bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional programs mediating neuronal toxicity and altered glial-neuronal signaling in aDrosophilaknock-in tauopathy model
Authors: Bukhari Hassan , Nithianandam Vanitha , Battaglia Rachel A. , Cicalo Anthony , Sarkar Souvarish , Comjean Aram , Hu Yanhui , Leventhal Matthew J. , Dong Xianjun , Feany Mel B. 
Published: February 2024

AbstractMissense mutations in the gene encoding the microtubule-associated protein tau cause autosomal dominant forms of frontotemporal dementia. Multiple models of frontotemporal dementia based on transgenic expression of human tau in experimental model organisms, includingDrosophila, have been described. These models replicate key features of the human disease, but do not faithfully recreate the genetic context of the human disorder. Here we use CRISPR-Cas mediated gene editing to model frontotemporal dementia caused by the tau P301L mutation by creating the orthologous mutation, P251L, in the endogenousDrosophila taugene. Flies heterozygous or homozygous for tau P251L display age-dependent neurodegeneration, metabolic defects and accumulate DNA damage in affected neurons. To understand the molecular events promoting neuronal dysfunction and death in knock-in flies we performed single-cell RNA sequencing on approximately 130,000 cells from brains of tau P251L mutant and control flies. We found that expression of disease-associated mutant tau altered gene expression cell autonomously in all neuronal cell types identified and non-cell autonomously in glial cells. Cell signaling pathways, including glial-neuronal signaling, were broadly dysregulated as were brain region and cell-type specific protein interaction networks and gene regulatory programs. In summary, we present here a genetic model of tauopathy, which faithfully recapitulates the genetic context and phenotypic features of the human disease and use the results of comprehensive single cell sequencing analysis to outline pathways of neurotoxicity and highlight the role of non-cell autonomous changes in glia.
Comprehensive analysis of the microbial consortium in the culture of flagellateMonocercomonoides exilis
Authors: Jiménez-González Alejandro , Treitli Sebastian Cristian , Peña-Diaz Priscila , Janovská Anna , Beneš Vladimír , Žáček Petr , Hampl Vladimír 
Published: February 2024

AbstractMonocercomonoides exilisis the only known amitochondriate eukaryote, making it an excellent model for studying the implications of mitochondrial reduction from a cellular and evolutionary point of view. AlthoughM. exilisis an endobiotic heterotroph, it can growin vitro, albeit with an uncharacterized and complex prokaryotic community. All attempts to growM. exilisaxenically have been unsuccessful. Here, we use metagenomic sequencing at different time points during culture growth to describe the composition and dynamics of this community. We assembled genomes of 24 from at least the 30 different bacterial species within. Based on DNA read abundances,M. exilisrepresents less than 1.5%, and the representation of dominant bacterial members changes over time. Genome-scale metabolic reconstruction, differential expression analysis and measurements of metabolites in the media showed that the community depends on organic carbon oxidation, fermentation, and hydrogen production without methanogenesis. This is consistent with the rapid decline of amino acids, nucleotides, glyceraldehyde, lactate, fatty acids, and alcohols in the media. The community depends on recycling the external supply of amino acids since it has a limited capacity to fix nitrogen gas and lacks ammonia oxidizers to close the nitrogen cycle. With the senescence of the culture, we observe changes in the expression of several metabolic pathways inM. exilis, particularly those adapting to starvation. We do not reveal any clear metabolic link to explain the dependence ofM. exilison prokaryotes.
Expression of novel androgen receptors in three GnRH neuron subtypes in the cichlid brain
Authors: Dussenne Mélanie , Alward Beau A. 
Published: February 2024

AbstractWithin a social hierarchy, an individuals’ social status determines its physiology and behavior. InA. burtoni, subordinate males can rise in rank to become dominant, which is accompanied by the upregulation of the entire HPG axis, including activation of GnRH1 neurons, a rise in circulating androgen levels and the display of specific aggressive and reproductive behaviors. Cichlids possess two other GnRH subtypes, GnRH2 and GnRH3, the latter being implicated in the display of male specific behaviors. Interestingly, some studies showed that these GnRH neurons are responsive to fluctuations in circulating androgen levels, suggesting a link between GnRH neurons and androgen receptors (ARs). Due to a teleost-specific whole genome duplication,A. burtonipossess two AR paralogs (ARα and ARβ) that are encoded by two different genes,ar1andar2, respectively. Even though social status has been strongly linked to androgens, whether ARα and/or ARβ are present in GnRH neurons remains unclear. Here, we used immunohistochemistry andin situhybridization chain reaction (HCR) to investigatear1andar2expression specifically in GnRH neurons. We find that all GnRH1 neurons intensely expressar1but only a few of them expressar2, suggesting the presence of genetically-distinct GnRH1 subtypes. Very fewar1andar2transcripts were found in GnRH2 neurons. GnRH3 neurons were found to express bothargenes. The presence of distinctargenes within GnRH neuron subtypes, most clearly observed for GnRH1 neurons, suggests differential control of these neurons by androgenic signaling. These findings provide valuable insight for future studies aimed at disentangling the androgenic control of GnRH neuron plasticity and reproductive plasticity across teleosts.
Anox2/cybbzebrafish mutant with defective neutrophil ROS production displays normal initial neutrophil recruitment to sterile tail injuries
Authors: Isiaku Abdulsalam I. , Zhang Zuobing , Pazhakh Vahid , Lieschke Graham J. 
Published: February 2024

AbstractReactive oxygen species (ROS) are important effectors and modifiers of the acute inflammatory response, recruiting neutrophils to sites of tissue injury. In turn, neutrophils are both consumers and producers of reactive oxygen species. Stimulated neutrophils generate reactive oxygen species in an oxidative burst through the activity of a multimeric phagocytic NADPH oxidase complex. Mutations in theNOX2/CYBB(previously gp91phox) NADPH oxidase subunit are the commonest cause of chronic granulomatous disease, a disease characterized by infection susceptibility and an inflammatory phenotype. To model chronic granulomatous disease, we made anox2/cybbzebrafish (Danio rerio) mutant and demonstrated it to have severely impaired neutrophil ROS production. Reduced early survival ofnox2mutant embryos indicated an essential requirement fornox2during early development. Innox2/cybbzebrafish mutants, the dynamics of initial neutrophil recruitment to both mild and severe surgical tailfin wounds was normal, suggesting that excessive neutrophil recruitment at the initiation of inflammation is not the primary cause of the “sterile” inflammatory phenotype of chronic granulomatous disease patients. Thisnox2zebrafish mutant adds to existing in vivo models for studying neutrophil reactive oxygen species function in development and disease.
Tryptanthrin Analogs Substoichiometrically Inhibit Seeded and Unseeded Tau4RD Aggregation
Authors: James Ellie I. , Baggett David W. , Chang Edcon , Schachter Joel , Nixey Thomas , Choi Karoline , Guttman Miklos , Nath Abhinav 
Published: February 2024

AbstractMicrotubule-associated protein tau is an intrinsically disordered protein (IDP) that forms characteristic fibrillar aggregates in several diseases, the most well-known of which is Alzheimer’s disease (AD). Despite keen interest in disrupting or inhibiting tau aggregation to treat AD and related dementias, there are currently no FDA-approved tau-targeting drugs. This is due, in part, to the fact that tau and other IDPs do not exhibit a single well-defined conformation but instead populate a fluctuating conformational ensemble that precludes finding a stable “druggable” pocket. Despite this challenge, we previously reported the discovery of two novel families of tau ligands, including a class of aggregation inhibitors, identified through a protocol that combines molecular dynamics, structural analysis, and machine learning. Here we extend our exploration of tau druggability with the identification of tryptanthrin and its analogs as potent, substoichiometric aggregation inhibitors, with the best compounds showing potencies in the low nanomolar range even at a ∼100-fold molar excess of tau4RD. Moreover, conservative changes in small molecule structure can have large impacts on inhibitory potency, demonstrating that similar structure-activity relationship (SAR) principles as used for traditional drug development also apply to tau and potentially to other IDPs.
Dynamic regulation of CeA gene expression during acute and protracted abstinence from chronic binge drinking of male and female C57BL/6J mice
Authors: Méndez Hernán G. , Neira Sofia , Flanigan Meghan E. , Haun Harold L. , Boyt Kristen M. , Thiele Todd E. , Kash Thomas L. 
Published: February 2024

AbstractBinge alcohol consumption is a major risk factor for developing Alcohol Use Disorder (AUD) and is associated with alcohol-related problems like accidental injury, acute alcohol poisoning, and black-outs. While there are numerous brain regions that have been shown to play a role in this AUD in humans and animal models, the central nucleus of the amygdala (CeA) has emerged as a critically important locus mediating binge alcohol consumption. In this study, we sought to understand how relative gene expression of key signaling molecules in the CeA changes during different periods of abstinence following bouts of binge drinking. To test this, we performed drinking in the dark (DID) on two separate cohorts of C57BL/6J mice and collected CeA brain tissue at one day (acute) and 7 days (protracted) abstinence after DID. We used qRTPCR to evaluate relative gene expression changes of 25 distinct genes of interest related to G protein-coupled receptors (GPCRs), neuropeptides, ion channel subunits, and enzymes that have been previously implicated in AUD. Our findings show that during acute abstinence CeA punches collected from female mice had upregulated relative mRNA expression of the gamma-aminobutyric acid receptor subunit alpha 2 (Gabra2), and the peptidase, angiotensinase c (Prcp). CeA punches from male mice at the same time point in abstinence had upregulated relative mRNA encoding for neuropeptide-related molecules, neuropeptide Y (Npy) and somatostatin (Sst), as well as the neuropeptide Y receptor Y2 (Npyr2) but downregulated, Glutamate ionotropic receptor NMDA type subunit 1 (Grin1). After protracted abstinence CeA punches collected from female mice had increased mRNA expression of corticotropin releasing hormone (Crh) and Npy. While CeA punches collected from male mice at the same timepoint had upregulated relative mRNA expression of Npy2r and downregulated mRNA expression of Gabra2, Grin1 and opioid receptor kappa 1 (Oprk1). Our findings support that there are differences in how the CeA of male and female respond to binge-alcohol exposure, highlighting the need to understand the implications of such differences in the context of AUD and binge drinking behavior.
Single-molecule chromatin configurations link transcription factor binding to expression in human cells
Authors: Doughty Benjamin R. , Hinks Michaela M. , Schaepe Julia M. , Marinov Georgi K. , Thurm Abby R. , Rios-Martinez Carolina , Parks Benjamin E. , Tan Yingxuan , Marklund Emil , Dubocanin Danilo , Bintu Lacramioara , Greenleaf William J. 
Published: February 2024

AbstractThe binding of multiple transcription factors (TFs) to genomic enhancers activates gene expression in mammalian cells. However, the molecular details that link enhancer sequence to TF binding, promoter state, and gene expression levels remain opaque. We applied single-molecule footprinting (SMF) to measure the simultaneous occupancy of TFs, nucleosomes, and components of the transcription machinery on engineered enhancer/promoter constructs with variable numbers of TF binding sites for both a synthetic and an endogenous TF. We find that activation domains enhance a TF’s capacity to compete with nucleosomes for binding to DNA in a BAF-dependent manner, TF binding on nucleosome-free DNA is consistent with independent binding between TFs, and average TF occupancy linearly contributes to promoter activation rates. We also decompose TF strength into separable binding and activation terms, which can be tuned and perturbed independently. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the binding microstates observed at the enhancer and subsequent time-dependent gene expression. This work provides a template for quantitative dissection of distinct contributors to gene activation, including the activity of chromatin remodelers, TF activation domains, chromatin acetylation, TF concentration, TF binding affinity, and TF binding site configuration.
Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
Authors: Yao Jianing , Yu Jinglun , Caffo Brian , Page Stephanie C. , Martinowich Keri , Hicks Stephanie C. 
Published: February 2024

AbstractRecent advances in spatially-resolved single-omics and multi-omics technologies have led to the emergence of computational tools to detect or predict spatial domains. Additionally, histological images and immunofluorescence (IF) staining of proteins and cell types provide multiple perspectives and a more complete understanding of tissue architecture. Here, we introduce Proust, a scalable tool to predict discrete domains using spatial multi-omics data by combining the low-dimensional representation of biological profiles based on graph-based contrastive self-supervised learning. Our scalable method integrates multiple data modalities, such as RNA, protein, and H&E images, and predicts spatial domains within tissue samples. Through the integration of multiple modalities, Proust consistently demonstrates enhanced accuracy in detecting spatial domains, as evidenced across various benchmark datasets and technological platforms.
Optogenetic Locus Coeruleus Stimulation Improves Pupil Size Tracking of Cortical State
Authors: Weiss Evan , (Andy) Liu Yuxiang , Wang Qi 
Published: February 2024

AbstractBrain state heavily influences our perception, cognition, and behavior. Multiple neuromodulatory systems, including the locus coeruleus – norepinephrine (LC-NE) system, contribute to the regulation of brain state. This research harnesses machine learning and optogenetics technologies to probe the impact of the LC on cortical state and pupillary responses in awake mice. Our integrative approach combines EEG recordings with pupillometry to capture the LC’s optogenetic activation, evoking notable EEG spectral power shifts synchronized with pupil dilation. These changes provide a noninvasive glimpse into the cortical states, modulated by the LC’s activity. Central to our methodology is the application of Support Vector Regression (SVR) modeling, which robustly correlates LC-induced pupillary changes with EEG power fluctuations. These insights help reinforce the LC’s crucial role in modulating prefrontal activity and its regulatory influence over arousal states. Beyond advancing our comprehension of the LC’s function, our work also highlights the potential for developing closed-loop stimulation systems. These systems, integrated with machine-learning techniques and multi-modal data, could offer precise therapeutic interventions for neurological disorders characterized by abnormal arousal states.
ComI inhibits transformation inBacillus subtilisby selectively killing competent cells
Authors: Smith Dominique R. , Kearns Daniel B. , Burton Briana M. 
Published: February 2024

AbstractMany bacteria build elaborate molecular machines to import DNA via natural competence, yet this activity is often not identified until strains have been handled and domesticated in laboratory settings. For example, one of the best studied Gram-positive model organisms,Bacillus subtilis,has a non-transformable ancestor. Transformation in the ancestral strain is inhibited by a transmembrane peptide, ComI, which is encoded on an extrachromosomal plasmid. Although ComI was shown to be necessary and sufficient to inhibit transformation when produced at high levels under an inducible promoter, the mechanism by which ComI inhibits transformation is unknown. Here, we examine the native regulation and mechanism of transformation inhibition by ComI. We find that under native regulation, ComI expression is restricted in the absence of the plasmid. In the presence of the plasmid, we find that ComI is preferentially expressed in cells that are differentiating into a competent state. The subcellular localization of ComI, however, does not depend on any other competence proteins and permeabilization activity is concentration dependent. Thus over time, the competent cells gradually producing ComI, are permeabilized and killed. Based on these observations we propose a new model for the mechanism of ComI, suggesting a response to competence activation that selectively eliminates the competent subpopulation.ImportanceNatural transformation mechanisms have been studied across several bacterial systems, but few examples of inhibition exist. This work investigates the mechanism of action of a plasmid-encoded transmembrane inhibitor of natural transformation. The data reveal that the peptide can cause cell permeabilization. Permeabilization is synergistic with entry ofBacillus subtilisinto the “competent” state, such that cells with ability to be transformed are preferentially killed. These findings reveal a self-preservation mechanism coupled to the physiological state of the cells that ensures the population can maintain unaltered plasmid and its predicted prophage.
Unraveling the impact of congenital deafness on individual brain organization
Authors: Amaral Lénia , Xiaosha Wang , Yanchao Bi , Ella Striem-Amit 
Published: February 2024

AbstractResearch on brain plasticity, particularly in the context of deafness, consistently emphasizes the reorganization of the auditory cortex. However, a critical question arises: to what extent do all individuals with deafness show the same level of reorganization? To address this question, we examined the individual differences in deafness functional connectivity (FC), specifically from the deprived auditory cortex. Our findings demonstrate a remarkable differentiation between individuals deriving from the absence of shared auditory experiences, resulting in heightened FC variability among deaf individuals, compared to more consistent FC in the hearing group. Notably, connectivity to language regions becomes more diverse across individuals in deafness. This does not stem from delayed language acquisition, as it is found in deaf native signers, who are exposed to rich natural language since birth. However, comparing FC diversity between deaf native signers and deaf delayed signers who were deprived of language in early development, we show that language experience also impacts individual differences, although to a more moderate extent. Overall, our research points out the intricate interplay between brain plasticity and individual differences, shedding light on the diverse ways reorganization manifests among individuals. It further joins findings in blindness, showing that individual differences are affected by sensory experience. Finally, these findings highlight the importance of considering individual differences in personalized rehabilitation for hearing loss.
Caspase-8 activity mediates TNFα production and restrictsCoxiella burnetiireplication during murine macrophage infection
Authors: Osbron Chelsea A. , Lawson Crystal , Hanna Nolan , Koehler Heather S. , Goodman Alan G. 
Published: February 2024

AbstractCoxiella burnetiiis an obligate intracellular bacteria which causes the global zoonotic disease Q Fever. Treatment options for infection are limited, and development of novel therapeutic strategies requires a greater understanding of howC. burnetiiinteracts with immune signaling. Cell death responses are known to be manipulated byC. burnetii, but the role of caspase-8, a central regulator of multiple cell death pathways, has not been investigated. In this research, we studied bacterial manipulation of caspase-8 signaling and the significance of caspase-8 toC. burnetiiinfection, examining bacterial replication, cell death induction, and cytokine signaling. We measured caspase, RIPK, and MLKL activation inC. burnetii-infected TNFα/CHX-treated THP-1 macrophage-like cells and TNFα/ZVAD-treated L929 cells to assess apoptosis and necroptosis signaling. Additionally, we measuredC. burnetiireplication, cell death, and TNFα induction over 12 days in RIPK1-kinase-dead, RIPK3-kinase-dead, or RIPK3-kinase-dead-caspase-8-/-BMDMs to understand the significance of caspase-8 and RIPK1/3 during infection. We found that caspase-8 is inhibited byC. burnetii, coinciding with inhibition of apoptosis and increased susceptibility to necroptosis. Furthermore,C. burnetiireplication was increased in BMDMs lacking caspase-8, but not in those lacking RIPK1/3 kinase activity, corresponding with decreased TNFα production and reduced cell death. As TNFα is associated with the control ofC. burnetii, this lack of a TNFα response may allow for the unchecked bacterial growth we saw in caspase-8-/-BMDMs. This research identifies and explores caspase-8 as a key regulator ofC. burnetiiinfection, opening novel therapeutic doors.
Primary auditory cortex is necessary for the acquisition and expression of categorical behavior
Authors: Krall Rebecca F. , Chambers Callista N. , Arnold Megan P. , Brougher Lauren I. , Chen Justin , Deshmukh Rishi , King Hailey B. , Morford Harry J. , Wiemann John M. , Williamson Ross S. 
Published: February 2024

SummaryThe primary auditory cortex (ACtx) is critically involved in the association of sensory information with specific behavioral outcomes. Such sensory-guided behaviors are necessarily brain-wide endeavors, requiring a plethora of distinct brain areas, including those that are involved in aspects of decision making, motor planning, motor initiation, and reward prediction. ACtx comprises a number of distinct excitatory cell-types that allow for the brain-wide propagation of behaviorally-relevant sensory information. Exactly how ACtx involvement changes as a function of learning, as well as the functional role of distinct excitatory cell-types is unclear. Here, we addressed these questions by designing a two-choice auditory task in which water-restricted, head-fixed mice were trained to categorize the temporal rate of a sinusoidal amplitude modulated (sAM) noise burst and used transient cell-type specific optogenetics to probe ACtx necessity across the duration of learning. Our data demonstrate that ACtx is necessary for the ability to categorize the rate of sAM noise, and this necessity grows across learning. ACtx silencing substantially altered the behavioral strategies used to solve the task by introducing a fluctuating choice bias and increasing dependence on prior decisions. Furthermore, ACtx silencing did not impact the animal’s motor report, suggesting that ACtx is necessary for the conversion of sensation to action. Targeted inhibition of extratelencephalic projections on just 20% of trials had a minimal effect on task performance, but significantly degraded learning. Taken together, our data suggest that distinct cortical cell-types synergistically control auditory-guided behavior and that extratelencephalic neurons play a critical role in learning and plasticity.