bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial DNA Breaks Activate an Integrated Stress Response to Reestablish Homeostasis
Authors: Fu Yi , Sacco Olivia , Kanshin Evgeny , Ueberheide Beatrix , Sfeir Agnel 
Published: October 2022

AbstractDouble-strand breaks in mitochondrial DNA (mtDSBs) lead to the degradation of the circular genomes and a reduction in copy number. However, it is unclear how mtDSBs are sensed and what signaling pathways are activated in response to mtDNA damage. In this study, we used mitochondrial-targeted restriction enzymes to investigate the cellular response to mtDSBs. Our results showed that a subset of cells with mtDSBs exhibited defects in mitochondrial protein import, reduced respiratory complexes, and loss of membrane potential. Electron microscopy revealed compromised mitochondrial membrane and cristae ultrastructure. We also found that mtDSBs activated the integrated stress response (ISR) through the phosphorylation of eIF2α by DELE1 and HRI. Notably, inhibition of the ISR exacerbated the mitochondrial import defect and delayed the recovery of mtDNA copy number following break formation. These findings suggest that the ISR plays a role in mitigating mitochondrial dysfunction following mtDNA damage and is critical to promoting mtDNA repopulation. Last, we used proteomics to survey the proteins present in the nucleoids shortly after mtDSBs and identified ATAD3A, a membrane-anchored protein interacting with nucleoids, as a potential factor in transmitting the signal from damaged genomes to the inner mitochondrial membrane. In summary, our study reveals the sequence of events linking damaged mitochondrial genomes with the cytoplasm and highlights the unexpected role of the ISR in reestablishing homeostasis in response to mitochondrial genome instability.
Flavonols contrary affect the interconnected glucosinolate and camalexin biosynthesis pathway inArabidopsis thaliana
Authors: Naik Jogindra , Tyagi Shivi , Rajput Ruchika , Kumar Pawan , Pucker Boas , Bisht Naveen C. , Misra Prashant , Stracke Ralf , Pandey Ashutosh 
Published: October 2022

AbstractFlavonols are structurally and functionally diverse molecules playing roles in plant biotic and abiotic stress tolerance, auxin transport inhibition, pollen development, etc. Despite their ubiquitous occurrence in land plants and multifunctionality, the effect of perturbation of flavonol biosynthesis over global gene expression and pathways other than flavonoid biosynthesis has not been studied in detail. To understand the signaling role of different flavonol metabolites, herein, we used the flavonol deficientArabidopsis thalianaloss-of-function mutantflavonol synthase1 (fls1-3)as object of study. Comparative transcriptome and metabolic profiling were used to study the effects of genetic flavonol deficiency and exogenous supplementation with flavonol derivatives (kaempferol, quercetin and rutin) on different cellular processes in the seedling. Various flavonol biosynthesis-related regulatory and structural genes were found to be up-regulated in thefls1-3mutant which could be reversed by exogenous flavonol feeding. Our manifold comparative studies indicated the modulation of various biological processes and metabolic pathways by flavonols. Camalexin biosynthesis was found to be negatively regulated by flavonols. Interestingly, flavonols appeared to promote the accumulation of aliphatic glucosinolate through transcription factor-mediated up-regulation of biosynthesis genes. Overall, this study provides new insights into molecular mechanisms by which flavonols interfere with the relevant signal chains and their molecular targets and adds new knowledge to the expanding plethora of biological activity of flavonols in plants.SignificanceComparative transcriptome and metabolomic profiling of genetic flavonol deficiency and exogenous flavonol supplementation inA. thalianaseedlings, for the first-time revealed the inverse regulation of interconnected specialized metabolite pathways by flavonol aglycones, and -glycosides. Flavonols negatively regulate camalexin biosynthesis, while promoting the accumulation of aliphatic glucosinolates. Our study adds new insights into the expanding plethora of biological activity of flavonols in plants and will help to uncover the molecular mechanisms by which flavonols interfere with the relevant signal chains and their molecular targets.
Quantitative fluorescence emission anisotropy microscopy for implementing homo-FRET measurements in living cells
Authors: van Zanten Thomas S , Pradeep S Greeshma , Mayor Satyajit 
Published: October 2022

AbstractQuantitative fluorescence emission anisotropy microscopy reveals the organization of fluorescently labelled cellular components and allows for their characterization in terms of changes in either rotational diffusion or homo-Förster’s energy transfer characteristics in living cells. These properties provide insights into molecular organization, such as orientation, confinement and oligomerization in situ. Here we elucidate how quantitative measurements of anisotropy using multiple microscope systems may be made, by bringing out the main parameters that influence the quantification of fluorescence emission anisotropy. We focus on a variety of parameters that contribute to errors associated with the measurement of emission anisotropy in a microscope. These include the requirement for adequate photon counts for the necessary discrimination of anisotropy values, the influence of extinction coefficients of the illumination source, the detector system, the role of numerical aperture and excitation wavelength. All these parameters also affect the ability to capture the dynamic range of emission anisotropy necessary for quantifying its reduction due to homo-FRET and other processes. Finally, we provide easily implementable tests to assess whether homo-FRET is a cause for the observed emission depolarization.
Modulation of tooth regeneration through opposing responses to Wnt and BMP signals in teleosts
Authors: Square Tyler A. , Mackey Emma J. , Sundaram Shivani , Weksler Naama C. , Chen Zoe Z. , Narayanan Sujanya , Miller Craig T. 
Published: October 2022

AbstractMost vertebrate species undergo tooth replacement throughout adult life. This process is marked by the shedding of existing teeth and the regeneration of tooth organs. However, little is known about the genetic circuitry regulating tooth replacement. Here we tested whether fish orthologs of genes known to regulate mammalian hair regeneration have effects on tooth replacement. Using two fish species that demonstrate distinct modes of tooth regeneration, threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), we found that transgenic overexpression of four different genes changed tooth replacement rates in direction predicted by a hair regeneration model:Wnt10aandGrem2aincreased tooth replacement rate, whileBmp6andDkk2strongly inhibited tooth formation. Thus, similar to known roles in hair regeneration, Wnt and BMP signals promote and inhibit regeneration, respectively. Regulation of total tooth number was separable from regulation of replacement rates. RNA-seq on stickleback dental tissue showed thatBmp6overexpression resulted in an upregulation of Wnt inhibitors. Together these data support a model where different epithelial organs like teeth and hair share genetic circuitry driving organ regeneration.
An FGF Timer for Zygotic Genome Activation
Authors: Treen Nicholas , Chavarria Emily , Weaver Claire J. , Brangwynne Clifford P. , Levine Michael 
Published: October 2022

AbstractZygotic genome activation has been extensively studied in a variety of systems including flies, frogs, and mammals. However, there is comparatively little known about the precise timings of gene induction during the earliest phases of embryogenesis. Here we employ high-resolution in situ detection methods, along with genetic and experimental manipulations, to study the timing of zygotic activation in the simple model chordate, Ciona intestinalis with minute-scale temporal precision. We found that two Prdm1 homologs in Ciona are the earliest genes that respond to FGF signaling. We present evidence for a FGF timing mechanism that is driven by derepression of the ERF repressor by ERK activity, which works in concert with localized activators such as Foxa.a. Absence of ERF results in derepression of target genes throughout the embryo. A highlight of this timer is the sharp transition in FGF responsiveness between the 8- and 16-cell stages of development. We propose that this timer is an innovation of chordates that is also employed by other vertebrates.
Single-cell chromatin accessibility of developing murine pancreas identifies cell state-specific gene regulatory programs
Authors: de la O Sean , Liu Zhe , Chang Sean , Sneddon Julie B. 
Published: October 2022

AbstractNumerous studies have characterized the existence of cell subtypes, along with their corresponding transcriptional profiles, within the developing mouse pancreas. The upstream mechanisms that initiate and maintain gene expression programs across cell states, however, remain largely unknown. Here, we generate single-nucleus ATAC-Sequencing data of developing murine pancreas and perform an integrated, multi-omic analysis of both chromatin accessibility and RNA expression to describe the chromatin landscape of both the developing epithelium and mesenchyme at E14.5 at single-cell resolution. We identify candidate transcription factors regulating cell fate and construct gene regulatory networks of active transcription factor binding to regulatory regions of downstream target genes. This work serves as a valuable resource for the field of pancreatic biology in general and contributes to our understanding of lineage plasticity among endocrine cell types. In addition, these data identify which epigenetic states should be represented in the differentiation of stem cells to the pancreatic beta cell fate in order to best recapitulate in vitro the gene regulatory networks that are critical for progression along the beta cell lineage in vivo.
Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics
Authors: Avraham-Davidi Inbal , Mages Simon , Klughammer Johanna , Moriel Noa , Imada Shinya , Hofree Matan , Murray Evan , Chen Jonathan , Pelka Karin , Mehta Arnav , Boland Genevieve M. , Delorey Toni , Caplan Leah , Dionne Danielle , Strasser Robert , Lalakova Jana , Niesnerova Anezka , Xu Hao , Rouault Morgane , Tirosh Itay , Hacohen Nir , Chen Fei , Yilmaz Omer , Roper Jatin , Rozenblatt-Rosen Orit , Nitzan Mor , Regev Aviv 
Published: October 2022

AbstractWhile advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single cell RNA-seq, spatial transcriptomics by Slide- seq, andin situmultiplex RNA analysis, to create a detailed spatial map of healthy and dysplastic colon cellular ecosystems and their association with disease progression. We profiled inducible genetic CRC mouse models that recapitulate key features of human CRC, assigned cell types and epithelial expression programs to spatial tissue locations in tumors, and computationally used them to identify the regional features spanning different cells in the same spatial niche. We find that tumors were organized in cellular neighborhoods, each with a distinct composition of cell subtypes, expression programs, and local cellular interactions. Comparing to scRNA-seq and Slide-seq data from human CRC, we find that both cell composition and layout features were conserved between the species, with mouse neighborhoods correlating with malignancy and clinical outcome in human patient tumors, highlighting the relevance of our findings to human disease. Our work offers a comprehensive framework that is applicable across various tissues, tumors, and disease conditions, with tools for the extrapolation of findings from experimental mouse models to human diseases.
Impact of acute complex exercise on inhibitory control and brain activation: a functional near-infrared spectroscopy study
Authors: Takahashi Shinji , Grove Philip M. 
Published: October 2022

AbstractA growing body of literature demonstrates that a single bout of exercise benefits executive function. While the acute effect of simple exercises like walking, running, and cycling has been well investigated, it is less clear how complex exercise, which requires open skills and various motions, impacts executive function and brain activation. Therefore, we compared the acute effects of a complex exercise on inhibitory control and brain activation with those of a simple exercise using functional near-infrared spectroscopy (fNIRS). Twenty-four young right-hand dominant adults (9 women) completed three interventions: badminton, running, and a seated rest control condition for 10 min each. During each intervention, oxygen uptake and heart rate were monitored. A Stroop task composed of neutral and incongruent conditions was administrated before and after each intervention. An fNIRS system recorded hemodynamics in the prefrontal cortex to evaluate brain activation during the Stroop task. The intensities of badminton and running were comparable. Performance on the Stroop task was significantly improved after badminton, specifically in the incongruent condition relative to in the neutral condition. On the other hand, neither running nor seated rest affected performance in the Stroop task. The fNIRS measures indicated that badminton and running had no significant influence on brain activation. These results show that a single bout of complex exercise enhances inhibitory control without increasing brain activation compared to simple exercise, suggesting that an acute complex exercise induces neural efficiency.
Distribution of intraperitoneally administered D2O in AQP4-knockout mouse brain after MCA occlusion
Authors: Urushihata Takuya , Takuwa Hiroyuki , Takahashi Manami , Kershaw Je◻ , Shibata Sayaka , Nitta Nobuhiro , Tachibana Yasuhiko , Yasui Masato , Higuchi Makoto , Takayuki Obata 
Published: October 2022

AbstractAs the movement of water in the brain is known to be involved in neural activity and various brain pathologies, the ability to assess water dynamics in the brain will be important for the understanding of brain function and the diagnosis and treatment of brain diseases. Aquaporin-4 (AQP4) is a membrane channel protein that is highly expressed in brain astrocytes and is important for the movement of water molecules in the brain. In this study, we investigated the contribution of AQP4 to brain water dynamics by administering deuterium-labeled water (D2O) intraperitoneally to wild-type and AQP4 knockout (AQP4-ko) mice that had undergone surgical occlusion of the middle cerebral artery. Water dynamics in the infarct region and on either side of the anterior cerebral artery (ACA) was monitored with proton-density-weighted imaging (PDWI) performed on a 7T animal MRI. D2O caused a negative signal change quickly after administration. The AQP4-ko mice showed a delay of the time-to-minimum in both contralateral and ipsilateral ACA region compared to wild-type mice. Also, only the AQP4-ko mice showed a delay of the time-to-minimum in the ipsilateral ACA region compared to the contralateral side. In only the wild-type mice, the signal minimum in the ipsilateral ACA region was higher than that in the contralateral ACA region. In the infarct region, the signal attenuation was slower for the AQP4-ko mice in comparison to the wild-type mice. These results suggest that AQP4 loss affects water dynamics in the ACA region not only in the infarct region. Dynamic PDWI after D2O administration may be a useful tool for showing the effects of AQP4 in vivo.HighlightsThe measurement of brain water dynamics with D2O.In vivo investigation of AQP4 loss and focal brain ischemia.AQP4 loss affects water dynamics in the ACA region not only in the infarct region.
Vascular tortuosity quantification as an outcome metric of the oxygen-induced retinopathy model of ischemic retinopathy
Authors: Marra Kyle V. , Chen Jimmy S. , Robles-Holmes Hailey K. , Miller Joseph , Wei Guoqin , Aguilar Edith , Ideguchi Yoichiro , Ly Kristine B. , Prenner Sofia , Erdogmus Deniz , Ferrara Napoleone , Campbell J. Peter , Friedlander Martin , Nudleman Eric 
Published: October 2022

ABSTRACTThe murine oxygen-induced retinopathy (OIR) model is one of the most widely used animal models of ischemic retinopathy, mimicking hallmark pathophysiology of initial vaso-obliteration (VO) resulting in ischemia that drives neovascularization (NV). In addition to NV and VO, human ischemic retinopathies including Retinopathy of Prematurity (ROP) are characterized by increased vascular tortuosity. Vascular tortuosity is an indicator of disease severity, need to treat, and treatment response in ROP. Current literature investigating novel therapeutics in the OIR model report their effects on NV and VO, but no standardized quantification of vascular tortuosity exists to date despite this metric’s relevance to human disease in clinics. The current proof-of-concept study applied a computer-based image analysis algorithm capable of calculating standardized measurements of vascular tortuosity. Quantification of vascular tortuosity correlated with disease activity in OIR analogously to that observed in infants with ROP. Treatment of OIR mice with anti-Vascular Endothelial Growth Factor (aflibercept) rescued vascular tortuosity in the model. Altogether, these data demonstrated that vascular tortuosity is a quantifiable feature of the OIR model and may be used as an outcome measurement in future studies investigating new treatment modalities for retinal ischemia.
Megakaryocyte and erythroblast DNA in plasma and platelets
Authors: Moss Joshua , Ben-Ami Roni , Shai Ela , Kalish Yosef , Klochender Agnes , Cann Gordon , Glaser Benjamin , Arad Ariela , Shemer Ruth , Dor Yuval 
Published: October 2022

ABSTRACTCirculating cell-free DNA (cfDNA) fragments are a biological analyte with extensive utility in diagnostic medicine. Understanding the source of cfDNA and mechanisms of release is crucial for designing and interpreting cfDNA-based liquid biopsy assays. Using cell type-specific methylation markers as well as genome-wide methylation analysis, we determined that megakaryocytes, the precursors of anuclear platelets, are major contributors to cfDNA (∼26%), while erythroblasts contribute 1-4% of cfDNA in healthy individuals. Surprisingly, we discovered that platelets contain genomic DNA fragments originating in megakaryocytes, contrary to the general understanding that platelets lack genomic DNA. Megakaryocyte-derived cfDNA is increased in pathologies involving increased platelet production (Essential Thrombocythemia, Idiopathic Thrombocytopenic Purpura) and decreased upon reduced platelet production due to chemotherapy-induced bone marrow suppression. Similarly, erythroblast cfDNA is reflective of erythrocyte production and is elevated in patients with Thalassemia. Megakaryocyte- and erythroblast-specific DNA methylation patterns can thus serve as novel biomarkers for pathologies involving increased or decreased thrombopoiesis and erythropoiesis, which can aid in determining the etiology of aberrant levels of erythrocytes and platelets.GRAPHICAL ABSTRACT
Single-cell analysis reveals dynamics of human B cell differentiation and identifies novel B and antibody-secreting cell intermediates
Authors: Verstegen Niels J.M. , Pollastro Sabrina , Unger Peter-Paul A. , Marsman Casper , Elias George , Jorritsma Tineke , Streutker Marij , Baβler Kevin , Händler Kristian , Rispens Theo , Schultze Joachim L. , ten Brinke Anja , Beyer Marc , van Ham S. Marieke 
Published: October 2022

ABSTRACTDifferentiation of B cells into antibody-secreting cells (ASCs) is a key process to generate protective humoral immunity. A detailed understanding of the cues controlling ASC differentiation is important to devise strategies to modulate antibody formation. Here, we dissected differentiation trajectories of human naive B cells into ASCs using single-cell RNA sequencing. By comparing transcriptomes of B cells at different stages of differentiation from an in vitro model with ex vivo B cells and ASCs, we uncovered a novel pre-ASC population present ex vivo in lymphoid tissues. For the first time, a germinal-center-like population is identified in vitro from human naive B cells and possibly progresses into a memory B cell population through an alternative route of differentiation, thus recapitulating in vivo human GC reactions. Our work allows further detailed characterization of human B cell differentiation into ASCs or memory B cells in both healthy and diseased conditions.
Chronically elevated corticosterone impairs dopaminergic transmission in the dorsomedial striatum by sex-divergent mechanisms
Authors: Holloway Ashley L. , Schaid Michael D. , Lerner Talia N. 
Published: October 2022

AbstractBackgroundMajor depressive disorder (MDD) is a leading cause of disability worldwide. Individuals with MDD exhibit decreased motivation and deficits in reward processing along with chronically elevated levels of the ‘stress hormone,’ cortisol. However, the mechanistic relationship between chronically elevated cortisol and behavioral deficits in motivation and reward processing remains unclear. Given that women are diagnosed with MDD at twice the rate of men, it is important to understand whether the mechanisms linking chronically elevated cortisol to the symptoms of MDD differ by sex.MethodsWe used subcutaneous implants to chronically elevate free plasma corticosterone (rodent homolog of cortisol; ‘CORT’) in male and female mice and examined changes in behavior and dopamine system function. We used operant training to assay reward-guided motivation and high-performance liquid chromatography to quantify striatal dopamine content. We assessed dopamine transporter (DAT) function using ex vivo slice imaging and in vivo fiber photometry in combination with a fluorescent dopamine sensor, dLight1.3b. We further quantified DAT expression and phosphorylation using western blot.ResultsWe found that chronic CORT treatment impaired reward-seeking in both sexes. In female but not male mice, CORT treatment reduced dopamine content in the dorsomedial striatum (DMS). In male but not female mice, the function of the dopamine transporter (DAT) was impaired in DMS.ConclusionsChronic elevation of CORT impairs reward-seeking by impairing dopaminergic transmission in the DMS, but via different mechanisms in male and female mice. A better understanding of these sex-specific mechanisms could lead to new directions in MDD diagnosis and treatment.