bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sound-Evoked Plasticity Differentiates Tinnitus from Non-Tinnitus Mice
Authors: Fabrizio-Stover Emily M. , Lee Christopher M. , Oliver Douglas L. , Burghard Alice L. 
Published: December 2024

AbstractTinnitus is the perception of non-meaningful sound in the absence of external stimuli. Although tinnitus behavior in animal models is associated with altered central nervous system activity, it is not currently possible to identify tinnitus using neuronal activity alone. In the mouse inferior colliculus (IC), a subpopulation of neurons demonstrates a sustained increase in spontaneous activity after a long-duration sound (LDS). Here, we use the “LDS test” to reveal tinnitus-specific differences in sound-evoked plasticity through IC extracellular recordings and the auditory brainstem response (ABRLDS) in CBA/CaJ mice after sound exposure and behavioral tinnitus assessment. Sound-exposed mice showed stronger and shorter tone-evoked responses in the IC compared to unexposed controls, but these differences were not strong predictors of tinnitus. In contrast, in the LDS test, non-tinnitus mice had a significantly stronger suppression in tone-evoked spike rate compared to tinnitus and unexposed control mice. ABR peak amplitudes also revealed robust differences between tinnitus and non-tinnitus mice, with ABR peaks from non-tinnitus mice exhibiting significantly stronger suppression in the LDS test compared to tinnitus and control mice. No significant differences were seen between cohorts in ABR amplitude, latency, wave V:I ratio, wave V:III ratio, I-V intra-peak latency, and I-VI intra-peak latency. We found high-frequency tone stimuli better suited to reveal tinnitus-specific differences for both extracellular IC and ABR recordings. We successfully used the LDS test to demonstrate that tinnitus-specific differences in sound-evoked plasticity can be shown using both multi-unit near-field recordings in the IC and non-invasive far-field recordings, providing a foundation for future electrophysiological research into the causes and treatment of tinnitus.
Glycosomal phosphoenolpyruvate carboxykinase CRISPR/Cas9-deletion and its role inTrypanosoma cruzimetacyclogenesis and infectivity in mammalian host
Authors: Vieira Carolina Silva Dias , Wang Wei , Sanchez-Valdez Fernando , Lim Jihyun , White Brooke E , da Silva Souza Camilla Garcia , Tarleton Rick L , Paes Marcia Cristina , Nogueira Natalia Pereira 
Published: December 2024

ABSTRACTTrypanosoma cruzi, the causative agent of Chagas disease, possesses glycosomes - unique organelles that house key metabolic enzymes, several of which are promising therapeutic targets. Among them, phosphoenolpyruvate carboxykinase (PEPCK) plays a central role in succinic fermentation, the main pathway for NAD+regeneration within the organelle. Using CRISPR/Cas9 editing, PEPCK gene was disrupted inT. cruzi, producing single- allele knockout epimastigotes (TcPEPCK-sKO) with reduced enzyme activity. This disruption impaired glucose consumption and mitochondrial respiration, particularly oxidative phosphorylation, reducing dependence on mitochondrial ATP production. To compensate, pyruvate phosphate dikinase was upregulated, increasing alanine production, possibly to maintain redox balance. Although TcPEPCK-sKO epimastigotes exhibited a minor reduction in growth, their differentiation (metacyclogenesis) and invasion were severely compromised. However, once inside the host cell, TcPEPCK-sKO amastigotes increased their replication, leading to enhanced trypomastigote production. The same was observed inin vivoinfection, where TcPEPCK-sKO infection in IFNγ-deficient mice caused uncontrolled parasitemia and severe pathology, highlighting the PEPCK critical role in host-pathogen interactions. However, an intact immune system effectively contained TcPEPCK-sKO infection. Taken together, our findings demonstrate that PEPCK is crucial forT. cruzienergy metabolism, enabling the parasite differentiation within the insect vector and controlling the infection of mammalian host cells.
Frataxin deficiency in the astrocytes drives neurocognitive impairment in sickle cell disease mice
Authors: Novelli Enrico M. , Lenhart Shane C , Foley Lesley M. , Sekar Nandinii , Mondal Paritosh , Wang Hong , Hitchens T. Kevin , Ghosh Samit , Chan Stephen Y. , Hu Xiaoming , Hazra Rimi 
Published: December 2024

AbstractIndividuals with sickle cell disease (SCD) suffer from a high burden of cerebrovascular lesions and cognitive impairment that vastly impact quality of life. Cerebrovascular lesions are characterized by microstructural neuroaxonal damage, but their pathogenesis has not been fully elucidated. Herein, we report that SCD mice (SS) have reduced expression of frataxin (FXN), a mitochondrial protein, in their astrocytes compared to control (AA) mice. Next, we generated chimeric mice with SS bone marrow and astrocyte-specific deletion of FXN (SSFXN-KO). Ex-vivo diffusion tensor magnetic resonance imaging and immunohistopathology of the brain showed that the SSFXN-KOmice have increased white matter neuroaxonal damage compared to the SS bone marrow chimera mice with wild-type FXN expression (SSFXN-WT). The SSFXN-KOmice also displayed poorer cognitive function as measured by the functional Y-maze and novel object recognition tests. Pharmacological induction of FXN by administration of insulin growth factor-1 improved cognitive function in the SSFXN-KOmice. Overall, our data demonstrate that FXN is a critical factor regulating neuroaxonal health and cognitive function in SCD mice. FXN may therefore be a novel pharmacologic target to prevent cerebrovascular complications in SCD.
Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data
Authors: Badia-i-Mompel Pau , Casals-Franch Roger , Wessels Lorna , Müller-Dott Sophia , Trimbour Rémi , Yang Yunxiao , Ramirez Flores Ricardo O. , Saez-Rodriguez Julio 
Published: December 2024

AbstractCells regulate their functions through gene expression, driven by a complex interplay of transcription factors and other regulatory mechanisms that together can be modeled as gene regulatory networks (GRNs). The emergence of single-cell multi-omics technologies has driven the development of several methods that integrate transcriptomics and chromatin accessibility data to infer GRNs. While these methods provide examples of their utility in discovering new regulatory interactions, a comprehensive benchmark evaluating their mechanistic and predictive properties as well as their ability to recover known interactions is lacking. To address this, we built a comprehensive framework, Gene Regulatory nETwork Analysis (GRETA), available as a Snakemake pipeline, that includes state of the art methods decomposing their different steps in a modular manner. With it, we found that the GRNs were highly sensitive to methods’ choices, such as changes in random seeds, or replacing steps in the inference pipelines, as well as whether they use paired or unpaired multimodal data. Although the obtained networks performed well in predictive evaluation tasks and partially recovered known interactions, they struggled to capture causal relationships from perturbation assays. Our work brings attention to the challenges of inferring GRNs from single-cell omics, offers guidelines, and presents a flexible framework for developing and testing new approaches.Graphical Abstract
Design of multimodal antibiotics against intracellular infections using deep learning
Authors: Cesaro Angela , Wan Fangping , Torres Marcelo D. T. , de la Fuente-Nunez Cesar 
Published: December 2024

AbstractThe rise of antimicrobial resistance has rendered many treatments ineffective, posing serious public health challenges. Intracellular infections are particularly difficult to treat since conventional antibiotics fail to neutralize pathogens hidden within human cells. However, designing molecules that penetrate human cells while retaining antimicrobial activity has historically been a major challenge. Here, we introduce APEXDUO, a multimodal artificial intelligence (AI) model for generating peptides with both cell-penetrating and antimicrobial properties. From a library of 50 million AI-generated compounds, we selected and characterized several candidates. Our lead, Turingcin, penetrated mammalian cells and eradicated intracellularStaphylococcus aureus. In mouse models of skin abscess and peritonitis, Turingcin reduced bacterial loads by up to two orders of magnitude. In sum, APEXDUOgenerated multimodal antibiotics, opening new avenues for molecular design.
ELONGATED HYPOCOTYL 5 regulates light-mediated squalene biosynthesis and development inArabidopsis thaliana
Authors: Pathak Pranshu Kumar , Khan Aruba , Sharma Ashish , Singh Nivedita , Sandhu Gurpreet , Trivedi Prabodh Kumar 
Published: December 2024

AbstractTerpenoids are diverse groups of metabolite families that are crucial for plant development and required in cosmetics and pharmacological industries. Various development processes and environmental factors, including light, have been shown to affect terpenoid biosynthesis. However, regulatory factors involved in such regulation have not been explored much. Squalene synthases (SQSs), key enzymes in the terpenoid pathway, are pivotal for sterol and triterpene biosynthesis across various organisms. In this study, we report thatAtSQS1expression and squalene content are higher in the dark, and light through ELONGATED HYPOCOTYL 5 (HY5) negatively regulates theAtSQS1gene and squalene biosynthesis inArabidopsis thaliana. Our study shows that theAtSQS1gene is unaffected in thehy5-215mutant during light and dark conditions, but it is down-regulated in WT and HY5OX lines. The histochemical GUS assays and GFP expression patterns indicate a negative regulation of squalene biosynthesis by AtHY5. Yeast one-hybrid assays, EMSA, and ChIP experiments have confirmed the physical binding of AtHY5 on light-responsive elements of theAtSQS1promoter. We have validated our results by developingAtSQS1promoter: reporter transgenic lines in WT,hy5-215mutants, and HY5OX backgrounds and conducted expression, metabolite quantification, and histochemical GUS assays. The metabolites quantification of squalene and phytosterols through GC-MS further confirms that AtHY5 negatively regulates the squalene biosynthesis in a light-dependent manner in Arabidopsis.
Early-life Oxytocin Rescues Hippocampal Synaptic Plasticity and Episodic Memory in a Mouse Model of Fragile X Syndrome
Authors: Chavez Jasmine , Le Aliza A. , Lauterborn Julie C. , Cox Brittney M. , Jia Yousheng , Lynch Gary , Gall Christine M. 
Published: December 2024

ABSTRACTCognitive disabilities including impairments to episodic memory are debilitating features of autism spectrum disorder (ASD). Here we report that early-life treatment with oxytocin (OXT) fully restores episodic memory and associated synaptic plasticity in a rodent model of an ASD.Fmr1-knockout (KO) mice -- which mimic the single gene mutation in Fragile X Syndrome -- failed to encode three basic elements of an episode (identity, location, and temporal order) during a first time, unrewarded encounter with a set of cues. Intranasal administration of OXT during the second postnatal week eliminated each of these impairments in mice tested in adulthood. OXT treatment during the second, but not fifth, postnatal week also corrected pronounced defects in two distinct forms of hippocampal Long-Term Potentiation (LTP). Rescue of LTP in lateral perforant path (LPP) to dentate gyrus synapses was linked to recovery of NMDAR-gated synaptic responses, which are otherwise profoundly reduced in the mutant LPP. LTP induced by a threshold theta burst stimulation protocol in CA3-CA1 synapses was severely impaired in adultFmr1-KOs as was a previously unreported post-induction growth phase for potentiation. Both effects were restored in adult Fmr1-KOs given early OXT treatment. Infusion of OXT into adultFmr1-KO hippocampal slices normalized LTP in CA1 but had no effect on the defective potentiation (or NMDAR-mediated EPSCs) at LPP-dentate gyrus synapses. These results show that severe, autism-related defects in cognition critical to memory, as evident in a rodent model, are reversible and that an early-life therapeutic intervention can effect an enduring restoration of function.
RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations
Authors: Taslim Cenny , Zhang Yuan , Kendall Genevieve C. , Theisen Emily R. 
Published: December 2024

AbstractRNA-Seq analysis has become a routine task in numerous genomic research labs, driven by the reduced cost of bulk RNA sequencing experiments. These generate billions of reads that require accurate, efficient, effective, and reproducible analysis. But the time required for comprehensive analysis remains a bottleneck. Many labs rely on in-house scripts, making standardization and reproducibility challenging. To address this, we developed RNA-SeqEZPZ, an automated pipeline with a user-friendly point-and-click interface, enabling rigorous and reproducible RNA-Seq analysis without requiring programming or bioinformatics expertise. For advanced users, the pipeline can also be executed from the command line, allowing customization of steps to suit specific requirements.This pipeline includes multiple steps from quality control, alignment, filtering, read counting to differential expression and pathway analysis. We offer two different implementations of the pipeline using either (1) bash and SLURM or (2) Nextflow. The two implementation options allow for straightforward installation, making it easy for individuals familiar with either language to modify and/or run the pipeline across various computing environments.RNA-SeqEZPZ provides an interactive visualization tool using R shiny to easily select the FASTQ files for analysis and compare differentially expressed genes and their functions across experimental conditions. The tools required by the pipeline are packaged into a Singularity image for ease of installation and to ensure replicability. Finally, the pipeline performs a thorough statistical analysis and provides an option to perform batch adjustment to minimize effects of noise due to technical variations across replicates.RNA-SeqEZPZ is freely available and can be downloaded fromhttps://github.com/cxtaslim/RNA-SeqEZPZ.
Combined inhibition of SHP2 overcomes adaptive resistance to type 1 BRAF inhibitors in BRAF V600E-driven high-grade glioma
Authors: Ayanlaja Abiola A. , Chang Michael , Lalwani Kriti , Ioannou Maria , Wang Jiawan , Jagtap Shreya , Yang Yanbo , Gartrell Robyn D. , Pratilas Christine A. , Schreck Karisa C. 
Published: December 2024

AbstractBRAF-mutant gliomas can be therapeutically targeted with BRAF mutant-selective inhibitors, yet responses are often transient due to short-term adaptive or long-term treatment-emergent resistance. We hypothesized that vertical inhibition of multiple signaling nodes could improve the durability of BRAF inhibition and prevent or overcome adaptive resistance. Using human tissue samples, we identified frequent RAS pathway reactivation in gliomas resistant to BRAF inhibitors, suggesting a common escape mechanism. Using patient-derived cell lines, we observed that upregulation of RAS activity was an adaptive response to BRAFi and that knockdown of SHP2, a central regulator of RAS activity, resulted in enhanced sensitivity to BRAF or MEK inhibition. Moreover, combined small molecule inhibition with SHP2 and BRAF or MEK inhibitors increased the depth and durability of ERK pathway inhibition, as well as prevented paradoxical upregulation of RAS activity. RNA sequencing analysis revealed deeper suppression of ERK transcriptional output with combined therapy, along with decreased reactivation of EGFR. Combined SHP2/BRAF small molecule inhibitors prevented growth and induced cell death in some cell line models. In cell lines with treatment-emergent resistance, moreover, combined SHP2 and BRAF inhibition overcame resistance to BRAF inhibitor monotherapy.In vivoorthotopic and patient-derived xenograft models confirmed enhanced tumor growth inhibition with combined therapy. Together, our findings demonstrate the critical role of RAS/ERK signaling reactivation in driving resistance to BRAF inhibition in glioma, and demonstrate the potential utility for adding SHP2 inhibitors to overcome resistance inBRAFV600E mutant glioma.SignificanceThe addition of a SHP2i to BRAFi in BRAF-V600E glioma cells prevents tumor growth and can overcome resistance to BRAFi in preclinical models in vitro and in vivo.
The biophysical mechanism of mitochondrial pearling
Authors: Sturm Gabriel , Hake Kayley , Lefebvre Austin E.Y.T. , Rux Caleb J. , Ivanova Daria , Millett-Sikking Alfred , Tharp Kevin M. , Rao Beiduo , Closser Michael , Waite Adam , Precido-Lopez Magdalena , Dumont Sophie , Lu Wen , Manley Suliana , Landoni Juan C. , Marshall Wallace F. 
Published: December 2024

AbstractMitochondrial networks exhibit remarkable dynamics that are driven in part by fission and fusion events. However, there are other reorganizations of the network that do not involve fission and fusion. One such exception is the elusive, “beads-on-a-string” morphological transition of mitochondria. During such transitions, the cylindrical tubes of the mitochondrial membrane transiently undergo shape changes to a string of “pearls” connected along thin tubes. These dynamics have been anecdotally observed in many contexts and given disparate explanations. Here we unify these observations by proposing a common underlying mechanism based on the biophysical properties of tubular fluid membranes for which it is known that, under particular regimes of tension and pressure, membranes reach an instability and undergo a shape transition to a string of connected pearls. First, we use high-speed light-sheet microscopy to show that transient, short-lived pearling events occur spontaneously in the mitochondrial network in every cell type we have examined, including primary fibroblasts, T-cells, neurons, and budding yeast. We present evidence that transient mitochondrial pearling occurs during important biological events, particularly during T cell activation and neuronal firing. Using our high-temporal resolution data, we identify two distinct categories of spontaneous pearling, i) internal pressure-driven pearling regulated by ionic flux, and ii) external tension-driven pearling regulated by molecular motors. By applying live-cell STED microscopy we document the structural reorganization of inner cristae membranes during mitochondrial pearling. We then compare numerous methods for inducing pearling, including the ability to induce these dynamics with single mitochondrion precision. These methods include ionophores, channel activators, osmotic shock, detergents, laser stimulation, membrane intercalating molecules, chemical fixation, and micro-needle force. These disparate inducers establish three main physical causes of pearling, i) ionic flux amplifying internal osmotic pressure, ii) membrane packing lowering bending elasticity, and iii) external mechanical force increasing membrane tension. Pearling dynamics thereby reveal a fundamental biophysical facet of mitochondrial biology. We suggest that pearling should take its place beside fission and fusion as a key process of mitochondrial dynamics, with implications for physiology, disease, and aging.
Expanding the capillarics toolbox: 3D-printed microfluidic phaseguides and self-coalescence modules
Authors: Craig Cosette , Leong Kelsey , Lin Carrie , Chang Megan , Olanrewaju Ayokunle 
Published: December 2024

AbstractCapillarics are microfluidic circuits that are assembled from individual fluidic elements, powered by surface tension forces encoded by microchannel geometry and surface chemistry, and enable instrument-free pre-programmed automation of multi-step liquid handling processes. 3D printing has recently transformed capillarics by enabling rapid and cost-effective prototyping, provided addition geometric degrees of freedom in multi-level fabrication, and facilitated new design paradigms with greater capabilities than traditional cleanroom fabrication. Despite widespread interest in 3D printing and development of custom high-resolution stereolithography printers for microfluidic applications, fluidic elements that require precise and tunable control over capillary pinning lines – such as fluidic phaseguides and self-coalescence modules (SCMs) – have so far only been manufactured with centralized and expensive cleanroom methods. Not only does this limit access to versatile capillaric features to only well-resourced settings, but it also slows innovation and widespread application of these fluid handling technologies. Here we expand the toolbox of 3D-printed capillarics to include phaseguides and SCMs, demonstrating their potential for precise instrument-free control over multi-step liquid handling and reagent rehydration. We employed benchtop stereolithography printers to prototype (up to 50X) scaled-up phaseguides and SCMs and integrated them into a capillaric circuit for inline reagent reconstitution, dynamic fluid control, and sequential drainage. We showcased scalable designs, customizable geometries, and robust self-coalescing flow for larger liquid volumes – up to 50 µL compared with 1.25 µL in cleanroom-fabricated SCMs. This work represents a significant advance in democratizing access to microfluidics, with potential for broad applications in diagnostics, assay automation, and organ-on-chip systems.
Developmental delay ensures global tissue size robustness upon local induction of apoptosis
Authors: Staneva Ralitza , Sobczyk-Moran Gabriel , Levillayer Florence , Villars Alexis , Davidović Anđela , Levayer Romain 
Published: December 2024

AbstractThe capacity of our tissues to cope with external and internal stress relies on the tight coupling between cell proliferation, cell growth and cell death. This coupling is assumed to be based on compensatory proliferation, where local mitogenic signals and mechanical inputs generated by dying cells promote neighbouring cell proliferation. However, compensatory proliferation was mostly studied in the context of massive death induction, irradiation, surgical tissue ablation or upon genetic perturbation of apoptosis execution. It remains thus unclear whether the same mechanism operates during physiological programmed cell death or upon mild induction of apoptosis, especiallyin vivo. Here, we use theDrosophilaprospective wing (the larval wing disc), to study the impact of local induction of apoptosis on tissue size and proliferation pattern. We first confirmed that the wing could recover its final size and compensate for mild induction of apoptosis. However, using spatial statistics we found surprisingly that local induction of death is not associated with any local increase of proliferation, could it be upon clonal or compartment induction of apoptosis. Compensation is driven instead by a JNK dependant delay of growth and lengthening of the larval stage which is required to reach the final tissue target size. These results suggest that compensation is here driven by a global response rather that a local proliferation induction. Accordingly, while total tissue size is maintained despite local induction of apoptosis, this mechanism fails to correct the local reduction of cell number, hence modulating wing shape and proportion. Overall, this study opens novel perspectives on tissue size regulation and outlines the context-dependency of compensatory mechanisms.