bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractActivated 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

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

SummaryMicroglia 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

AbstractSevere 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

AbstractActive 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

ABSTRACTThe 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

SummaryUrban 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

AbstractThe 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

AbstractProtein 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

AbstractWhile 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 statementGlutathione 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

AbstractObjectivesReceptor 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.MethodsSubcellular 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.ResultsGCGR 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.ConclusionsBy 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 abstractIcons sourced from [1]
Genome-wide association mapping and systems-level analysis reveal genetic architecture and physiological mechanisms linked with tolerance to flooding during germination in rice
Authors: Entila Frederickson D. , Pacleb Myrish A. , Ella Evangelina S. , Ismail Abdelbagi M. 
Published: May 2021

ABSTRACTRice is the staple food of more than half of the world’s population; yet, it faces numerous challenges to meet the rising food demands and worsening climates. An urgent global imperative is to address imminent food shortages through intensive and sustainable agri-food systems and steady genetic gains. Intensification of rice production through direct-seeded rice (DSR) has been progressively practiced but is hindered by poor germination of existing high-yielding varieties in flooded soils. Identifying donors of anaerobic germination (AG) tolerance in rice will expedite the development of varieties suitable for DSR and will lead to enhanced and sustained agricultural productivity. This study aims to dissect the genetic architecture and physiological mechanisms of AG tolerance using systems biology and omics approaches. A Rice Diversity Panel (343 accessions) consisting of 5 subpopulations was screened for AG tolerance under greenhouse conditions, mapped through genome-wide association study (GWAS), and profiled for metabolites. Analyses revealed that most of the AG-tolerant varieties are japonicas with few indicas) and aus. Tolerant japonicas employed better root growth or rapid shoot extension, while tolerant indicas exhibited only the latter. A total of 51 significant GWAS peaks were detected across the genome, some of which were co-localized with known quantitative trait loci while others were novel, more so tolerance was found to involve different genetic controls across subpopulations. AG stress causes distinct biochemical signatures for tolerant genotypes and the profiles contrast among subpopulations implicating divergent metabolic adjustments, including shifts in sugars, intermediates, amino acids, antioxidants, and hormones. This study provides a systems-level approach for underpinning physiological mechanisms of AG tolerance; elucidating phenotypic heterogeneity, genetic architecture, transcriptomic networks, and metabolic landscapes from a genome-wide perspective.ONE SENTENCE SUMMARYThe integration of GWA mapping, gene network analysis and, non-targeted metabolite profiling elucidates genetic architecture and physiological mechanisms of tolerance to germination and early seedling growth under anaerobic conditions in rice.
Extracellular vesicles from neuronal cells promote neural induction of mESCs through cyclinD1
Authors: Song Lu , Tian Xinran , Schekman Randy 
Published: May 2021

AbstractExtracellular vesicles (EVs) that are thought to mediate the transport of proteins and RNAs involved in intercellular communication. Here, we show dynamic changes in the buoyant density and abundance of extracellular vesicles that are secreted by PC12 cells stimulated with nerve growth factor (NGF), N2A cells treated with retinoic acid to induce neural differentiation and mESCs differentiated into neuronal cells. EVs secreted from in vitro differentiated cells promote neural induction of mouse embryonic stem cells (mESCs). Cyclin D1 enriched within the EVs derived from differentiated neuronal cells contributes to this induction. EVs purified from cells overexpressing cyclin D1 are more potent in neural induction of mESC cells. Depletion of cyclin D1 from the EVs reduced the neural induction effect. Our results suggest that extracellular vesicles regulate neural development through sorting of cyclin D1.SummaryExtracellular vesicles (EVs) may mediate intercellular communication through the transfer of cargo molecules. Here, we report that cyclinD1 is sorted into EVs during neuronal differentiation and that these EVs help to promote the neural induction of mouse embryonic stem cells.
A novel approach to the functional classification of retinal ganglion cells
Authors: Hilgen Gerrit , Kartsaki Evgenia , Kartysh Viktoriia , Cessac Bruno , Sernagor Evelyne 
Published: May 2021

AbstractRetinal neurons are remarkedly diverse based on structure, function and genetic identity. Classifying these cells is a challenging task, requiring multimodal methodology. Here, we introduce a novel approach for retinal ganglion cell (RGC) classification, based on pharmacogenetics combined with immunohistochemistry and large-scale retinal electrophysiology. Our novel strategy allows grouping of cells sharing gene expression and understanding how these cell classes respond to basic and complex visual scenes. Our approach consists of several consecutive steps. First, the spike firing frequency is increased in RGCs co-expressing a certain gene (Scnn1a or Grik4) using excitatory DREADDs (Designer Receptors Exclusively Activated by Designer Drugs) in order to single out activity originating specifically from these cells. Their spike location is then combined with post hoc immunostaining, to unequivocally characterize their anatomical and functional features. We grouped these isolated RGCs into multiple clusters based on spike train similarities. Using this novel approach. we were able to extend the pre-existing list of Grik4 expressing RGC types to a total of 8 and, for the first time, we provide a phenotypical description of 13 Scnn1a-expressing RGCs. The insights and methods gained here can guide not only RGC classification but neuronal classification challenges in other brain regions as well.