bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps
Authors: Spitzer Hannah , Berry Scott , Donoghoe Mark , Pelkmans Lucas , Theis Fabian J. 
Published: May 2022

AbstractHighly multiplexed quantitative subcellular imaging holds enormous promise for understanding how spatial context shapes the activity of our genome and its products at multiple scales. Yet unbiased analysis of subcellular organisation across experimental conditions remains challenging, because differences in molecular profiles between conditions confound differences in molecular profiles across space. Here, we introduce a deep-learning framework called CAMPA (Conditional Autoencoder for Multiplexed Pixel Analysis), which uses a variational autoencoder conditioned on cellular states and perturbations to learn consistent molecular signatures. Clustering the learned representations into subcellular landmarks allows quantitative comparisons of landmark sizes, shapes, molecular compositions and relative spatial organisation between conditions. By performing high-resolution multiplexed immunofluorescence on human cells, we use CAMPA to reveal how subnuclear organisation changes upon different perturbations of RNA production or processing, and how different membraneless organelles scale with cell size. Furthermore, by integrating information across the cellular and subcellular scales, we uncover new links between the molecular composition of membraneless organelles and bulk RNA synthesis rates of single cells. We anticipate that CAMPA will greatly accelerate the systematic mapping of multiscale atlases of biological organisation to identify the rules by which context shapes physiology and disease.
Allele-specific knockouts reveal a role for apontic-like in the evolutionary loss of larval pigmentation in the domesticated silkworm, Bombyx mori
Authors: Tomihara Kenta , Andolfatto Peter , Kiuchi Takashi 
Published: May 2022

AbstractThe domesticated silkworm, Bombyx mori, and its wild progenitor, B. mandarina, are extensively studied as a model case of the evolutionary process of domestication. A conspicuous difference between these species is the dramatic reduction in pigmentation in both larval and adult B. mori. Here we evaluate the efficiency of CRISPR/Cas9-targeted knockouts of pigment-related genes as a tool to understand their potential contributions to domestication-associated pigmentation loss in B. mori. To demonstrate the efficacy of targeted knockouts in B. mandarina, we generated a homozygous CRISPR/Cas9-targeted knockout of yellow-y. In yellow-y knockout mutants, black body color became lighter throughout the larval, pupal and adult stages, confirming a role for this gene in pigment formation. Further, we performed allele-specific CRISPR/Cas9-targeted knockouts of the pigment-related transcription factor, apontic-like (apt-like) in B. mori × B. mandarina F1 hybrid individuals. Knockout of the B. mandarina allele of apt-like in F1 embryos results in depigmented patches on the dorsal integument of larvae, whereas corresponding knockouts of the B. mori allele consistently exhibit normal F1 larval pigmentation. These results demonstrate a contribution of apt-like to the evolution of reduced pigmentation in B. mori. Together, our results demonstrate the feasibility of CRISPR/Cas9-targeted knockouts as a tool for understanding the genetic basis of traits associated with B. mori domestication.Brief abstractBombyx mori and its wild progenitor are an important model for the study of phenotypic evolution associated with domestication. As proof-of-principle, we used CRISPR/Cas9 to generate targeted knockouts of two pigmentation-related genes. By generating a homozygous knockout of yellow-y in B. mandarina, we confirmed this gene”s role in pigment formation. Further, by generating allele-specific knockouts of apontic-like (apt-like) in B. mori × B. mandarina F1 hybrids, we establish that evolution of apt-like contributed to reduced pigmentation during B. mori domestication.Graphical TOC/Abstract
A zebrafish embryo screen utilizing gastrulation for identification of anti-metastasis drugs
Authors: Nakayama Joji , Makinoshima Hideki , Gong Zhiyuan 
Published: May 2022

AbstractFew models exist that allow for rapid and effective screening of anti-metastasis drugs. Here, we present a phenotype-based chemical screen utilizing gastrulation of zebrafish embryos for identification of anti-metastasis drugs. Based on the evidence that metastasis proceeds through utilizing the molecular mechanisms of gastrulation, we hypothesize that chemicals which interrupt zebrafish gastrulation might suppress metastasis of cancer cells. Thus, we developed a drug screening protocol which uses epiboly, the first morphogenetic movement in gastrulation, as a marker. The screen only needs zebrafish embryos and enables hundreds of chemicals to be tested in five hours through observing epiboly progression of a test chemical-treated embryos. In the screen, embryos at the two-cell stage are firstly corrected and then developed to the sphere stage. The embryos are treated with a test chemical and incubated in the presence of the chemical until vehicle-treated embryos develop to 90% epiboly stage. Finally, positive ‘hit’ chemicals that interrupt epiboly progression are selected through comparing epiboly progression of the chemical-treated embryos with that of vehicle-treated embryos under a stereoscopic microscope. Previous study subjected 1,280 FDA-approved drugs to the screen and identified Adrenosterone and Pizotifen as epiboly-interrupting drugs. These drugs were validated to suppress metastasis of breast cancer cells in mice models of metastasis. Furthermore, 11β–Hydroxysteroid Dehydrogenase 1 (HSD11β1) and serotonin receptor 2C (HTR2C), which are primary target of Adrenosterone and Pizotifen respectively, promotes metastasis through induction of epithelial-mesenchymal transition (EMT). That indicates the screen could be diverted to a chemical genetic screening platform for identification of metastasis-promoting genes.
The rescue of epigenomic abnormalities in ICF1 patient iPSCs following DNMT3B correction is incomplete at a residual fraction of H3K4me3-enriched regions
Authors: Krishnan Varsha Poondi , Morone Barbara , Toubiana Shir , Krzak Monika , Strazzullo Maria , Angelini Claudia , Selig Sara , Matarazzo Maria R. 
Published: May 2022

ABSTRACTBackgroundBi-allelic hypomorphic mutations in DNMT3B disrupt DNA methyltransferase activity and lead to Immunodeficiency, Centromeric instability, Facial anomalies syndrome, type 1 (ICF1). While several ICF1 phenotypes have been linked to abnormally hypomethylated repetitive regions, the unique genomic regions responsible for the remaining disease phenotypes remain largely uncharacterized. Here we explored two ICF1 patient-induced pluripotent stem cells (iPSCs) and their CRISPR/Cas9 corrected clones to determine whether gene correction can overcome DNA methylation defects and related/associated changes in the epigenome of non-repetitive regions.ResultsHypomethylated regions throughout the genome are highly comparable between ICF1 iPSCs carrying different DNMT3B variants, and significantly overlap with those in ICF1-peripheral blood and lymphoblastoid cell lines. These regions include large CpG island domains, as well as promoters and enhancers of several lineage-specific genes, in particular immune-related, suggesting that they are pre- marked during early development. The gene corrected ICF1 iPSCs reveal that the majority of phenotype- related hypomethylated regions re-acquire normal DNA methylation levels following editing. However, at the most severely hypomethylated regions in ICF1 iPSCs, which also display the highest increased H3K4me3 levels and enrichment of CTCF-binding motifs, the epigenetic memory persisted, and hypomethylation was uncorrected.ConclusionsRestoring the catalytic activity of DNMT3B rescues the majority of the aberrant ICF1 epigenome. However, a small fraction of the genome is resilient to this reversal, highlighting the challenge of reverting disease states that are due to genome-wide epigenetic perturbations. Uncovering the basis for the persistent epigenetic memory will promote the development of strategies to overcome this obstacle.
Oxytocin attenuates microglial activation and restores social and non-social memory in the APP/PS1 mouse model of Alzheimer’s disease
Authors: Selles Maria Clara , Fortuna Juliana T.S. , de Faria Yasmin P.R. , Longo Beatriz Monteiro , Froemke Robert C. , Chao Moses V. , Ferreira Sergio T. 
Published: May 2022

AbstractAlzheimer’s disease (AD) is the main cause of dementia in the elderly and is characterized by memory loss, social withdrawal and neurodegeneration, eventually leading to death. Brain inflammation has emerged as a key pathogenic mechanism in AD. We hypothesized that oxytocin, a pro-social hypothalamic neuropeptide with anti-inflammatory properties, could have therapeutic actions in AD. We investigated oxytocin production in mouse models of AD, and evaluated the therapeutic potential of intranasal oxytocin. We observed lower levels of hypothalamic oxytocin in wild-type mice following brain infusion of amyloid-β oligomers (AβOs), as well as in APP/PS1 AD model mice. Treatment of APP/PS1 mice with intranasal oxytocin reduced microglial activation and favored deposition of Aβ in dense core plaques, a potentially neuroprotective mechanism. Oxytocin further alleviated social and non-social memory impairments in APP/PS1 mice. Our findings point to oxytocin as a potential therapeutic target to reduce brain inflammation and correct memory deficits in AD.
Exploring the utility of recombinantly expressed snake venom serine protease toxins as immunogens for generating experimental snakebite antivenoms
Authors: Alomran Nessrin , Blundell Patricia , Alsolaiss Jaffer , Crittenden Edouard , Ainsworth Stuart , Dawson Charlotte A. , Edge Rebecca J. , Hall Steven R. , Harrison Robert A. , Wilkinson Mark C. , Menzies Stefanie K. , Casewell Nicholas R. 
Published: May 2022

AbstractSnakebite is a neglected tropical disease that causes high rates of global mortality and morbidity. Although snakebite can cause a variety of pathologies in victims, haemotoxic effects are particularly common and are typically characterised by haemorrhage and/or venom-induced consumption coagulopathy. Despite polyclonal antibody-based antivenoms being the mainstay life-saving therapy for snakebite, they are associated with limited cross-snake species efficacy, as there is often extensive toxin variation between snake venoms, including those used as immunogens for antivenom production. This restricts the therapeutic utility of any antivenom to certain geographical regions. In this study, we explored the feasibility of using recombinantly expressed toxins as immunogens to stimulate focused, pathology-specific, antibodies to broadly counteract specific toxins associated with snakebite envenoming. Three snake venom serine proteases (SVSP) toxins, sourced from geographically diverse and medically important viper snake venoms were successfully expressed in HEK293F mammalian cells and used for murine immunisation. Analyses of the resulting antibody responses revealed that ancrod and RVV-V stimulated the strongest immune responses, and that experimental antivenoms directed against these recombinant SVSP toxins, and a mixture of the three different immunogens, extensively recognised and exhibited immunological binding towards a variety of native snake venoms. While the experimental antivenoms showed some reduction in abnormal clotting parameters stimulated by the toxin immunogens and crude venom, specifically reducing the depletion of fibrinogen levels and prolongation of prothrombin times, fibrinogen degradation experiments revealed they broadly protected against venom- and toxin-induced fibrinogenolytic functional activities. Overall, our findings further strengthen the case for the use of recombinant venom toxins as supplemental immunogens to stimulate focused and desirable antibody responses capable of neutralising venom-induced pathological effects, and therefore potentially circumventing some of the limitations associated with current snakebite therapies.
Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace
Authors: Liao Jie , Qian Jingyang , Liu Ziqi , Chi Ying , Zheng Yanrong , Shao Xin , Cheng Junyun , Cui Yongjin , Guo Wenbo , Yang Penghui , Hu Yining , Bao Hudong , Chen Qian , Li Mingxiao , Zhang Bing , Fan Xiaohui 
Published: May 2022

AbstractTissues are highly complicated with spatial heterogeneity in gene expression. However, the cutting-edge single-cell RNA-seq technology eliminates the spatial information of individual cells, which contributes to the characterization of cell identities. Herein, we propose single-cell spatial position associated co-embeddings (scSpace), an integrative algorithm to distinguish spatially variable cell subclusters by reconstructing cells onto a pseudo-space with spatial transcriptome references (Visium, STARmap, Slide-seq, etc.). We demonstrated that scSpace can define biologically meaningful cell subpopulations neglected by single-cell RNA-seq or spatially resolved transcriptomics. The use of scSpace to uncover the spatial association within single-cell data, reproduced, the hierarchical distribution of cells in the brain cortex and liver lobules, and the regional variation of cells in heart ventricles and the intestinal villus. scSpace identified cell subclusters in intratelencephalic neurons, which were confirmed by their biomarkers. The application of scSpace in melanoma and Covid-19 exhibited a broad prospect in the discovery of spatial therapeutic markers.
Limited overlap of eQTLs and GWAS hits due to systematic differences in discovery
Authors: Mostafavi Hakhamanesh , Spence Jeffrey P. , Naqvi Sahin , Pritchard Jonathan K. 
Published: May 2022

AbstractMost signals in genome-wide association studies (GWAS) of complex traits point to noncoding genetic variants with putative gene regulatory effects. However, currently identified expression quantitative trait loci (eQTLs) explain only a small fraction of GWAS signals. By analyzing GWAS hits for complex traits in the UK Biobank, and cis-eQTLs from the GTEx consortium, we show that these assays systematically discover different types of genes and variants: eQTLs cluster strongly near transcription start sites, while GWAS hits do not. Genes near GWAS hits are enriched in numerous functional annotations, are under strong selective constraint and have a complex regulatory landscape across different tissue/cell types, while genes near eQTLs are depleted of most functional annotations, show relaxed constraint, and have simpler regulatory landscapes. We describe a model to understand these observations, including how natural selection on complex traits hinders discovery of functionally-relevant eQTLs. Our results imply that GWAS and eQTL studies are systematically biased toward different types of variants, and support the use of complementary functional approaches alongside the next generation of eQTL studies.
Chemical structures of cyclic ADP ribose (cADPR) isomers and the molecular basis of their production and signaling
Authors: Manik Mohammad K. , Shi Yun , Li Sulin , Zaydman Mark A. , Damaraju Neha , Eastman Samuel , Smith Thomas G. , Gu Weixi , Masic Veronika , Mosaiab Tamim , Weagley James S. , Hancock Steven J. , Vasquez Eduardo , Hartley-Tassell Lauren , Maruta Natsumi , Lim Bryan Y. J. , Burdett Hayden , Lansdberg Michael J. , Schembri Mark A. , Prokes Ivan , Song Lijiang , Grant Murray , DiAntonio Aaron , Nanson Jeffrey D. , Guo Ming , Milbrandt Jeffrey , Ve Thomas , Kobe Bostjan 
Published: May 2022

AbstractCyclic ADP ribose (cADPR) isomers are important signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via NAD+ hydrolysis, yet their chemical structures are unknown. We show that v-cADPR (2’cADPR) and v2-cADPR (3’cADPR) isomers are cyclized by O-glycosidic bond formation between the ribose moieties in ADPR. Structures of v-cADPR (2’cADPR)-producing TIR domains reveal that conformational changes are required for the formation of the active assembly that resembles those of Toll-like receptor adaptor TIR domains, and mutagenesis data demonstrate that a conserved tryptophan is essential for cyclization. We show that v2-cADPR (3’cADPR) is a potent activator of ThsA effector proteins from Thoeris anti-phage defence systems and is responsible for suppression of plant immunity by the effector HopAM1. Collectively, our results define new enzymatic activities of TIR domains, reveal the molecular basis of cADPR isomer production, and establish v2-cADPR (3’cADPR) as an antiviral signaling molecule and an effector-mediated signaling molecule for plant immunity suppression.One-Sentence SummaryThe chemical structures of two O-glycosidic bond-containing cyclic ADP ribose isomers, the molecular basis of their production, and their function in antiviral and plant immunity suppression by bacteria are reported.
Dynamic emergence of relational structure network in human brains
Authors: Ren Xiangjuan , Zhang Hang , Luo Huan 
Published: May 2022

AbstractReasoning the hidden relational structure from sequences of events is a crucial ability humans possess, which help them to predict the future and make inferences. Besides simple statistical properties, humans also excel in learning more complex relational networks. Several brain regions are engaged in the process, yet the time-resolved neural implementation of relational structure learning and its behavioral relevance remains unknown. Here human subjects performed a probabilistic sequential prediction task on image sequences generated from a transition graph-like network, with their brain activities recorded using electroencephalography (EEG). We demonstrate the emergence of two key aspects of relational knowledge – lower-order transition probability and higher-order community structure, which arise around 840 msec after image onset and well predict behavioral performance. Furthermore, computational modeling suggests that the formed higher-order community structure, i.e., compressed clusters in the network, could be well characterized by a successor representation operation. Overall, human brains are constantly computing the temporal statistical relationship among discrete inputs, based on which new abstract knowledge could be inferred.
Pupil size as a robust marker of attentional bias toward nicotine-related stimuli in smokers
Authors: Blini Elvio , Zorzi Marco 
Published: May 2022

AbstractSpatial attention can be magnetically attracted by behaviorally salient stimuli. This phenomenon occasionally conflicts with behavioral goals, leading to maladaptive consequences, as in the case of addiction, in which attentional biases have been described and linked with clinically meaningful variables, such as craving level or dependence intensity. Here, we sought to probe the markers of attentional priority in smokers through eye-tracking measures, by leveraging the established link between eye movements and spatial attention. We were particularly interested in potential markers related to pupil size, because pupil diameter reflects a range of autonomic, affective, and cognitive/attentional reactions to behaviorally significant stimuli and is a robust marker of appetitive and aversive learning. We found that changes in pupil size to nicotine-related visual stimuli could reliably predict, in crossvalidated logistic regression, the smoking status of young smokers (showing pupil constriction) better than more traditional proxy measures. The possibility that pupil constriction may reflect a bias toward central vision, e.g. attentional capture, is discussed in terms of sensory tuning with respect to nicotine-related stimuli. Pupil size was more sensitive at lower nicotine dependence levels, and at increased abstinence time (though these two variables were collinear). We conclude that pupillometry can provide a robust marker for attentional priority computation and useful indications regarding motivational states and individual attitudes toward conditioned stimuli.
FIB-SEM analysis on three-dimensional structures of growing organelles in wild Chlorella pyrenoidosa cells
Authors: Feng Lingchong , Guo Wangbiao , Guo Jiansheng , Zhang Xing , Zou Xiangbo , Rao Mumin , Ye Ji , Kuang Cao , Chen Gongda , Chen Chuangting , Qin Shiwei , Yang Weijuan , Cheng Jun 
Published: May 2022

AbstractTo clarify dynamic changes of organelle microstructures in Chlorella pyrenoidosa cells during photosynthetic growth with CO2 fixation, three-dimensional organelle microstructures in three growth periods of meristem, elongation and maturity were quantitatively determined and comprehensively reconstructed with focused ion beam scanning electron microscopy (FIB-SEM). The single round-pancake mitochondria in each cell split into a dumbbell and then into a circular ring, while barycenter distance of mitochondria to chloroplast and nucleus was reduced to 45.5% and 88.3% to strengthen energy transfer, respectively. The single pyrenoid consisting of a large part and another small part in each chloroplast gradually developed to a mature state in which the two parts were nearly equal in size. The nucleolus progressively became larger with euchromatin replication. The number of starch grains gradually increased, but average grain volume remained nearly unchanged.
On the limits of fitting complex models of population history to genetic data
Authors: Maier Robert , Flegontov Pavel , Flegontova Olga , Changmai Piya , Reich David 
Published: May 2022

AbstractOur understanding of human population history in deep time has been assisted by fitting “admixture graphs” to data: models that specify the ordering of population splits and mixtures which is the only information needed to capture the patterns of allele frequency correlation among populations. Not needing to specify population size changes, split times, or whether admixture events were sudden or drawn out simplifies the space of models that need to be searched. However, the space of possible admixture graphs relating populations is vast and cannot be sampled fully, and thus most published studies have identified fitting admixture graphs through a manual process driven by prior hypotheses, leaving the vast majority of alternative models unexplored. Here, we develop a method for systematically searching the space of all admixture graphs that can incorporate non-genetic information in the form of topology constraints. We implement this findGraphs tool within a software package, ADMIXTOOLS 2, which is a reimplementation of the ADMIXTOOLS software with new features and large performance gains. We apply this methodology to identify alternative models to admixture graphs that played key roles in eight published studies and find that graphs modeling more than six populations and two or three admixture events are often not unique, with many alternative models fitting nominally or significantly better than the published one. Our results suggest that strong claims about population history from admixture graphs should only be made when all well-fitting and temporally plausible models share common topological features. Our re-evaluation of published data also provides insight into the population histories of humans, dogs, and horses, identifying features that are stable across the models we explored, as well as scenarios of populations relationships that differ in important ways from models that have been highlighted in the literature, that fit the allele frequency correlation data, and that are not obviously wrong.