by BET inhibitors leads to broad suppression of the NEUROD1-target genes, especially those associated with superenhancers, and reduces SCLC growth in vitro and in vivo. LSAMP, a membrane protein in the IgLON family, was identified as one of the NEUROD1-target genes mediating BET inhibitor sensitivity in SCLC. Altogether, our study reveals that targeting transcriptional coactivators could be a novel approach to blocking the master transcription factors in SCLC for therapeutic purposes.

Significance

Small cell lung cancer (SCLC) is the most aggressive form of lung malignancies, and little progress has been made to improve its outcome in the past two decades. It is now recognized that SCLC is not a single disease but has at least four molecular subtypes, and each subtype features the expression of one master transcription factor. Unfortunately, these master transcription factors are not directly druggable. Here, we identified BET bromodomain proteins as the transcriptional coactivators of NEUROD1, one of the master transcription factors in SCLC. Blocking BET bromodomain proteins with inhibitors suppresses NEUROD1-target genes and reduces tumor growth. Our results demonstrate that blocking transcriptional coactivators could be an alternative approach to targeting the master transcription factors in SCLC.
pH dependence of C•A, G•A and A•A mismatches in the stem of precursor microRNA-31
Authors: Kotar Anita , Ma Sicong , Keane Sarah C.
Published: October 2021

MicroRNAs (miRNAs) are important regulators of post-transcriptional gene expression. Mature miRNAs are generated from longer transcripts (primary, pri- and precursor, pre-miRNAs) through a series of highly coordinated enzymatic processing steps. The sequence and structure of these pri- and pre-miRNAs play important roles in controlling their processing. Both pri- and pre-miRNAs adopt hairpin structures with imperfect base pairing in the helical stem. Here, we investigated the role of three base pair mismatches (A∙A, G∙A, and C∙A) present in pre-miRNA-31. Using a combination of NMR spectroscopy and thermal denaturation, we found that the three base pair mismatches displayed unique structural properties, including varying dynamics and sensitivity to solution pH. These studies deepen our understanding of how the physical and chemical properties of base pair mismatches influence RNA structural stability.

Graphical abstract
OC_Finder: A deep learning-based software for osteoclast segmentation, counting, and classification
Authors: Wang Xiao , Kittaka Mizuho , He Yilin , Zhang Yiwei , Ueki Yasuyoshi , Kihara Daisuke
Published: October 2021

Osteoclasts are multinucleated cells that exclusively resorb bone matrix proteins and minerals on the bone surface. They differentiate from monocyte/macrophage-lineage cells in the presence of osteoclastogenic cytokines such as the receptor activator of nuclear factor-κB ligand (RANKL) and are stained positive for tartrate-resistant acid phosphatase (TRAP). In vitro, osteoclast formation assays are commonly used to assess the capacity of osteoclast precursor cells for differentiating into osteoclasts wherein the number of TRAP-positive multinucleated cells are counted as osteoclasts. Osteoclasts are manually identified on cell culture dishes by human eyes, which is a labor-intensive process. Moreover, the manual procedure is not objective and result in lack of reproducibility. To accelerate the process and reduce the workload for counting the number of osteoclasts, we developed OC_Finder, a fully automated system for identifying osteoclasts in microscopic images. OC_Finder consists of segmentation and classification steps. OC_Finder detected osteoclasts differentiated from wild-type and Sh3bp2KI/+ precursor cells at a 99.4% accuracy for segmentation and at a 98.1% accuracy for classification. The number of osteoclasts classified by OC_Finder was at the same accuracy level with manual counting by a human expert. Together, successful development of OC_Finder suggests that deep learning is a useful tool to perform prompt and accurate unbiased classification and detection of specific cell types in microscopic images.
Biophysical Kv channel alterations dampen excitability of cortical PV interneurons and contribute to network hyperexcitability in early Alzheimer’s
Authors: Oláh Viktor Janos , Goettemoeller Annie M , Dimidschstein Jordane , Rowan Matthew JM
Published: October 2021

In Alzheimer’s disease (AD), a multitude of genetic risk factors and early biomarkers are known. Nevertheless, the causal factors responsible for initiating cognitive decline in AD remain controversial. Toxic plaques and tangles correlate with progressive neuropathology, yet disruptions in circuit activity emerge before their deposition in AD models and patients. Parvalbumin (PV) interneurons are potential candidates for dysregulating cortical excitability, as they display altered AP firing before neighboring excitatory neurons in prodromal AD. Here we report a novel mechanism responsible for PV hypoexcitability in young adult familial AD mice. We found that biophysical modulation of K+ channels, but not changes in mRNA expression, are responsible for dampened excitability. These K+ conductances could efficiently regulate near-threshold AP firing, resulting in gamma-frequency specific network hyperexcitability. Our findings suggest that posttranslational modulation of ion channels can reshape cortical network activity prior to changes in their gene expression in early AD.
Dissecting the Roles of the Tuberin Protein in the Subcellular Localization of the G2/M Cyclin, Cyclin B1
Authors: Dare-Shih Jessica , Pillon Adam , Fong Jackie , da Silva Elizabeth Fidalgo , Porter Lisa A.
Published: October 2021

Tuberin is a major component of the protein regulatory complex known as the Tuberous Sclerosis Complex and plays a crucial role in cell cycle progression and protein synthesis. Mutations in the Tuberin gene, TSC2, lead to the formation of benign tumors in many organ systems and causes the Tuberous Sclerosis Complex disorder. Genotypes ranging from point mutations to large deletions in the TSC2 gene have been clinically characterized with a wide range of phenotypes from skin tumors to large brain tumors. Our current work investigates the molecular mechanisms behind Tuberin and its ability to regulate the cell cycle through its binding to the G2/M cyclin, Cyclin B1. After creating an early stop codon in a critical region of the Tuberin, our results show the in vitro phenotype that occurs from a truncated Tuberin protein. Herein we demonstrate that this clinically relevant truncated form of Tuberin promotes an increased nuclear accumulation of Cyclin B1 and a subsequent increase in cell proliferation supporting the phenotypic data seen in the clinic with Tuberous Sclerosis Complex patients showing deletions within the TSC2 gene. This data provides an insight into some of the functional and molecular consequences of truncated proteins that are seen in clinical patients.
Transcriptomically unique endolysosomal and homeostatic microglia populations in Alzheimer’s disease and aged human brain
Authors: Prater Katherine E. , Green Kevin J. , Mamde Sainath , Sun Wei , Cochoit Alexandra , Smith Carole L. , Chiou Kenneth L. , Heath Laura , Rose Shannon E. , Wiley Jesse , Keene C. Dirk , Kwon Ronald Y. , Snyder-Mackler Noah , Blue Elizabeth E. , Logsdon Benjamin , Young Jessica E. , Shojaie Ali , Garden Gwenn A. , Jayadev Suman
Published: October 2021

Microglia contribute to Alzheimer’s Disease (AD) progression and are candidate therapeutic targets. Human microglia exhibit an array of transcriptional phenotypes implying that accurate manipulation of microglial function will require clarity of their molecular states and context dependent regulation. To increase the number of microglia analyzed per subject we employed fluorescence activated nuclei sorting prior to single-nucleus RNA-seq on human prefrontal cortices. We observed microglia phenotypes previously unrecognized in human brain gene expression studies and mapped their transcriptomic relationships by trajectory inference. Three clusters were enriched for endolysosomal pathways, one of which showed differential expression of AD GWAS genes in addition to genes implicated in nucleic acid detection and interferon signaling. Analysis of the “homeostatic” microglia cluster revealed a uniquely AD subcluster. Our study demonstrates the value of deeply profiling microglia to explore the biological implications of microglia transcriptomic diversity.
Structural Dynamics of Real and Modeled Solanum Stamens: Implications for Pollen Ejection by Buzzing Bees
Authors: Jankauski Mark , Ferguson Riggs , Russell Avery , Buchmann Stephen
Published: October 2021

An estimated 10% of flowering plant species conceal their pollen within tube-like anthers that dehisce through small apical pores (poricidal anthers). Bees extract pollen from poricidal anthers through a complex motor routine called floral buzzing, whereby the bee applies vibratory forces to the flower stamen by rapidly contracting its flight muscles. The resulting deformation depend on the stamen’s natural frequencies and vibration mode shapes, yet for most poricidal species these properties have not been sufficiently characterized. We performed experimental modal analysis on Solanum elaeagnifolium stamens to quantify their natural frequencies and vibration modes. Based on morphometric and dynamic measurements, we developed a finite element model of the stamen to identify how variable material properties, geometry and bee weight could affect its dynamics. In general, stamen natural frequencies fell outside the reported floral buzzing range, and variations in stamen geometry and material properties were unlikely to bring natural frequencies within this range. However, inclusion of bee mass reduced natural frequencies to within the floral buzzing frequency range and gave rise to an axial-bending vibration mode. We hypothesize that floral buzzing bees exploit the large vibration amplification factor of this mode to increase anther deformation, which may facilitate pollen ejection.
Riemannian Geometries of Visual Space: Variable Curvature and Horizon
Authors: Turski Jacek
Published: October 2021

This is a study of the phenomenal geometries constructed in the Riemannian geometry framework from simulated iso-disparity conics in the horizontal visual plane of the binocular system with the asymmetric eyes (AEs). For the eyes’ resting vergence posture, which depends on parameters of the AE, the iso-disparity conics are frontal straight lines in physical space. For all other fixations, the simulated iso-disparity conics consist of families of the ellipses or hyperbolas depending on both the AE’s parameters and the bifoveal fixation. However, the iso-disparity conic’s arcs are perceived in the gaze direction as the frontal lines. Thus, geometries of physical and visual spaces are different. An assumption underlying the relevant architecture of the human visual system is combined with results from simulated iso-disparity straight lines, giving the relative depth as a function of the AE’s parameters and the distance. This establishes the metric tensor in binocular space of fixations for the eyes’ resting vergence posture. The resulting geodesics in the gaze direction, give the distance to the horizon and zero curvature. For all other fixations, only the sign of the curvature may be inferred from the global behavior of the simulated iso-disparity conics.
Structural snapshots of V/A-ATPase reveal a new paradigm for rotary catalysis
Authors: Kishikawa J. , Nakanishi A. , Nakano A. , Saeki S. , Furuta A. , Kato T. , Mistuoka K. , Yokoyama K.
Published: October 2021

V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with FoF1 ATP synthase. When powered by ATP hydrolysis, the V1 moiety rotates the central rotor against the A3B3 hexamer, composed of three catalytic AB dimers adopting different conformations (ABopen, ABsemi, and ABclosed). Here we have determined the atomic models of 18 catalytic intermediates of the V1 moiety of V/A-ATPase under different reaction conditions by single particle Cryo-EM, which revealed that the rotor does not rotate immediately after binding of ATP to the V1. Instead, three events proceed simultaneously with the 120° rotation of the shaft: hydrolysis of ATP in ABsemi, zipper movement in ABopen by the binding ATP, and unzipper movement in ABclosed with release of both ADP and Pi. This indicates the unidirectional rotation of V/A-ATPase by a ratchet-like mechanism owing to ATP hydrolysis in ABsemi, rather than the power stroke model proposed previously for F1-ATPase.
In silico analyses of maleidride biosynthetic gene clusters
Authors: Williams Katherine , de Mattos-Shipley Kate M. J. , Willis Christine L. , Bailey Andrew M.
Published: October 2021

Maleidrides are a family of structurally related fungal natural products, many of which possess diverse, potent bioactivities. Previous identification of several maleidride biosynthetic gene clusters, and subsequent experimental work, has determined the ‘core’ set of genes required to construct the characteristic medium-sized alicyclic ring with maleic anhydride moieties. Through genome mining, this work has used these core genes to discover ten entirely novel maleidride biosynthetic gene clusters, amongst both publicly available genomes, and encoded within the genome of the previously un-sequenced epiheveadride producer Wicklowia aquatica CBS125634. We have undertaken phylogenetic analyses and comparative bioinformatics on all known and putative maleidride biosynthetic gene clusters to gain further insights regarding these unique biosynthetic pathways.